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Today’s we will learn to download FASTQ files from a published paper:

Manuscript: Heikema et al. (2020). https://www.mdpi.com/2073-4425/11/9/1105

STEP 1 : Find where the data is available for download in the above manuscript

Click on the link above and search for “accession”, “Data availability”, “BioProject ID” or “GEO accession code”
If, only a GEO accession code is available, go to the GEO database and look for BioProject ID - Note, ENA (Step2) requires this identifier to download the data.

Which BioProject ID host the data used in the above manuscript?

PRJEB28612

STEP 2: Search for data for the identified BioProject ID at the European Nucleotide Archive (ENA) database

Go to https://www.ebi.ac.uk/ena/browser/home and search for the BioProject ID using the search option on the top right corner and click on ‘view’:

STEP 3: Download sample report - metadata information

118 samples in this study - metagenomics data generated using Illumina and Nanopore sequencing technologies:

run_accession	sample_accession	experiment_accession	study_accession	tax_id	scientific_name	fastq_ftp	submitted_ftp	sra_ftp	bam_ftp
ERR2850008	SAMEA4984173	ERX2856660	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850008/ERR2850008.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850008/Illumina4.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850008	
ERR2850012	SAMEA4984177	ERX2856664	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850012/ERR2850012.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850012/Illumina8.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850012	
ERR2850017	SAMEA4984182	ERX2856669	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850017/ERR2850017.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850017/Illumina13.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850017	
ERR2850022	SAMEA4984187	ERX2856674	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850022/ERR2850022.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850022/Illumina18.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850022	
ERR2850025	SAMEA4984190	ERX2856677	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850025/ERR2850025.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850025/Illumina21.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850025	
ERR2850026	SAMEA4984191	ERX2856678	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850026/ERR2850026.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850026/Illumina22.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850026	
ERR2850028	SAMEA4984193	ERX2856680	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850028/ERR2850028.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850028/Illumina24.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850028	
ERR2850030	SAMEA4984195	ERX2856682	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850030/ERR2850030.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850030/Illumina26.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850030	
ERR2850031	SAMEA4984196	ERX2856683	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850031/ERR2850031.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850031/Illumina27.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850031	
ERR2850034	SAMEA4984199	ERX2856686	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850034/ERR2850034.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850034/Illumina30.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850034	
ERR2850039	SAMEA4984204	ERX2856691	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850039/ERR2850039.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850039/Illumina35.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850039	
ERR2850041	SAMEA4984206	ERX2856693	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850041/ERR2850041.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850041/Illumina37.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850041	
ERR2850042	SAMEA4984207	ERX2856694	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850042/ERR2850042.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850042/Illumina38.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850042	
ERR2850046	SAMEA4984211	ERX2856698	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850046/ERR2850046.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850046/Illumina42.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850046	
ERR2850047	SAMEA4984212	ERX2856699	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850047/ERR2850047.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850047/Illumina43.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850047	
ERR2850006	SAMEA4984171	ERX2856658	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850006/ERR2850006.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850006/Illumina2.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850006	
ERR2850052	SAMEA4984217	ERX2856704	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850052/ERR2850052.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850052/Illumina48.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850052	
ERR2850054	SAMEA4984219	ERX2856706	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850054/ERR2850054.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850054/Illumina50.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850054	
ERR2850007	SAMEA4984172	ERX2856659	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850007/ERR2850007.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850007/Illumina3.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850007	
ERR2850009	SAMEA4984174	ERX2856661	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850009/ERR2850009.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850009/Illumina5.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850009	
ERR2850059	SAMEA4984224	ERX2856711	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850059/ERR2850059.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850059/Illumina55.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850059	
ERR2850010	SAMEA4984175	ERX2856662	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850010/ERR2850010.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850010/Illumina6.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850010	
ERR2850080	SAMEA4984245	ERX2856732	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850080/ERR2850080.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850080/Nanopore1.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850080	
ERR2850081	SAMEA4984246	ERX2856733	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850081/ERR2850081.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850081/Nanopore2.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850081	
ERR2850011	SAMEA4984176	ERX2856663	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850011/ERR2850011.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850011/Illumina7.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850011	
ERR2850083	SAMEA4984248	ERX2856735	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850083/ERR2850083.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850083/Nanopore4.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850083	
ERR2850015	SAMEA4984180	ERX2856667	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850015/ERR2850015.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850015/Illumina11.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850015	
ERR2850084	SAMEA4984249	ERX2856736	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850084/ERR2850084.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850084/Nanopore5.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850084	
ERR2850018	SAMEA4984183	ERX2856670	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850018/ERR2850018.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850018/Illumina14.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850018	
ERR2850019	SAMEA4984184	ERX2856671	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850019/ERR2850019.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850019/Illumina15.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850019	
ERR2850086	SAMEA4984251	ERX2856738	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850086/ERR2850086.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850086/Nanopore7.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850086	
ERR2850020	SAMEA4984185	ERX2856672	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850020/ERR2850020.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850020/Illumina16.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850020	
ERR2850087	SAMEA4984252	ERX2856739	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850087/ERR2850087.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850087/Nanopore8.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850087	
ERR2850088	SAMEA4984253	ERX2856740	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850088/ERR2850088.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850088/Nanopore9.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850088	
ERR2850024	SAMEA4984189	ERX2856676	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850024/ERR2850024.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850024/Illumina20.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850024	
ERR2850005	SAMEA4984170	ERX2856657	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850005/ERR2850005.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850005/Illumina1.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850005	
ERR2850032	SAMEA4984197	ERX2856684	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850032/ERR2850032.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850032/Illumina28.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850032	
ERR2850090	SAMEA4984255	ERX2856742	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850090/ERR2850090.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850090/Nanopore11.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850090	
ERR2850091	SAMEA4984256	ERX2856743	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850091/ERR2850091.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850091/Nanopore12.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850091	
ERR2850035	SAMEA4984200	ERX2856687	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850035/ERR2850035.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850035/Illumina31.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850035	
ERR2850100	SAMEA4984265	ERX2856752	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850100/ERR2850100.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850100/Nanopore21.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850100	
ERR2850037	SAMEA4984202	ERX2856689	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850037/ERR2850037.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850037/Illumina33.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850037	
ERR2850105	SAMEA4984270	ERX2856757	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850105/ERR2850105.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850105/Nanopore26.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850105	
ERR2850043	SAMEA4984208	ERX2856695	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850043/ERR2850043.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850043/Illumina39.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850043	
ERR2850013	SAMEA4984178	ERX2856665	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850013/ERR2850013.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850013/Illumina9.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850013	
ERR2850050	SAMEA4984215	ERX2856702	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850050/ERR2850050.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850050/Illumina46.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850050	
ERR2850106	SAMEA4984271	ERX2856758	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850106/ERR2850106.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850106/Nanopore27.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850106	
ERR2850055	SAMEA4984220	ERX2856707	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850055/ERR2850055.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850055/Illumina51.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850055	
ERR2850014	SAMEA4984179	ERX2856666	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850014/ERR2850014.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850014/Illumina10.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850014	
ERR2850111	SAMEA4984276	ERX2856763	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850111/ERR2850111.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850111/Nanopore32.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850111	
ERR2850056	SAMEA4984221	ERX2856708	PRJEB28612	1869227	bacterium	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850056/ERR2850056.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850056/Illumina52.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850056	
ERR2850016	SAMEA4984181	ERX2856668	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850016/ERR2850016.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850016/Illumina12.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850016	
ERR2850119	SAMEA4984284	ERX2856771	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850119/ERR2850119.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850119/Nanopore40.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850119	
ERR2850021	SAMEA4984186	ERX2856673	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850021/ERR2850021.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850021/Illumina17.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850021	
ERR2850060	SAMEA4984225	ERX2856712	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850060/ERR2850060.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850060/Illumina56.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850060	
ERR2850121	SAMEA4984286	ERX2856773	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850121/ERR2850121.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850121/Nanopore42.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850121	
ERR2850023	SAMEA4984188	ERX2856675	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850023/ERR2850023.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850023/Illumina19.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850023	
ERR2850063	SAMEA4984228	ERX2856715	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850063/ERR2850063.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850063/Illumina59.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850063	
ERR2850122	SAMEA4984287	ERX2856774	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850122/ERR2850122.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850122/Nanopore43.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850122	
ERR2850027	SAMEA4984192	ERX2856679	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850027/ERR2850027.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850027/Illumina23.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850027	
ERR2850126	SAMEA4984291	ERX2856778	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850126/ERR2850126.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850126/Nanopore47.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850126	
ERR2850093	SAMEA4984258	ERX2856745	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850093/ERR2850093.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850093/Nanopore14.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850093	
ERR2850029	SAMEA4984194	ERX2856681	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850029/ERR2850029.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850029/Illumina25.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850029	
ERR2850127	SAMEA4984292	ERX2856779	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850127/ERR2850127.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850127/Nanopore48.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850127	
ERR2850033	SAMEA4984198	ERX2856685	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850033/ERR2850033.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850033/Illumina29.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850033	
ERR2850096	SAMEA4984261	ERX2856748	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850096/ERR2850096.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850096/Nanopore17.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850096	
ERR2850036	SAMEA4984201	ERX2856688	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850036/ERR2850036.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850036/Illumina32.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850036	
ERR2850097	SAMEA4984262	ERX2856749	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850097/ERR2850097.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850097/Nanopore18.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850097	
ERR2850137	SAMEA4984302	ERX2856789	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850137/ERR2850137.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850137/Nanopore58.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850137	
ERR2850101	SAMEA4984266	ERX2856753	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850101/ERR2850101.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850101/Nanopore22.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850101	
ERR2850104	SAMEA4984269	ERX2856756	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850104/ERR2850104.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850104/Nanopore25.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850104	
ERR2850108	SAMEA4984273	ERX2856760	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850108/ERR2850108.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850108/Nanopore29.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850108	
ERR2850038	SAMEA4984203	ERX2856690	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850038/ERR2850038.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850038/Illumina34.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850038	
ERR2850109	SAMEA4984274	ERX2856761	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850109/ERR2850109.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850109/Nanopore30.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850109	
ERR2850040	SAMEA4984205	ERX2856692	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850040/ERR2850040.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850040/Illumina36.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850040	
ERR2850112	SAMEA4984277	ERX2856764	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850112/ERR2850112.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850112/Nanopore33.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850112	
ERR2850044	SAMEA4984209	ERX2856696	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850044/ERR2850044.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850044/Illumina40.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850044	
ERR2850117	SAMEA4984282	ERX2856769	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850117/ERR2850117.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850117/Nanopore38.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850117	
ERR2850123	SAMEA4984288	ERX2856775	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850123/ERR2850123.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850123/Nanopore44.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850123	
ERR2850045	SAMEA4984210	ERX2856697	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850045/ERR2850045.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850045/Illumina41.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850045	
ERR2850128	SAMEA4984293	ERX2856780	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850128/ERR2850128.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850128/Nanopore49.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850128	
ERR2850048	SAMEA4984213	ERX2856700	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850048/ERR2850048.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850048/Illumina44.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850048	
ERR2850129	SAMEA4984294	ERX2856781	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850129/ERR2850129.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850129/Nanopore50.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850129	
ERR2850131	SAMEA4984296	ERX2856783	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850131/ERR2850131.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850131/Nanopore52.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850131	
ERR2850049	SAMEA4984214	ERX2856701	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850049/ERR2850049.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850049/Illumina45.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850049	
ERR2850132	SAMEA4984297	ERX2856784	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850132/ERR2850132.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850132/Nanopore53.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850132	
ERR2850051	SAMEA4984216	ERX2856703	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850051/ERR2850051.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850051/Illumina47.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850051	
ERR2850133	SAMEA4984298	ERX2856785	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850133/ERR2850133.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850133/Nanopore54.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850133	
ERR2850053	SAMEA4984218	ERX2856705	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850053/ERR2850053.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850053/Illumina49.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850053	
ERR2850134	SAMEA4984299	ERX2856786	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850134/ERR2850134.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850134/Nanopore55.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850134	
ERR2850057	SAMEA4984222	ERX2856709	PRJEB28612	1869227	bacterium	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850057/ERR2850057.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850057/Illumina53.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850057	
ERR2850136	SAMEA4984301	ERX2856788	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850136/ERR2850136.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850136/Nanopore57.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850136	
ERR2850058	SAMEA4984223	ERX2856710	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850058/ERR2850058.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850058/Illumina54.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850058	
ERR2850061	SAMEA4984226	ERX2856713	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850061/ERR2850061.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850061/Illumina57.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/001/ERR2850061	
ERR2850062	SAMEA4984227	ERX2856714	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850062/ERR2850062.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850062/Illumina58.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850062	
ERR2850082	SAMEA4984247	ERX2856734	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850082/ERR2850082.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850082/Nanopore3.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850082	
ERR2850085	SAMEA4984250	ERX2856737	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850085/ERR2850085.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850085/Nanopore6.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850085	
ERR2850089	SAMEA4984254	ERX2856741	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850089/ERR2850089.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850089/Nanopore10.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850089	
ERR2850092	SAMEA4984257	ERX2856744	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850092/ERR2850092.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850092/Nanopore13.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850092	
ERR2850094	SAMEA4984259	ERX2856746	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850094/ERR2850094.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850094/Nanopore15.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850094	
ERR2850095	SAMEA4984260	ERX2856747	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850095/ERR2850095.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850095/Nanopore16.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850095	
ERR2850098	SAMEA4984263	ERX2856750	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850098/ERR2850098.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850098/Nanopore19.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850098	
ERR2850099	SAMEA4984264	ERX2856751	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850099/ERR2850099.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850099/Nanopore20.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/009/ERR2850099	
ERR2850102	SAMEA4984267	ERX2856754	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850102/ERR2850102.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850102/Nanopore23.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/002/ERR2850102	
ERR2850103	SAMEA4984268	ERX2856755	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850103/ERR2850103.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850103/Nanopore24.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850103	
ERR2850107	SAMEA4984272	ERX2856759	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850107/ERR2850107.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850107/Nanopore28.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/007/ERR2850107	
ERR2850110	SAMEA4984275	ERX2856762	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850110/ERR2850110.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850110/Nanopore31.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850110	
ERR2850113	SAMEA4984278	ERX2856765	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850113/ERR2850113.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850113/Nanopore34.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/003/ERR2850113	
ERR2850114	SAMEA4984279	ERX2856766	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850114/ERR2850114.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850114/Nanopore35.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850114	
ERR2850115	SAMEA4984280	ERX2856767	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850115/ERR2850115.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850115/Nanopore36.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850115	
ERR2850116	SAMEA4984281	ERX2856768	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850116/ERR2850116.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850116/Nanopore37.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/006/ERR2850116	
ERR2850118	SAMEA4984283	ERX2856770	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850118/ERR2850118.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850118/Nanopore39.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850118	
ERR2850120	SAMEA4984285	ERX2856772	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850120/ERR2850120.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850120/Nanopore41.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850120	
ERR2850124	SAMEA4984289	ERX2856776	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850124/ERR2850124.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850124/Nanopore45.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/004/ERR2850124	
ERR2850125	SAMEA4984290	ERX2856777	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850125/ERR2850125.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850125/Nanopore46.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850125	
ERR2850130	SAMEA4984295	ERX2856782	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850130/ERR2850130.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850130/Nanopore51.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/000/ERR2850130	
ERR2850135	SAMEA4984300	ERX2856787	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850135/ERR2850135.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850135/Nanopore56.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/005/ERR2850135	
ERR2850138	SAMEA4984303	ERX2856790	PRJEB28612	1131769	human nasopharyngeal metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850138/ERR2850138.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR285/ERR2850138/Nanopore59.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR285/008/ERR2850138

STEP 4: Select FASTQ files (tick boxes next to the file names) and click on “Get download script”. This will download a bash script (e.g., )

STEP 5: Open the downloaded ena file using TextEdit (NotePad or similar app). The downloaded script looks like this:

wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850034/ERR2850034.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850053/ERR2850053.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850015/ERR2850015.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850024/ERR2850024.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850063/ERR2850063.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850059/ERR2850059.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850005/ERR2850005.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850014/ERR2850014.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850010/ERR2850010.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850049/ERR2850049.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850020/ERR2850020.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850029/ERR2850029.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850054/ERR2850054.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850033/ERR2850033.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850035/ERR2850035.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850052/ERR2850052.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850048/ERR2850048.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850016/ERR2850016.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850047/ERR2850047.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850040/ERR2850040.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850021/ERR2850021.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850056/ERR2850056.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850028/ERR2850028.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850012/ERR2850012.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850031/ERR2850031.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850009/ERR2850009.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850050/ERR2850050.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850037/ERR2850037.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850022/ERR2850022.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850018/ERR2850018.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850060/ERR2850060.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850027/ERR2850027.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850008/ERR2850008.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850041/ERR2850041.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850046/ERR2850046.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850013/ERR2850013.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850032/ERR2850032.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850055/ERR2850055.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850036/ERR2850036.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850017/ERR2850017.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850051/ERR2850051.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850023/ERR2850023.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850045/ERR2850045.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850026/ERR2850026.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850061/ERR2850061.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850042/ERR2850042.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850058/ERR2850058.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850039/ERR2850039.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850007/ERR2850007.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850011/ERR2850011.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850038/ERR2850038.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850043/ERR2850043.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850044/ERR2850044.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850030/ERR2850030.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850057/ERR2850057.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850006/ERR2850006.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850062/ERR2850062.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850025/ERR2850025.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850019/ERR2850019.fastq.gz

wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850034/ERR2850034.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850053/ERR2850053.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850015/ERR2850015.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850024/ERR2850024.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850063/ERR2850063.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850059/ERR2850059.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850005/ERR2850005.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850014/ERR2850014.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850010/ERR2850010.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850049/ERR2850049.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850020/ERR2850020.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850029/ERR2850029.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850054/ERR2850054.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850033/ERR2850033.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850035/ERR2850035.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850052/ERR2850052.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850048/ERR2850048.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850016/ERR2850016.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850047/ERR2850047.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850040/ERR2850040.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850021/ERR2850021.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850056/ERR2850056.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850028/ERR2850028.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850012/ERR2850012.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850031/ERR2850031.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850009/ERR2850009.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850050/ERR2850050.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850037/ERR2850037.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850022/ERR2850022.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850018/ERR2850018.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850060/ERR2850060.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850027/ERR2850027.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850008/ERR2850008.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850041/ERR2850041.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850046/ERR2850046.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850013/ERR2850013.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850032/ERR2850032.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850055/ERR2850055.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850036/ERR2850036.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850017/ERR2850017.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850051/ERR2850051.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850023/ERR2850023.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850045/ERR2850045.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850026/ERR2850026.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850061/ERR2850061.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850042/ERR2850042.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850058/ERR2850058.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850039/ERR2850039.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850007/ERR2850007.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850011/ERR2850011.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850038/ERR2850038.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850043/ERR2850043.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850044/ERR2850044.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850030/ERR2850030.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850006/ERR2850006.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850062/ERR2850062.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850025/ERR2850025.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850019/ERR2850019.fastq.gz

Now using the TextEdit or NotePad app, we will add the following lines to the top of the script - copy and paste the following to the above script:

#!/bin/bash -l
#PBS -N ENA_data_download
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
#work on current directory (folder)
cd $PBS_O_WORKDIR

You should have this:

#!/bin/bash -l
#PBS -N ENA_data_download
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
#work on current directory (folder)
cd $PBS_O_WORKDIR

wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850034/ERR2850034.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850053/ERR2850053.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850015/ERR2850015.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850024/ERR2850024.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850063/ERR2850063.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850059/ERR2850059.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850005/ERR2850005.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850014/ERR2850014.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850010/ERR2850010.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850049/ERR2850049.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850020/ERR2850020.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850029/ERR2850029.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850054/ERR2850054.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850033/ERR2850033.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850035/ERR2850035.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850052/ERR2850052.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850048/ERR2850048.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850016/ERR2850016.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850047/ERR2850047.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850040/ERR2850040.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850021/ERR2850021.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850056/ERR2850056.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850028/ERR2850028.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850012/ERR2850012.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850031/ERR2850031.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850009/ERR2850009.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850050/ERR2850050.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850037/ERR2850037.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850022/ERR2850022.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850018/ERR2850018.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850060/ERR2850060.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850027/ERR2850027.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850008/ERR2850008.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850041/ERR2850041.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850046/ERR2850046.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850013/ERR2850013.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850032/ERR2850032.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850055/ERR2850055.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850036/ERR2850036.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850017/ERR2850017.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850051/ERR2850051.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850023/ERR2850023.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850045/ERR2850045.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850026/ERR2850026.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850061/ERR2850061.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850042/ERR2850042.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850058/ERR2850058.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850039/ERR2850039.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/007/ERR2850007/ERR2850007.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/001/ERR2850011/ERR2850011.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/008/ERR2850038/ERR2850038.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/003/ERR2850043/ERR2850043.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/004/ERR2850044/ERR2850044.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/000/ERR2850030/ERR2850030.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/006/ERR2850006/ERR2850006.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/002/ERR2850062/ERR2850062.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/005/ERR2850025/ERR2850025.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR285/009/ERR2850019/ERR2850019.fastq.gz

STEP 6: Save the file and now let’s transfer it to the HPC. See below:

NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.

Windows PC: open file finder and type the address below to connect to your home directory in the HPC, and then browse to the /workshop/2024-2/session4_RNAseq/data/mydata folder

\\hpc-fs\home\

Mac: open file finder and press “command” + “k” to open prompt, then type the below command, and then browse to the /workshop/2024-2/session4_RNAseq/data/mydata folder

smb://hpc-fs/home/

Drag and drop the script into the /workshop/2025/S1W1/metagenomics/data/mydata folder

STEP 7: We will ensure the copied file from our laptop / desktop does not have unwanted characters. Let’s move to the data folder:

cd $HOME/workshop/2025/S1W1/metagenomics/data/mydata

To simplify next steps let’s modify the name of the downloaded file:

mv ena-file-download-selected-files* ena-file-download-selected-files_mydata.pbs

STEP 8: Removing hidden characters from the downloaded file. We use the dos2unix conversion:

dos2unix ena-file-download-selected-files_mydata.pbs

Note: If you create a file using Microsoft Excel, it is likely that it will add ASCII characters, use dos2unix to remove such characters.

If you had issues with the steps above an end-file-download is available. Copy it as follows:

cp /work/training/2025/S1W1/session3_metagenomics/scripts/ena-file-download-selected-files_mydata.pbs .

STEP 9: Submit the download job to the cluster

Now we are ready to submit to the HPC cluster the script to download FASTQ files:

qsub ena-file-download-selected-files_mydata.pbs

Monitor progress of job:

qjobs

Note: Downloading the above datasets will take about ~50 minutes.

Alternatively, use the qstat command:

qstat -u username

Tip: Do the following to know the number oj jobs on the cluster:

qstat  | wc -l

where: we use the qstat command to list all jobs, then we pipe the list to the wc- l command to count the number of lines (equivalent to number of jobs -1)

Other ways to download genomics data

Find in the link below alternative approaches to download data from SRA, BaseSpace or use the nf-core/fetchngs pipeline:

Data Download

Other ways to download genomics data

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