Question

headers missing in efetch results for SRA database

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2.3 years ago

gernophil ▴ 90

Hey everyone, I am trying to retrieve a SRA table via esearch and efetch, as I did many times before. However, when I do this now, the headers in my table are missing. And I can't find any flag or similar that would make them reappear. Did SRA change anything here?

My command is:

esearch -db bioproject -query [PRJN or SRP] | efetch -format runinfo > file.csv

SRA Entrez.Direct efetch • 1.4k views

ADD COMMENT • link updated 2.3 years ago by PeterC_NCBI ▴ 510 • written 2.3 years ago by gernophil ▴ 90

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While I have not done this specific search, are you saying that you used to get something like the following with that query?

$ esearch -db sra -query PRJNA253315 | efetch -format runInfo | head -3
SRR1448774,2014-11-12 16:42:10,2014-06-23 16:59:00,59803030,3049954530,0,51,1902,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR001/448/SRR1448774.sralite.1,SRX620734,,ChIP-Seq,ChIP,GENOMIC,SINGLE,0,0,ILLUMINA,Illumina HiSeq 2000,SRP043510,PRJNA253315,2,253315,SRS645140,SAMN02870079,simple,9606,Homo sapiens,GSM1418957,,,,,,,no,,,,,GEO,SRA172049,,public,8015BDF5C26D74EA2C32420993B7B044,FCC5BDCBF2064FBA9F03892CDB1AE898
SRR1448775,2014-11-12 16:42:10,2014-06-23 17:02:07,63157308,3221022708,0,51,2014,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR144/8775/SRR1448775.sralite.1,SRX620735,,ChIP-Seq,ChIP,GENOMIC,SINGLE,0,0,ILLUMINA,Illumina HiSeq 2000,SRP043510,PRJNA253315,2,253315,SRS645141,SAMN02870084,simple,9606,Homo sapiens,GSM1418958,,,,,,,no,,,,,GEO,SRA172049,,public,DB43B8469F5A907F2E48F463655F5145,0A5F480C86FF6D3577D1AFD53CECE112

ADD REPLY • link 2.3 years ago by GenoMax 146k

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Yes, but with headers like

Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,...

They were included in the exact same command, but since about two weaks the headers are missing somehow. That makes it really hard to identify the columns :).

ADD REPLY • link 2.3 years ago by gernophil ▴ 90

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Please report this to NCBI help desk. Be aware that it may take them up to 48h to respond at times. Looks like the -format runInfo header is not working (even in case of search I posted above).

ADD REPLY • link 2.3 years ago by GenoMax 146k

score 1 · Answer 1 · 2022-07-13

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2.3 years ago

PeterC_NCBI ▴ 510

Thanks for pointing out this problem with the headers. We are working on a fix. Hope to have it corrected soon.

ADD COMMENT • link 2.3 years ago by PeterC_NCBI ▴ 510

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Looks like they are back. However, the headers are tab separated now, but the rest of the output is comma separated :).

ADD REPLY • link 2.3 years ago by gernophil ▴ 90

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Maybe it's helpful for you to name my NCBI case number here so you can link the cases: #CAS-921910-D4T1M8