SRA toolkit fastq files download error
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6 weeks ago

Hello everyone, I am trying to download multiple fastq files using SRA toolkit. while some of the files were downloaded successfully, some showed error as:

2021-02-25T19:17:50 fasterq-dump.2.10.4 err: cmn_iter.c cmn_read_String( #794965 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted) 
2021-02-25T19:17:51 fasterq-dump.2.10.4 err: cmn_iter.c cmn_read_String( #687977 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted) 
2021-02-25T19:17:51 fasterq-dump.2.10.4 err: cmn_iter.c cmn_read_uint8_array( #915768 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted) 
2021-02-25T19:17:51 fasterq-dump.2.10.4 err: row #915768 : READ.len(200) != QUALITY.len(0) (D) 
2021-02-25T19:17:51 fasterq-dump.2.10.4 fatal: SIGNAL - Segmentation fault 
fasterq-dump (PID 24285) quit with error code 1

What might be the reason for this error. Also if any apt alternative could be provided.

any help would be highly appreciated. Thank you

RNA-Seq SRA • 126 views
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could be a network issue, try again or fetch fro ENA

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6 weeks ago

Thank you for that. Actually in ENA i will have to download manually on my machine as it cannot be downloaded directly on server, and there are about 8300*2 files. That is why I had used SRA toolkit. :(

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You can just copy ENA fastq ftp links and downloaded them with curl or wget directly to the server (if you use a Linux machine). No need to anything manually.

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Yes that only I will have to copy for 8000 files their ftp link. :'(

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use the API to go over the 8000 files

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