SRA toolkit fastq files download error
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
• 2,914 views
•
link
written
by
sidrah.maryam •
1 answer
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. :(
• 0 views
•
link
written
by
sidrah.maryam •
Yes that only I will have to copy for 8000 files their ftp link. :'(
• 0 views
•
link
written
by
sidrah.maryam •
Log in to answer this question.
More posts like this
-
fasterq-dump quit with error code 3
written by Aki •
-
Basic fasterq-dump command is failing from `SIGNAL - Segmentation fault`
written by O.rka
-
efetch sra suddenly stopping
written by barry •
could be a network issue, try again or fetch fro ENA