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rvalieris / parallel-fastq-dump

parallel fastq-dump wrapper
MIT License
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fastq-dump error! exit code: 3 #57

Open binbinL opened 2 months ago

binbinL commented 2 months ago

Hi, I have downloaded SRR files and now tend to use parallel-fastq-dump convert them to .fastq.gz files when i run "parallel-fastq-dump -t 4 -O ./fastq --split-files --gzip -s /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793" under /tmp dir

error ： 2024-07-25 16:13:51,267 - SRR ids: ['/public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793'] 2024-07-25 16:13:51,267 - extra args: ['--split-files', '--gzip'] 2024-07-25 16:13:51,268 - tempdir: /tmp/pfd_wyozb3vj 2024-07-25 16:13:51,268 - CMD: sra-stat --meta --quick /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 2024-07-25 16:13:51,292 - /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 spots: 34906477 2024-07-25 16:13:51,292 - blocks: [[1, 8726619], [8726620, 17453238], [17453239, 26179857], [26179858, 34906477]] 2024-07-25 16:13:51,292 - CMD: fastq-dump -N 1 -X 8726619 -O /tmp/pfd_wyozb3vj/0 --split-files --gzip /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 2024-07-25 16:13:51,293 - CMD: fastq-dump -N 8726620 -X 17453238 -O /tmp/pfd_wyozb3vj/1 --split-files --gzip /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 2024-07-25 16:13:51,293 - CMD: fastq-dump -N 17453239 -X 26179857 -O /tmp/pfd_wyozb3vj/2 --split-files --gzip /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 2024-07-25 16:13:51,294 - CMD: fastq-dump -N 26179858 -X 34906477 -O /tmp/pfd_wyozb3vj/3 --split-files --gzip /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 2024-07-25T08:13:51 fastq-dump.2.8.0 err: column not found while opening table within short read archive module - failed /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 2024-07-25T08:13:51 fastq-dump.2.8.0 err: column not found while opening table within short read archive module - failed /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 2024-07-25T08:13:51 fastq-dump.2.8.0 err: column not found while opening table within short read archive module - failed /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 2024-07-25T08:13:51 fastq-dump.2.8.0 err: column not found while opening table within short read archive module - failed /public/home/mengqx/dengxsh/WorkSpace/Data/tmp/SRR18141793 ... fastq-dump error! exit code: 3

Version parallel-fastq-dump : 0.6.7 fastq-dump : 2.8.0

Thanks!

rvalieris commented 2 months ago

Hello, I believe this issue can be resolved by updating fastq-dump, the version 2.8.0 that you are using is very old.