fastq-dump error

[msfuentealba]

Hi all,

I'm trying to run the monorail-external with SRA input but I'm getting the following error. Any ideas? Thanks

I'm running the command /bin/bash ../monorail-external-master/singularity/run_recount_pump.sh ../recount-pump_1.1.1.sif SRR21355139 SRP394927 grcm38 20 ../monorail-external-master/

Other datasets work fine.

2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL_START
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL_LEN
2023-06-01T02:05:29 fastq-dump.2.9.1 err: column not found while opening table within short read archive module - column READ
2023-06-01T02:05:29 fastq-dump.2.9.1 err: column not found while opening table within short read archive module - failed /container-mounts/recount/temp_big/dl-SRR21355139/SRR21355139/SRR21355139.sra
2023-06-01T02:05:29 fastq-dump.2.9.1 info: KConfig(repository) found: using VResolver
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL_START
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL_LEN
2023-06-01T02:05:29 fastq-dump.2.9.1 err: column not found while opening table within short read archive module - column READ
2023-06-01T02:05:29 fastq-dump.2.9.1 err: column not found while opening table within short read archive module - failed /container-mounts/recount/temp_big/dl-SRR21355139/SRR21355139/SRR21355139.sra
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL_START
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL_LEN
2023-06-01T02:05:29 fastq-dump.2.9.1 err: column not found while opening table within short read archive module - column READ
2023-06-01T02:05:29 fastq-dump.2.9.1 err: column not found while opening table within short read archive module - failed /container-mounts/recount/temp_big/dl-SRR21355139/SRR21355139/SRR21355139.sra
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL_START
2023-06-01T02:05:29 fastq-dump.2.9.1 warn: column not found while opening table within short read archive module - column LABEL_LEN
2023-06-01T02:05:29 fastq-dump.2.9.1 err: column not found while opening table within short read archive module - column READ
2023-06-01T02:05:29 fastq-dump.2.9.1 err: column not found while opening table within short read archive module - failed /container-mounts/recount/temp_big/dl-SRR21355139/SRR21355139/SRR21355139.sra
2023-06-01T02:05:29 fastq-dump.2.9.1 info: KConfig(repository) found: using VResolver
2023-06-01T02:05:29 fastq-dump.2.9.1 info: KConfig(repository) found: using VResolver
2023-06-01T02:05:29 fastq-dump.2.9.1 info: KConfig(repository) found: using VResolver

[ChristopherWilks]

Hi @msfuentealba,

The issue is most likely the use of the 2.9.1 version of fastq-dump/sra-toolkit in that container.
I've got an updated version (uses sra-toolkit 3.0.x), but I need to test it out before pushing it to the public repo.

I'll try to do that in the next couple of days.

[ChristopherWilks]

Hi @msfuentealba

I've updated the pump docker image to be 1.1.3 which now uses SRAtoolkit 3.0.2 for both prefetch and fastq-dump, so hopefully should fix this error.

Please give the new image a try and let me know.

Thanks,
Chris