LoadSQM issue

[tboonf]

SqueezeMeta completed successfully with all the necessary outputs. However i have issue with loading it to SQMTools (both squeezemeta and sqmtools are the latest versions):

ABC = loadSQM('./Project', engine = 'data.table')
Generating tabular outputs for project in ./Project
Traceback (most recent call last):
File "/home/nova/miniconda3/envs/SqueezeMeta/SqueezeMeta/utils/sqm2tables.py", line 223, in
main(parse_args())
File "/home/nova/miniconda3/envs/SqueezeMeta/SqueezeMeta/utils/sqm2tables.py", line 70, in main
sampleNames, orfs, kegg, cog, pfam, custom, noCDSorfs, noCDScontigs = parse_orf_table(perlVars['$mergedfile'], total_reads, total_bases, nokegg, nocog, nopfam,
File "/home/nova/miniconda3/envs/SqueezeMeta/SqueezeMeta/utils/../lib/utils.py", line 199, in parse_orf_table
abundances = array([int(line[idx[sample]]) for sample in samples])
File "/home/nova/miniconda3/envs/SqueezeMeta/SqueezeMeta/utils/../lib/utils.py", line 199, in
abundances = array([int(line[idx[sample]]) for sample in samples])
IndexError: list index out of range

[fpusan]

What version of SqueezeMeta did you use to generate this project?
Any chance you can share the full directory with us using something like dropbox, wetransfer, etc?

[tboonf]

Thanks for fast responding..is it possible to send the link to your private email due to data confidentiality?

[fpusan]

Of course [email protected]

[fpusan]

Did you send it in the end? it doesn't seem so but maybe it went to my spam folder?

[fpusan]

I see what's happening now. The last line on your results/13.*.orftable file is truncated. I wonder how the data got corrupted.
Maybe your process was killed in the middle of that step, and you restarted the pipeline?

[tboonf]

Thank you for checking. Appreciated it. I will rerun.

…

On Fri, Jan 17, 2025 at 6:42 PM Fernando Puente-Sánchez < ***@***.***> wrote: I see what's happening on. The last line on your results/13.*.orftable file is truncated. I wonder how the data got corrupted. Maybe your process was killed in the middle of that step, and you restarted the pipeline? — Reply to this email directly, view it on GitHub <#920 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AASWIMXCX5DP6JK3OC5ENVL2LDNB3AVCNFSM6AAAAABVC2RHO6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKOJXHE3TOOBXHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>