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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Squeezemeta warning for STEP15 #693

Closed sarpiens closed 1 year ago

sarpiens commented 1 year ago

Hello,

We were using the squeezemeta pipeline(squeezemeta1.6.2post1) with a set of metatranscriptomic samples, using the following parameters: -m coassembly, -a rnaspades --nobins -t 16 -b 25

However, despite de fact that tables were generated we found and errorr regarding "STEP15 -> DAS_TOOL MERGING: 15.dastool.pl":

warning_squeezemeta

In'm wondering if it is okey to continue because the warning makes sense since we used the option --nobins. Is it okey to continue or should we adjust some parameters?

Thanks in advance. Best regards.

fpusan commented 1 year ago

It is fine to continue, I think. But if you added --nobins then it shouldn't have attempted binning in the first place. What version are you using?

jtamames commented 1 year ago

Hello Yes, it is ok to continue. Did you see any messages regarding step 14 (binning)? Could you send the syslog file to us? Best, J

sarpiens commented 1 year ago

Hi again, we used squeezemeta1.6.2post1 in a conda env. We did not see any messages regarding step 14.

I attach the log file of the run: squeezemeta_Alicia_MTT_coassembly.log

Thanks in advance. Best, Sam

jtamames commented 1 year ago

Hello Sam Oh yes, there is a misplaced bracket in the SqueezeMeta.pl script causing this. My bad. I will correct it asap. But it does not have any influence in your results, which you can trust fully. Thanks for reporting!

Best, J