restart

[HannahBenisty]

Hi!

I am trying to use --restart with: SqueezeMeta.pl --restart -p obs_09 -step 6

but I get the following error: Can't open samples file (-s) in obs_09/data/00..samples. Please check that it is the correct file squeezemeta.e90917011 (END)

Do you know if there is anything I need to change in the files before trying to restart?

Thanks!

[jtamames]

Hello Which version are you using?

[HannahBenisty]

Hi! 1.6.1, February 2023, thanks!

[jtamames]

Are you in the directory in which you run the project for first time?

[HannahBenisty]

Yes. And the sample file indicated by the error looks fine to me. Can't open samples file (-s) in obs_09/data/00..samples.

[jtamames]

Please send us the syslog file

[HannahBenisty]

[13 hours, 35 minutes, 34 seconds]: STEP2 -> 02.rnas.pl

[13 hours, 53 minutes, 56 seconds]: STEP3 -> 03.run_prodigal.pl

[15 hours, 40 minutes, 4 seconds]: STEP4 -> 04.rundiamond.pl

[2 days, 0 hours, 23 minutes, 58 seconds]: STEP5 -> 05.run_hmmer.pl

[2 days, 20 hours, 42 minutes, 16 seconds]: STEP6 -> 06.lca.pl syslog (END)

[jtamames]

No, I mean the syslog file you will find in the obs_09 directory

[HannahBenisty]

syslog.txt

[jtamames]

Move to directory /nfs/users/rg/hbenisty/HAB23-094_test and try again. Yours is a sequential project, which means that each sample will have its own directory

[HannahBenisty]

Thanks a lot, I'll try!

[HannahBenisty]

One question, I have only one sample (long read from PacBio) and I used sequential mode. Is this correct or should I use a different mode?

[jtamames]

It's OK to use sequential. Perhaps I will try to assemble it externally using a long-read PacBio assembler and providing the result to SqueezeMeta.

[HannahBenisty]

Thanks!

I have tried again and still the same error message as before. Would you restart the pipeline from scratch?

[jtamames]

It should work. But if you can, save a copy of the results you already have