exit status (137)

[ntromas]

Hi,

I just got this error and I wonder how to fix it. Thanks for the help! In the working dir "70c33636e9449f7ab62b01d9375d6e" I do have tmp_allctgs.txt file that is not empty.

Cheers

Nico

_Error executing process > 'identify_fasta_MSF:samtools (1)'

Caused by: Process identify_fasta_MSF:samtools (1) terminated with an error exit status (137)

Command executed:

cat metaphinder-own-DB.txt metaphinder.txt phigaro.txt seeker.txt sourmash.txt vibrant-virome.txt vibrant.txt virfinder.txt virsorter-virome.txt virsorter.txt virsorter2.txt | sort | uniq > tmp_allctgs.txt cat Preselection_dvf_filtered.fa > all.fasta

get samtools but ignore "samtool fails"

while read fastaheader; do
if grep -qw ">$fastaheader" all.fasta; then samtools faidx all.fasta $fastaheader >> Preselection_dvf_positive_contigs.fa else echo "$fastaheader not found" >> error_code_samtools.txt fi done < tmp_allctgs.txt

old command

xargs samtools faidx all.fasta < tmp_allctgs.txt > Preselection_dvf_positive_contigs.fa

Command exit status: 137

Command output: (empty)

Work dir: /mnt/1bcce214-6fb0-454a-99a7-df65602d98b6/What_the_Phage-master/work2/2e/70c33636e9449f7ab62b01d9375d6e

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line_

[replikation]

hi, exit statements of 137 or more generally exit> 100 are usually related to the computer hardware (e.g. not enough RAM).

what system are you running on?

[ntromas]

Hi,

Worstation with Ubuntu 20.04 , 128Gb RAM, 26 cores.

Nico

Le lun. 8 nov. 2021 08 h 52, Christian Brandt @.***> a écrit :

hi, exit statements of 137 or more generally exit> 100 are usually related to the computer hardware (e.g. not enough RAM).

what system are you running on?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/replikation/What_the_Phage/issues/151#issuecomment-963169636, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABY5D6EW4WX3PHZYJKOZEO3UK7I2HANCNFSM5HSWMF4Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[replikation]

can you also paste the command used and the WtP version that you used? @ntromas

[ntromas]

Sure:

nextflow run replikation/What_the_Phage --fasta Preselection_dvf.fa --cores 12 -profile local,docker -r v1.0.2 --dv --filter 1500 --databases database_wtp/ --workdir work2/ --output results/

N E X T F L O W ~ version 20.07.1

Launching replikation/What_the_Phage [distraught_pauling] - revision: fc18d6a2a6 [v1.0.2]

---

---

/ \ / __ _/____ \

\ \/\/ / | | | ___/

\ / | | | |

__/\ / || ||

    \/

---

Profile: local,docker

Current User: nico

Nextflow-version: 20.07.1

WtP intended for Nextflow-version: 20.01.0

Starting time: 24-07-2020 15:18 UTC

Workdir location [--workdir]:

/tmp/nextflow-phages-nico

Output location [--output]:

results

Database location [--databases]:

nextflow-autodownload-databases

CPUs to use: 12, maximal CPUs to use: 28

Le lun. 8 nov. 2021 à 09:01, Christian Brandt @.***> a écrit :

can you also paste the command used and the WtP version that you used? @ntromas https://github.com/ntromas

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/replikation/What_the_Phage/issues/151#issuecomment-963176977, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABY5D6BCVXUUKKFEYMNYGUTUK7J2XANCNFSM5HSWMF4Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

--

---

Nicolas Tromas PhD Université de Montréal Département de sciences biologiques Microbial Evolutionary Genomics Group-Laboratoire de Jesse Shapiro Pavillon Marie-Victorin 90 Vincent-d'Indy, Montréal, Québec, H2V 2S9 Phone: (514) 343 6111 3188 E-mail: @. @.> Researchgate: NTromasPage https://www.researchgate.net/profile/Nicolas_Tromas Web: http://www.shapirolab.ca/

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[mult1fractal]

I'm running now your command on our workstation and try to reproduce the error.

you could try to reboot your workstation and run your command again since error 137 should be related to ram

[mult1fractal]

Hey,

I was unable to reproduce your error. The workflow finished without any problems with your command.

Have you tried to reboot your workstation and re-run WTP

[ntromas]

Will try that...

Le mar. 9 nov. 2021 04 h 05, Mike Marquet @.***> a écrit :

Hey,

I was unable to reproduce your error. The workflow finished without any problems with your command.

Have you tried to reboot your workstation and re-run WTP

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