Closed xlinxlin closed 5 years ago
drpatelh
commented
5 years ago Hi @xlinxlin What error were you seeing? @apeltzer now maintains the pipeline but he is on annual leave. Would you mind creating a PR to the dev branch of the pipeline that updates this?
This just means we can get the dev version of the pipeline working for you and everyone else :+1: . Also, the Docker container for the pipeline will be rebuilt after the merge.
Thank you!
xlinxlin
commented
5 years ago Hi @drpatelh the error was something like this:
executor > local (14)
[93/046c90] process > get_software_versions [100%] 1 of 1, cached: 1 ✔
[8f/c1d737] process > trim_and_combine (SH_1_S1) [100%] 13 of 13, cached: 13 ✔
[5a/2ba574] process > fastqc (SH_10_S10) [100%] 13 of 13, cached: 13 ✔
[32/4b6fe8] process > unicycler (SH_5_S5) [100%] 13 of 13, cached: 13 ✔
[d9/94ccef] process > quast (quast for each SH_3_S3) [100%] 13 of 13, cached: 7 ✔
[78/4c1ef4] process > prokka (SH_10_S10) [100%] 8 of 8, failed: 8
[- ] process > multiqc -
[c2/19421b] process > output_documentation (1) [100%] 1 of 1, cached: 1 ✔
[0;35m[nf-core/bacass] Pipeline completed with errors
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'prokka (SH_15_S15)'
Caused by:
Process `prokka (SH_15_S15)` terminated with an error exit status (2)
Command executed:
prokka --cpus 16 --prefix "SH_15_S15" --outdir SH_15_S15_annotation /home/sysgen/nf-core/bacass/bacass-master/work/6a/f365330352c310cff160d9ac21d682/SH_15_S15_assembly.fasta
Command exit status:
2
Command output:
(empty)
Command error:
[14:43:53] Fixed 2 duplicate /gene - tagE_1 tagE_2
[14:43:53] Fixed 3 duplicate /gene - xerC_1 xerC_2 xerC_3
[14:43:53] Fixed 2 duplicate /gene - femA_1 femA_2
[14:43:53] Fixed 2 duplicate /gene - glnQ_1 glnQ_2
[14:43:53] Fixed 3 duplicate /gene - bin3_1 bin3_2 bin3_3
[14:43:53] Fixed 2 duplicate /gene - arcB_1 arcB_2
[14:43:53] Fixed 2 duplicate /gene - phnE_1 phnE_2
[14:43:53] Fixed 2 duplicate /gene - znuA_1 znuA_2
[14:43:53] Fixed 2 duplicate /gene - metP_1 metP_2
[14:43:53] Fixed 2 duplicate /gene - yqfL_1 yqfL_2
[14:43:53] Fixed 2 duplicate /gene - xylB_1 xylB_2
[14:43:53] Fixed 2 duplicate /gene - copA_1 copA_2
[14:43:53] Fixed 2 duplicate /gene - bmrA_1 bmrA_2
[14:43:53] Fixed 2 duplicate /gene - brnQ_1 brnQ_2
[14:43:53] Fixed 3 duplicate /gene - mqo2_1 mqo2_2 mqo2_3
[14:43:53] Fixed 2 duplicate /gene - gtf2_1 gtf2_2
[14:43:53] Fixed 3 duplicate /gene - bceB_1 bceB_2 bceB_3
[14:43:53] Fixed 2 duplicate /gene - dapH_1 dapH_2
[14:43:53] Fixed 2 duplicate /gene - tagG_1 tagG_2
[14:43:53] Fixed 2 duplicate /gene - tadA_1 tadA_2
[14:43:53] Fixed 9 duplicate /gene - btuD_1 btuD_2 btuD_3 btuD_4 btuD_5 btuD_6 btuD_7 btuD_8 btuD_9
[14:43:53] Fixed 2 duplicate /gene - graS_1 graS_2
[14:43:53] Fixed 2 duplicate /gene - queE_1 queE_2
[14:43:53] Fixed 3 duplicate /gene - argR_1 argR_2 argR_3
[14:43:53] Fixed 5 duplicate /gene - zwf_1 zwf_2 zwf_3 zwf_4 zwf_5
[14:43:53] Fixed 2 duplicate /gene - cls_1 cls_2
[14:43:53] Fixed 2 duplicate /gene - graR_1 graR_2
[14:43:53] Fixed 2 duplicate /gene - pepA_1 pepA_2
[14:43:53] Fixed 2 duplicate /gene - mleN_1 mleN_2
[14:43:53] Fixed 2 duplicate /gene - guaB_1 guaB_2
[14:43:53] Fixed 2 duplicate /gene - suhB_1 suhB_2
[14:43:53] Fixed 2 duplicate /gene - opuCD_1 opuCD_2
[14:43:53] Fixed 2 duplicate /gene - macB_1 macB_2
[14:43:53] Fixed 2 duplicate /gene - lacC_1 lacC_2
[14:43:53] Fixed 2 duplicate /gene - oatA_1 oatA_2
[14:43:53] Fixed 3 duplicate /gene - arsB_1 arsB_2 arsB_3
[14:43:53] Fixed 2 duplicate /gene - mscS_1 mscS_2
[14:43:53] Fixed 2 duplicate /gene - yciC_1 yciC_2
[14:43:53] Fixed 2 duplicate /gene - uvrA_1 uvrA_2
[14:43:53] Fixed 2 duplicate /gene - copZ_1 copZ_2
[14:43:53] Fixed 2 duplicate /gene - ecfT_1 ecfT_2
[14:43:53] Fixed 3 duplicate /gene - czcD_1 czcD_2 czcD_3
[14:43:53] Fixed 119 colliding /gene names.
[14:43:53] Adding /locus_tag identifiers
[14:43:53] Assigned 2358 locus_tags to CDS and RNA features.
[14:43:53] Writing outputs to SH_15_S15_annotation/
[14:43:56] Generating annotation statistics file
[14:43:56] Generating Genbank and Sequin files
[14:43:56] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka' -Z SH_15_S15_annotation\/SH_15_S15\.err -i SH_15_S15_annotation\/SH_15_S15\.fsa 2> /dev/null
[14:44:05] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka' -Z SH_15_S15_annotation\/SH_15_S15\.err -i SH_15_S15_annotation\/SH_15_S15\.fsa 2> /dev/null
Work dir:
/home/sysgen/nf-core/bacass/bacass-master/work/70/ad80c24bb1be6558027e5267d6da14
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
The log file please see the attachment. I have made a pull request, but I am not sure if this error was due to the Prokka version but it did work after the upgrade.
Pipeline Name : nf-core/bacass
Run Name : stoic_pasteur
Skip Kraken2 : true
Kraken2 DB :
Extra Unicycler arguments:
Extra Prokka arguments:
Max Resources : 64 GB memory, 32 cpus, 1d time per job
Launch dir : /home/sysgen/Desktop/201907_SH_WGS/bacass/bacass-master
Output dir : ./results
Working dir : /home/sysgen/Desktop/201907_SH_WGS/bacass/bacass-master/work
Script dir : /home/sysgen/Desktop/201907_SH_WGS/bacass/bacass-master
User : sysgen
Config Profile : standard
----------------------------------------------------
executor > local (45)
[df/22723e] process > get_software_versions [100%] 1 of 1, cached: 1 ✔
[23/9a1587] process > trim_and_combine (SH_4_S4) [100%] 13 of 13, cached: 13 ✔
[29/e92308] process > fastqc (SH_8_S8) [100%] 13 of 13, cached: 8 ✔
[9e/d22243] process > unicycler (SH_2_S2) [100%] 13 of 13 ✔
[89/eaf049] process > quast (quast for each SH_2_S2) [100%] 13 of 13 ✔
[39/309e00] process > prokka (SH_2_S2) [100%] 13 of 13 ✔
[71/cfe07c] process > multiqc (1) [100%] 1 of 1 ✔
[86/977aca] process > output_documentation (1) [100%] 1 of 1, cached: 1 ✔
[0;35mWarning, pipeline completed, but with errored process(es)
[0;31mNumber of ignored errored process(es) : 0
[0;32mNumber of successfully ran process(es) : 45
[0;35m[nf-core/bacass] Pipeline completed successfully
Completed at: 13-Aug-2019 10:33:27
Duration : 1h 18m 1s
CPU hours : 131.1 (0.6% cached)
Succeeded : 45
Cached : 23Ah, yes the error in the PR is because the tests will still be using the old Docker container. It will only be rebuilt after we have merged the PR.
Hi, yesterday we failed with this pipeline in the Prokka process. After we rewrote the environment.yml file and made it to Prokka 1.14.0, then it works perfect now.