sajjadasaf
commented
1 month ago Open sajjadasaf opened 1 month ago
sajjadasaf
commented
1 month ago 
fmalmeida
commented
1 month ago Hi @sajjadasaf ,
It seems you ran out of memory. Can you attach here the .nextflow.log file and the .command.? files of this process so I can check?
Then I can propose something if that is the case.
sajjadasaf
commented
1 month ago How much memory it needed? Where I can find .command. file?
fmalmeida
commented
1 month ago The amount of memory necessary, is dependent on the amount of data given as input and genome size.
For example, for a bacteria with 5.5m I can generally run with no more than 10.Gb. But, it always depends on amount of data and genome size.
In any case, I just noted this: string: Execution is retried (1)
Did the pipeline shut down, or still running? I expect with this message that the pipeline should still try once with the max allowed memory.
If it is still running, let's wait to check if it works.
If the pipeline indeed shuts down, please attach the logs I mentioned, the main pipeline .nextflow.log file and the .command.? files of the specific process that shuts the pipeline down.
By the error, it seems to me that it only requires more memory than the first try.
fmalmeida
commented
1 month ago How much memory it needed? Where I can find .command. file?
I just checked the log. It seems the pipeline is still running. Let's first see if it works on not on the automatic second try. If not, we can assess the process logs to check what is the error.
The .command.? files are placed in the working directories. The working directories one can find in the .nextflow.log. For example, here:
sajjadasaf
commented
1 month ago Thank you for your kind reply. Yes the pipeline still running and trying. It is fungi data with 35m genome.
fmalmeida
commented
1 month ago Thank you for your kind reply. Yes the pipeline still running and trying. It is fungi data with 35m genome.
Perfect. Let's wait a bit more then. If it indeed fail shutting down incomplete, we can collect all the logs. Then I can take a look at it!
Thanks for using it.
sajjadasaf
commented
3 weeks ago You were right it was a memory error. I increased the memory and the process almost complete but at the end it show the following error.
executor > local (2)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
[- ] LONGREADS_ONLY:canu -
[- ] LONGREADS_ONLY:flye -
[- ] LONGREADS_ONLY:unicycler -
[- ] LONGREADS_ONLY:raven -
[- ] LONGREADS_ONLY:shasta -
[- ] LONGREADS_ONLY:wtdbg2 -
[- ] LONGREADS_ONLY:hifiasm -
[- ] LONGREADS_ONLY:medaka -
[- ] LONGREADS_ONLY:nanopolish -
[- ] LONGREADS_ONLY:gcpp -
[21/3016b3] HYB…gillus_terreus:strategy_1) | 1 of 1, cached: 1 ✔
[03/badcd2] HYB…gillus_terreus:strategy_1) | 1 of 1, cached: 1 ✔
[6c/0227b1] HYB…gillus_terreus:strategy_2) | 1 of 1, cached: 1 ✔
[2d/84db3d] HYB…gillus_terreus:strategy_2) | 1 of 1, cached: 1 ✔
[55/c38b23] HYB…gillus_terreus:strategy_2) | 1 of 1, cached: 1 ✔
[19/746669] HYB…gillus_terreus:strategy_2) | 1 of 1, cached: 1 ✔
[- ] HYBRID:strategy_2_shasta -
[b4/85bcc0] HYB…gillus_terreus:strategy_2) | 1 of 1, cached: 1 ✔
[80/2e77ed] HYB…gillus_terreus:strategy_2) | 5 of 5, cached: 5 ✔
[5e/d425c6] HYB…gillus_terreus:strategy_2) | 5 of 5, cached: 5 ✔
[34/fa7243] ASS…gillus_terreus:strategy_1) | 17 of 17, cached: 16, failed: 1 ✘
[26/9b7334] ASS…M_DUMPSOFTWAREVERSIONS (1) | 1 of 1 ✔
[- ] ASSEMBLY_QC:multiqc | 0 of 1
Plus 4 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
Pipeline completed at: 2024-06-07T14:08:33.269330969+04:00
Execution status: failed
Execution duration: 41m 43s
Do not give up, we can fix it!
ERROR ~ Error executing process > 'ASSEMBLY_QC:quast (aspergillus_terreus:strategy_1)'
Caused by:
Process `ASSEMBLY_QC:quast (aspergillus_terreus:strategy_1)` terminated with an error exit status (1)
Command executed:
# run quast
quast.py \
-o unicycler \
-t 4 \
--pacbio Genomic-DNA-8_LGE6249-PacBio.hifi_reads.fastq \
--pe1 Genomic-DNA-8-LGE6249_L4_1.fq --pe2 Genomic-DNA-8-LGE6249_L4_2.fq \
\
--rna-finding \
--min-contig 100 \
\
unicycler_assembly.fasta
# run busco
cp -r /opt/busco_db .
busco \
--tar \
--download_path ./ \
-i unicycler_assembly.fasta \
-m genome \
-l ./busco_db/bacteria_odb10 \
-o unicycler/busco_stats/run_unicycler
# change names
for i in $( find unicycler/busco_stats/run_unicycler -name 'short*.json' ) ; do
path=$( dirname $i ) ;
mv $i ${path}/short_summary_unicycler.json ;
done
for i in $( find unicycler/busco_stats/run_unicycler -name 'short*.txt' ) ; do
path=$( dirname $i ) ;
mv $i ${path}/short_summary_unicycler.txt ;
done
# save assembly
mkdir -p input_assembly
cp unicycler_assembly.fasta input_assembly/unicycler_assembly.fasta
# get version
cat <<-END_VERSIONS > versions.yml
"ASSEMBLY_QC:quast":
quast: $( quast.py --version | tail -n+2 | cut -f 2 -d ' ' )
busco: $( busco --version | cut -f 2 -d ' ' )
END_VERSIONS
Command exit status:
1
Command output:
2024-06-07 10:08:19
Running Basic statistics processor...
Contig files:
unicycler_assembly
Calculating N50 and L50...
unicycler_assembly, N50 = 1902357, L50 = 8, auN = 1720046.8, Total length = 33445707, GC % = 52.29, # N's per 100 kbp = 0.00
Drawing Nx plot...
saved to unicycler/basic_stats/Nx_plot.pdf
Drawing cumulative plot...
saved to unicycler/basic_stats/cumulative_plot.pdf
Drawing GC content plot...
saved to unicycler/basic_stats/GC_content_plot.pdf
Drawing unicycler_assembly GC content plot...
saved to unicycler/basic_stats/unicycler_assembly_GC_content_plot.pdf
Done.
NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
2024-06-07 10:08:21
Running Barrnap...
Logging to unicycler/predicted_genes/barrnap.log...
Ribosomal RNA genes = 25
Predicted genes (GFF): unicycler/predicted_genes/unicycler_assembly.rna.gff
Done.
2024-06-07 10:08:28
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
1 of 2: Creating PDF with all tables and plots...
2 of 2: Creating Icarus viewers...
Done
2024-06-07 10:08:29
RESULTS:
Text versions of total report are saved to unicycler/report.txt, report.tsv, and report.tex
Text versions of transposed total report are saved to unicycler/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
HTML version (interactive tables and plots) is saved to unicycler/report.html
PDF version (tables and plots) is saved to unicycler/report.pdf
Icarus (contig browser) is saved to unicycler/icarus.html
Log is saved to unicycler/quast.log
Finished: 2024-06-07 10:08:29
Elapsed time: 0:41:28.089135
NOTICEs: 5; WARNINGs: 2; non-fatal ERRORs: 0
Thank you for using QUAST!
2024-06-07 10:08:32 INFO: ***** Start a BUSCO v5.6.1 analysis, current time: 06/07/2024 10:08:32 *****
2024-06-07 10:08:32 INFO: Configuring BUSCO with local environment
2024-06-07 10:08:32 INFO: Running genome mode
Command error:
Calculating N50 and L50...
unicycler_assembly, N50 = 1902357, L50 = 8, auN = 1720046.8, Total length = 33445707, GC % = 52.29, # N's per 100 kbp = 0.00
Drawing Nx plot...
saved to unicycler/basic_stats/Nx_plot.pdf
Drawing cumulative plot...
saved to unicycler/basic_stats/cumulative_plot.pdf
Drawing GC content plot...
saved to unicycler/basic_stats/GC_content_plot.pdf
Drawing unicycler_assembly GC content plot...
saved to unicycler/basic_stats/unicycler_assembly_GC_content_plot.pdf
Done.
NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
2024-06-07 10:08:21
Running Barrnap...
Logging to unicycler/predicted_genes/barrnap.log...
Ribosomal RNA genes = 25
Predicted genes (GFF): unicycler/predicted_genes/unicycler_assembly.rna.gff
Done.
2024-06-07 10:08:28
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
1 of 2: Creating PDF with all tables and plots...
2 of 2: Creating Icarus viewers...
Done
2024-06-07 10:08:29
RESULTS:
Text versions of total report are saved to unicycler/report.txt, report.tsv, and report.tex
Text versions of transposed total report are saved to unicycler/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
HTML version (interactive tables and plots) is saved to unicycler/report.html
PDF version (tables and plots) is saved to unicycler/report.pdf
Icarus (contig browser) is saved to unicycler/icarus.html
Log is saved to unicycler/quast.log
Finished: 2024-06-07 10:08:29
Elapsed time: 0:41:28.089135
NOTICEs: 5; WARNINGs: 2; non-fatal ERRORs: 0
Thank you for using QUAST!
2024-06-07 10:08:32 INFO: ***** Start a BUSCO v5.6.1 analysis, current time: 06/07/2024 10:08:32 *****
2024-06-07 10:08:32 INFO: Configuring BUSCO with local environment
2024-06-07 10:08:32 INFO: Running genome mode
2024-06-07 10:08:32 ERROR: A run with the name unicycler/busco_stats/run_unicycler already exists...
If you are sure you wish to overwrite existing files, please use the -f (force) option
2024-06-07 10:08:32 ERROR: BUSCO analysis failed!
2024-06-07 10:08:32 ERROR: Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues
Work dir:
/home/omic/funig8/work/34/fa7243238dbef8437ae5534af56df3
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for detailsHi @sajjadasaf ,
I think if I just add a '-f' param to BUSCO and Quast might solve this issue.
I am making a new branch with this feature. Can you try to see if it works?
You have to include the -r issue-77 -latest and -resume param to, respectively, use the correct source branch, and make nextflow try to load all successful processes, starting only the failed ones. -latest makes nextflow download the latest version of selected code.
E.g. nextflow run fmalmeida/mpgap run -r issue-77 -latest -resume ... < all your other params >.
Let me know what happens, if it works, I can make a hotfix release.