Closed UniAlberta closed 3 weeks ago
Are there any files in the 00_LOGS directory?
No, nothing is created.
On Mon, Aug 19, 2024, 23:38 A. Murat Eren (Meren) @.***> wrote:
Are there any files in the 00_LOGS directory?
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The folder 00_LOGS is created but empty.
On Mon, Aug 19, 2024, 23:44 Nafsa Khazaei @.***> wrote:
No, nothing is created.
On Mon, Aug 19, 2024, 23:38 A. Murat Eren (Meren) < @.***> wrote:
Are there any files in the 00_LOGS directory?
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This means the problem is occurring before anvi'o processes could actually start running. Can you please run the workflow in an interactive shell rather than sending the command to the queue to see the error messages?
I'm running in an interactive shell. The output file has no error messages, but has warning messages.
On Tue, Aug 20, 2024, 02:00 A. Murat Eren (Meren) @.***> wrote:
This means the problem is occurring before anvi'o processes could actually start running. Can you please run the workflow in an interactive shell rather than sending the command to the queue to see the error messages?
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Here it is.
On Tue, Aug 20, 2024 at 5:23 AM Nafsa Khazaei @.***> wrote:
I'm running in an interactive shell. The output file has no error messages, but has warning messages.
On Tue, Aug 20, 2024, 02:00 A. Murat Eren (Meren) < @.***> wrote:
This means the problem is occurring before anvi'o processes could actually start running. Can you please run the workflow in an interactive shell rather than sending the command to the queue to see the error messages?
— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2333#issuecomment-2298217891, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZVXR3V4ZDEPHQG6TM3NLLLZSLZRDAVCNFSM6AAAAABMYRY6VSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJYGIYTOOBZGE . You are receiving this because you authored the thread.Message ID: @.***>
Your message says here it is but I don't see anything. Am I fired?
Oh no, I wrote here it is in your reply as I attached the output file for you.
On Tue, Aug 20, 2024, 06:51 A. Murat Eren (Meren) @.***> wrote:
Your message says here it is but I don't see anything. Am I fired?
— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2333#issuecomment-2298784071, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZVXR3XJU2ZGAIF3ES7TWX3ZSM3TPAVCNFSM6AAAAABMYRY6VSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJYG44DIMBXGE . You are receiving this because you authored the thread.Message ID: @.***>
Are you able to see the attached OUT file? If not, I copied the content here.
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
If you publish results from this workflow, please do not forget to cite snakemake (doi:10.1093/bioinformatics/bts480)
HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None) HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None) HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None) HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None)
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
We are initiating parameters for the metagenomics workflow
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
We are initiating parameters for the metagenomics workflow
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
We are initiating parameters for the metagenomics workflow
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None)
We are initiating parameters for the metagenomics workflow
HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None) HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None)
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
We are initiating parameters for the metagenomics workflow
We are initiating parameters for the metagenomics workflow
HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None) HMM profiles .................................: 9 sources have been loaded: Ribosomal_RNA_16S (3 genes, domain: None), Ribosomal_RNA_28S (1 genes, domain: None), Ribosomal_RNA_18S (1 genes, domain: None), Protista_83 (83 genes, domain: eukarya), Ribosomal_RNA_23S (2 genes, domain: None), Bacteria_71 (71 genes, domain: bacteria), Archaea_76 (76 genes, domain: archaea), Ribosomal_RNA_5S (5 genes, domain: None), Ribosomal_RNA_12S (1 genes, domain: None)
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
We are initiating parameters for the metagenomics workflow
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
We are initiating parameters for the metagenomics workflow
OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. So make sure that these don't include anything that you didn't mean to include as an additional param: --cores, 12, --keep-going, --rerun-incomplete, --unlock.
We are initiating parameters for the metagenomics workflow
/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/workflows/metagenomics/Snakefile:1111: SyntaxWarning: "is not" with a literal. Did you mean "!="? params:
We are initiating parameters for the metagenomics workflow
/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/workflows/metagenomics/Snakefile:1111: SyntaxWarning: "is not" with a literal. Did you mean "!="? params:
We are initiating parameters for the metagenomics workflow
/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/workflows/metagenomics/Snakefile:1111: SyntaxWarning: "is not" with a literal. Did you mean "!="? params:
We are initiating parameters for the metagenomics workflow
/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/workflows/metagenomics/Snakefile:1111: SyntaxWarning: "is not" with a literal. Did you mean "!="? params:
We are initiating parameters for the metagenomics workflow
Needed .......................................: gunzip, anvi-script-reformat-fasta, anvi-script-reformat-fasta, anvi-gen-contigs-database, anvi-import-functions, anvi-get-sequences-for-gene-calls, centrifuge, anvi-import-taxonomy-for-genes, anvi-run-hmms, anvi-run-pfams, anvi-run-kegg-kofams, anvi-run-ncbi-cogs, anvi-run-scg-taxonomy, anvi-scan-trnas, anvi-get-sequences-for-gene-calls, iu-gen-configs, iu-filter-quality-minoche, gzip, bowtie2-build, bowtie2, samtools, anvi-init-bam, anvi-profile, echo, anvi-import-collection, anvi-script-add-default-collection, anvi-summarize, anvi-split, mv, krakenuniq, krakenuniq-mpa-report, anvi-import-taxonomy-for-layers, anvi-cluster-contigs Missing ......................................: centrifuge, krakenuniq, krakenuniq-mpa-report
Needed .......................................: gunzip, anvi-script-reformat-fasta, anvi-script-reformat-fasta, anvi-gen-contigs-database, anvi-import-functions, anvi-get-sequences-for-gene-calls, centrifuge, anvi-import-taxonomy-for-genes, anvi-run-hmms, anvi-run-pfams, anvi-run-kegg-kofams, anvi-run-ncbi-cogs, anvi-run-scg-taxonomy, anvi-scan-trnas, anvi-get-sequences-for-gene-calls, iu-gen-configs, iu-filter-quality-minoche, gzip, bowtie2-build, bowtie2, samtools, anvi-init-bam, anvi-profile, echo, anvi-import-collection, anvi-script-add-default-collection, anvi-summarize, anvi-split, mv, krakenuniq, krakenuniq-mpa-report, anvi-import-taxonomy-for-layers, anvi-cluster-contigs Missing ......................................: centrifuge, krakenuniq, krakenuniq-mpa-report
/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/workflows/metagenomics/Snakefile:1111: SyntaxWarning: "is not" with a literal. Did you mean "!="? params:
We are initiating parameters for the metagenomics workflow
Needed .......................................: gunzip, anvi-script-reformat-fasta, anvi-script-reformat-fasta, anvi-gen-contigs-database, anvi-import-functions, anvi-get-sequences-for-gene-calls, centrifuge, anvi-import-taxonomy-for-genes, anvi-run-hmms, anvi-run-pfams, anvi-run-kegg-kofams, anvi-run-ncbi-cogs, anvi-run-scg-taxonomy, anvi-scan-trnas, anvi-get-sequences-for-gene-calls, iu-gen-configs, iu-filter-quality-minoche, gzip, bowtie2-build, bowtie2, samtools, anvi-init-bam, anvi-profile, echo, anvi-import-collection, anvi-script-add-default-collection, anvi-summarize, anvi-split, mv, krakenuniq, krakenuniq-mpa-report, anvi-import-taxonomy-for-layers, anvi-cluster-contigs Missing ......................................: centrifuge, krakenuniq, krakenuniq-mpa-report
On Tue, Aug 20, 2024 at 9:13 AM Nafsa Khazaei @.***> wrote:
Oh no, I wrote here it is in your reply as I attached the output file for you.
On Tue, Aug 20, 2024, 06:51 A. Murat Eren (Meren) < @.***> wrote:
Your message says here it is but I don't see anything. Am I fired?
— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2333#issuecomment-2298784071, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZVXR3XJU2ZGAIF3ES7TWX3ZSM3TPAVCNFSM6AAAAABMYRY6VSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJYG44DIMBXGE . You are receiving this because you authored the thread.Message ID: @.***>
I see --unlock
in your additional parameters. It is simply asking snakemake to remove a stale lock (if exists), and quit. Please read the snakemake help from more details (and perhaps remove that parameter and try again after).
Needed .......................................: gunzip, anvi-script-reformat-fasta, anvi-script-reformat-fasta, anvi-gen-contigs-database, anvi-import-functions, anvi-get-sequences-for-gene-calls, centrifuge, anvi-import-taxonomy-for-genes, anvi-run-hmms, anvi-run-pfams, anvi-run-kegg-kofams, anvi-run-ncbi-cogs, anvi-run-scg-taxonomy, anvi-scan-trnas, anvi-get-sequences-for-gene-calls, iu-gen-configs, iu-filter-quality-minoche, gzip, bowtie2-build, bowtie2, samtools, anvi-init-bam, anvi-profile, echo, anvi-import-collection, anvi-script-add-default-collection, anvi-summarize, anvi-split, mv, krakenuniq, krakenuniq-mpa-report, anvi-import-taxonomy-for-layers, anvi-cluster-contigs Missing ......................................: centrifuge, krakenuniq, krakenuniq-mpa-report
However, I see the folders such as 00_LOGS, 02_FASTA, 03_CONTIGS and 04_MAPPING have been created with files in them and the workflow is running. Is that fine?
On Wed, Aug 21, 2024 at 2:23 AM A. Murat Eren (Meren) < @.***> wrote:
I see --unlock in your additional parameters. It is simply asking snakemake to remove a stale lock (if exists), and quit. Please read the snakemake help from more details (and perhaps remove that parameter and try again after).
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No this is not fine :( I'm afraid you need to talk to a local bioinformatics person. This needs some interactive debugging to figure out what is happening with your snakemake. Sorry.
Hi,
I
m running anvio-8 to do assembly and binning. I can successfully submit the job script with no errors but it fails after a few seconds. There is no error in the output file so I
m really confused about it. Could you please give me some guidance?