MOP_MOD error msgs

[tzcoolman]

Hi Luca,

I was trying to run the MOP_MOD module and got the following error message:

**task: name=NANOCOMPORE_VER:getVersion; work-dir=null
error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to pull singularity image
command: singularity pull --name quay.io-biocontainers-nanocompore-1.0.0rc3.post1--py38_0.img.pulling.1714006415484 docker://quay.io/biocontainers/nanocompore:1.0.0rc3.post1--py38_0 > /dev/null
status : 255
message:
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
Copying blob sha256:dbd31e1d863d4a41565c08ad1d419c3a3538abfdd4a7971de63b8c5c8a43caec
Copying blob sha256:cfb1ba34637d96787f6e780192bc5f09c04fe0b40c4e1acdcbc88953bce25b5b
Copying blob sha256:75c080ef15ebb28daeadc91eeda0ca95a893fe1f4e55845da3feb58069d42fdc
Copying blob sha256:1dbcab28ce46b65c0174e5e82658492107396fead31e9144c343e6bc96e471c7
Copying blob sha256:ace2d8a63dd59063206661355f22da9e1c75c56d6cae5116d91db7a65f640667
Copying blob sha256:316957f8baafcefd4c9f72b7e3f3fafb7fcb3ca805dc69d242aef656e0736490
Copying blob sha256:2f8531d5a6ece34772cf99a2d30e3057c636f1ad05cdec0c8009eab401e616a7
Copying blob sha256:1dbcab28ce46b65c0174e5e82658492107396fead31e9144c343e6bc96e471c7
Copying blob sha256:2e178fd72baf28bc587b5d274574f1a3d3e25ac802fdaf154af258a3c5891831
Copying blob sha256:06c77ba29d605f0bbac81931217851e0d66a9afdfaddc3d106e02b29f4abc64f
Copying config sha256:bef1cf6ff5db5659b393f305d95b31546adfb2271aa2a721b68c9c235d0cff85
Writing manifest to image destination
Storing signatures
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: no descriptor found for reference "f9c358ce0a2673dec110b3642d94890ecb42ee2d9d787a6f21121828607c8814"

Apr-24 20:53:44.583 [Actor Thread 17] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NANOCOMPORE_VER:getVersion'**

Looks like the error came from singularity pulling nanocompare. I ran mop_preprocess and mop_tail, where multiple tools were pulled and no error occured. Is there any reason for that?

Best

[lucacozzuto]

Hi,

It might be some temporary hiccups... Try to download it by yourself. If you still get the error you might have the singularity temporary folder filled.

I'm the upcoming version I'll add a script for downloading images in advance.

Best,
Luca

[tzcoolman]

Unfortunetely, we only have singularity/apptainer for downloading img files, so I tried the following commands:

singularity pull https://quay.io/biocontainers/nanocompore:1.0.0rc3.post1--py38_0

singularity pull docker://quay.io/biocontainers/nanocompore

apptainer pull docker://quay.io/biocontainers/nanocompore

But none of them worked. could you please help me with that? Thanks

[lucacozzuto]

Hi, what is the error you get? Can it be that your singularity cache dir is full?

[tzcoolman]

Thanks for your reply.

I mannually downloaded nanocompore & epinano then ran the module.
singularity pull --name biocorecrg-mopmod-0.6.img.pulling.1715790772835 docker://biocorecrg/mopmod:0.6

singularity pull docker://quay.io/biocontainers/nanocompore:1.0.0rc3.post1--py38_0

singularity pull --name biocorecrg-mopepinano-0.2.img.pulling.1715789865283 docker://biocorecrg/mopepinano:0.2

It worked until error message occured again:
executor > local (978)
[8d/f57dc5] che…ary_assembly.genome.fa.gz) | 1 of 1 ✔
[2f/e3418e] epi…Splitting of reference.fa) | 1 of 1 ✔
[bb/e2bfcb] epi…trol_s.bam on pieces76.fa) | 154 of 154 ✔
[aa/228e01] epi…nce (Indexing pieces76.fa) | 77 of 77 ✔
[- ] epi…INANO_CALC_VAR_FREQUENCIES | 0 of 154
[- ] epinano_flow:joinEpinanoRes -
[- ] epi…_flow:makeEpinanoPlots_ins -
[- ] epi…_flow:makeEpinanoPlots_mis -
[- ] epi…_flow:makeEpinanoPlots_del -
[1c/01b8ff] com…etChromInfo (reference.fa) | 1 of 1 ✔
[fe/8fd472] com…EVENTALIGN:index (control) | 2 of 2 ✔
[dc/0e0083] com…6945dd9bd63f7bf_144.fast5) | 245 of 245 ✔
[- ] com…NTALIGN:eventalignCollapse | 0 of 2
[05/89b2ea] com…w:mean_per_pos (treatment) | 1 of 245, failed: 1
[- ] com…h_flow:concat_mean_per_pos -
[- ] com…lish_flow:concat_csv_files -
[- ] com…MPLE_COMPARE:sampleCompare -
[cc/8c53f1] tom…b6e8ad6945dd9bd63f7bf_149) | 245 of 245 ✔
[90/69f3ac] tom…b6e8ad6945dd9bd63f7bf_115) | 244 of 245
[df/9229ad] getChromInfo (reference.fa) | 1 of 1 ✔
[ae/b30f74] EPINANO_VER:getVersion | 1 of 1 ✔
[86/b06ee3] NANOPOLISH_VER:getVersion | 1 of 1 ✔
[49/890720] NANOCOMPORE_VER:getVersion | 1 of 1 ✔
[8e/142bd5] TOMBO_VER:getVersion | 1 of 1 ✔
Plus 7 more processes waiting for tasks…
ERROR ~ Error executing process > 'compore_polish_flow:mean_per_pos (treatment)'

Caused by:
Process compore_polish_flow:mean_per_pos (treatment) terminated with an error exit status (127)

Command executed:

mean_per_pos.py -i treatment_FAK48830_943e5944c778fed434e61ec2402d253bb0446cec_50.fast5_event_align.tsv.gz -o basename treatment_FAK48830_943e5944c778fed434e61ec2402d253bb0446cec_50.fast5_event_ali gn.tsv.gz .fast5_event_align.tsv.gz
#gzip *_processed_perpos_median.tsv

Looks like mean_per_pos.py is your in-house script. And the whole task failed because of that. any suggestions?

[lucacozzuto]

Can you see if it just ran out of RAM or time? The error code is suggesting me this

[tzcoolman]

Can you see if it just ran out of RAM or time? The error code is suggesting me this

I tried to increase memory to 200GB, 24cores and let it run for 96hrs. The program stopped after 12hrs. I will try 400GB again and see what happens.

[lucacozzuto]

@ADelgadoT do you have experience with this problem?

[tzcoolman]

@ADelgadoT do you have experience with this problem?

This Error was caused due to incorrect python scripts downloaded to the bin folder under mop_mod. When I downloaded again from github, the error was gone. However, new errors arose:

May-30 14:10:41.395 [FinalizeTask-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=epinano_flow:EPINANO_CALC_VAR_FREQUENCIES (treatment___pieces27_s.bam on treatment); work-dir=/N/slate/ONT_mop/MOP2/mop_mod/work/02/7993cfcce9dc46a799c04b0cf54fd2
error [nextflow.exception.ProcessFailedException]: Process epinano_flow:EPINANO_CALC_VAR_FREQUENCIES (treatment___pieces27_s.bam on treatment) failed

Is it because I didn't use a correct epinano version? I manually downloaded epinano used in the docker script:
'biocorecrg-mopepinano-0.2.img'