PbJelly resumen and error

Lissa Cruz — Wed, 12 Jun 2024 15:46:09 -0000

Hi everyone

I was running a mapping step for PbJelly gap filling. However, It stop after three days with the following error:

File "/home/lissa/ENV/lib/python3.8/site-packages/pbjelly-16.0b1-py3.8.egg/EGG-INFO/scripts/m4pie.py", line 120, in uniteTails
data = datGrab.search(read.qname).groupdict()
AttributeError: 'NoneType' object has no attribute 'groupdict'
Do you know if there is some way to resume PbJelly?. I think it already finished a big part of the mapping. Additionally, do you know how I can resolve this problem?.

Thanks in advance for your answer.

Error during output step

Valentina — Wed, 28 Aug 2019 08:26:50 -0000

Hi Seyhan,

have you ever solved the issue? I'm facing the same

blasr warning, stopped in mapping stage

Lan Wu-Cavener — Mon, 05 Aug 2019 16:04:41 -0000

I am running PBJ to fill gaps of a draft genome assembly using Pacbio long reads on PBS one node 40 cores. The multiple job spun out from the main script has the following error:

[INFO] 2019-08-05T11:50:06 [blasr] started.
Warning: When attempting to select equivalently scoring reads at random
the bestn parameter should be greater than one.

And all stopped without any output. Did anyone run into the same problem? Could anyone give me some advice? I'd appreciate any help!

Lan

mapping stage warning and stopped on single node with multiple cores

Lan Wu-Cavener — Fri, 02 Aug 2019 21:36:26 -0000

Hi,
Run PBJelly mapping stage on a single node with 40 cores as part of PBS cluster. It generated
mapping_chunkXX.sh for each of the input fasta file. But there is no output (fasta.m4 file, .fasta.out file)
Please help me to diagnose the problem. Thanks!

Lan

All the mapping_chunkX.err show the same message:

[INFO] 2019-08-02T16:06:56 [blasr] started.
Warning: When attempting to select equivalently scoring reads at random
the bestn parameter should be greater than one.

The mapping_chunk0.sh is below:

!/bin/bash

blasr /gpfs/group/restricted/drc9/restricted/Lan/default/PBJ_k99/reads_PB/oPB1ccs0.fasta /gpf
s/group/restricted/drc9/restricted/Lan/default/PBJ_k99/ref/o3PE_scafSeq.fasta --sa /gpfs/grou
p/restricted/drc9/restricted/Lan/default/PBJ_k99/ref/o3PE_scafSeq.fasta.sa -m 4 --out /gpfs/g
roup/restricted/drc9/restricted/Lan/default/PBJ_k99/mapping/oPB1ccs0.fasta.m4 --minMatch 12 -
-minAlnLength 5 --minPctSimilarity 70 --maxAnchorsPerPosition 700 --hitPolicy randombest --be
stn 1 --nCandidates 20 --maxScore -500 --nproc 39 --noSplitSubreads
m4pie.py /gpfs/group/restricted/drc9/restricted/Lan/default/PBJ_k99/mapping/oPB1ccs0.fasta.m4
/gpfs/group/restricted/drc9/restricted/Lan/default/PBJ_k99/reads_PB/oPB1ccs0.fasta /gpfs/gro
up/restricted/drc9/restricted/Lan/default/PBJ_k99/ref/o3PE_scafSeq.fasta --nproc 39 -i

Here is the xml: (I removed some input files since they are in sequence)

<jellyprotocol>
/gpfs/group/restricted/drc9/restricted/Lan/default/PBJ_k99/
<reference>/gpfs/group/restricted/drc9/restricted/Lan/default/PBJ_k99/ref/o3PE_scafSeq.fa
sta</reference>
<outputdir>/gpfs/group/restricted/drc9/restricted/Lan/default/PBJ_k99/</outputdir>
<cluster>
${CMD} ${JOBNAME} 2> ${STDERR} 1> ${STDOUT} &
<njobs>39</njobs>
</cluster>
<blasr>--minMatch 12 --minAlnLength 5 --minPctSimilarity 70 --maxAnchorsPerPosition 700 -
-hitPolicy randombest --bestn 1 --nCandidates 20 --maxScore -500 --nproc 39 --noSplitSubreads
</blasr>
<input basedir="/gpfs/group/restricted/drc9/restricted/Lan/default/PBJ_k99/reads_PB">
<job>oPB1ccs0.fasta</job>
<job>oPB1ccs1.fasta</job>
... ...
<job>oPB1ccs7.fasta</job>
<job>oPB2ccs0.fasta</job>
<job>oPB2ccs1.fasta</job>
... ...
<job>oPB2ccs7.fasta</job>

</jellyprotocol>

Jelly quits during assembly, PBS scheduler

Zachary Calamari — Fri, 02 Aug 2019 15:17:16 -0000

Unfortunately, I was not able to get PBJelly to work. Sorry!

Jelly quits during assembly, PBS scheduler

Lan Wu-Cavener — Fri, 02 Aug 2019 14:57:59 -0000

Have you solved the problem? It looks like you have completed previous stages using cluster. Could you please post your protocol file. I am using PBS cluster and trying to get PBJ to work, yet not successful.
Thanks!
Lan

Jelly quits during assembly, PBS scheduler

Zachary Calamari — Sat, 27 Apr 2019 02:59:48 -0000

Hello,

I am trying to run Jelly on a computer using the PBS scheduler. I called Jelly.py assembly protocol.xml with and without the -x "--nproc 16" flag, and the assembly keeps failing with the message =>> PBS: job killed: ncpus 86.0 exceeded limit 16 (burst). Is there a reason the assembly script is attempting to use more CPUs than I've set with the nproc command? I appreciate any assistance!

Best,
Zac

Continued problems with Support step: PBJelly in PBSuite

Niraj Rayamajhi — Thu, 21 Mar 2019 16:46:56 -0000

The problem is solved by lowering--minMapq value!

Continued problems with Support step: PBJelly in PBSuite

Niraj Rayamajhi — Wed, 20 Mar 2019 20:47:59 -0000

Hi All,

I am having the same issue: support.py generates .gml file without any information on graph. It just generates .gml file which contains graph [ ]

You have solved this issue, could you please let me know about it?

Regards,
Niraj

Extraction does not finish

Gina Pham — Tue, 19 Mar 2019 12:13:20 -0000

I ran this in debug mode a few times and got this type of error message in the Jelly.py error log:

2019-03-18 13:24:31,945 [DEBUG] CommandRunner Returned: [(137, '/bin/sh: line 1: 38454 Killed Extraction.py /data/scratch/gpham/pepsi_dm/pbjelly/jelly_protocol3.xml --debug > /data/scratch/gpham/pepsi_dm/pbjelly/dm5_unmasked_hic_oriented_gapfill/assembly/extraction.out 2> /data/scratch/gpham/pepsi_dm/pbjelly/dm5_unmasked_hic_oriented_gapfill/assembly/extraction.err\n', None)]

It looked like a memory issue, though the job was crashing with only about half of the server's memory used. I switched to a server with 1 TB memory and the same command finished.

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PbJelly resumen and error

Error during output step

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!/bin/bash

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Extraction does not finish