Activity for PBSuite
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Lissa Cruz posted a comment on discussion General Discussion
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...
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Valentina posted a comment on discussion PBJelly Tickets
Hi Seyhan, have you ever solved the issue? I'm facing the same
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Lan Wu-Cavener posted a comment on discussion General Discussion
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
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Hi, I have problem with running PBJelly mapping stage on a single node with 40 cores as part of PBS cluster. I used the <cluster> ... </cluster> as shown in xml file (attached). It seems working but having problem to get blasr running. The blasr complained about "bestn" parameter. The run generated mapping_chunkXX.sh for each of the input fasta file. But there is no output (fasta.m4 file, .fasta.out file). I need your advice on how to fix it. Could anyone who successfully get PBJ running with cluster...
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Hi, I have problem with running PBJelly mapping stage on a single node with 40 cores as part of PBS cluster. The run generated mapping_chunkXX.sh for each of the input fasta file. But there is no output (fasta.m4 file, .fasta.out file) The same data set was used to run mapping stage without cluster successfully. So the problem should be in those mapping_chunkXX.sh. I need advice on how to fix it. The .err file does not show the early steps such as Extracting tails, Parsing XX reads, etc. Only showes...
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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) The same data set was used to run mapping stage without cluster successfully. Please help me to diagnose the problem. The .err file does not show the early steps such as Extracting tails, Parsing XX reads, etc. Only showes the blasr started. All the mapping_chunkX.err show the same message: I...
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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:...
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Zachary Calamari posted a comment on discussion PBJelly Tickets
Unfortunately, I was not able to get PBJelly to work. Sorry!
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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
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Vidhya Jagannathan posted a comment on ticket #4
Did you find a solution for this ? I have run into a similar error and do not know how to solve it. Thank you very much for your answer
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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
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Niraj Rayamajhi posted a comment on discussion PBJelly Tickets
The problem is solved by lowering--minMapq value!
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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 [ ] If you have solved this issue, could you please let me know about it? Regards, Niraj
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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
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Gina Pham posted a comment on discussion PBJelly Tickets
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...
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I cannot get the "extraction" step to finish. The log in assembly/extraction.err shows this as the last line: 2019-03-15 16:11:57,053 [INFO] Parsing /data/scratch/gpham/pepsi_dm/pbjelly/all_dm_pacbio_concat_ec2.fasta There are no messages following this line. Any ideas as to what could be wrong?
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Hannes Becher modified a comment on discussion PBJelly Tickets
I have the same problem. Has a solution been found since the last post? Many thanks!
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I have the same problem. Has a solution been found since this post? Many thanks!
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I have the same problem. Has a sulution been found since this post? Many thanks!
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Roy Francis posted a comment on a wiki page
Are the above instructions/dependencies/versions still valid for Dec 2018?
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Mirian Tsuchiya posted a comment on discussion PBJelly Tickets
Hi, I have encountered the same issue. Any suggestion on what could be wrong? Thank you so much!
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Amandine Velt posted a comment on discussion General Discussion
Hello all, I have an assembled genome of 500Mb of size and PacBio 30x data to improve the scaffolding. After the scaffolding, I would like to do the gap filling step with PBJelly. The problem is that when I use PBJelly with the default settings, it fills very well the Ns (70% of Ns are filled, what I want) but also modifies the sequences of my genome around the N (what I don’t want at all!). I just want, basically, replace the Ns with real bases, without modifying anything else. I tried the option...
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Priscila Santos posted a comment on discussion PBJelly Tickets
Dear all. The assembly step ran for 20 days in the cluster (maximal time in the cluster) and did not finish. So I restarted, indicating the path to the tmp folder, to follow if this step was actually running. Now it has being running for 6 days and I do not have any update in the tmp folder for 4 days. I do not have any issue on the previous steps. Someone experienced the same issue? Any advices? Thank you. Priscila
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Hello all, I have an assembled genome of 500Mb of size and PacBio 30x data to improve the scaffolding. After the scaffolding, I would like to do the gap filling step with PBJelly. The problem is that when I use PBJelly with the default settings, it fills very well the Ns (70% of Ns are filled, what I want) but also modifies the sequences of my genome around the N (what I don’t want at all!). I just want, basically, replace the Ns with real bases, without modifying anything else. I tried the option...
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John Martin posted a comment on discussion PBJelly Tickets
Just wanted to report back that LSF works fine for PBSuite, my problem was just some bad syntax
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And actually, if it doesn't support LSF could I manually run all the shell scripts in such a way that PBJelly could pick up and continue on with the steps after mapping?
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I'm trying to submit the mapping portion of pbjelly to an LSF cluster (using 'bsub'). I've split the subreads fastq into 200 parts and I had thought I setup the Protocols.xml file correctly. But when I run Jelly.py mapping Protocol.xml it builds all the shell scripts but doesn't launch anything. Does PBJelly support LSF/bsub? Here is how I setup my cluster command: <cluster> echo '${CMD}' | bsub -N "${JOBNAME}" -o ${STDOUT} -e ${STDERR} -n 200 -M 31000000 -R 'rusage[mem=30000]' -a 'docker(jmartin7/ubuntu:pbsuite)'...
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Thiru Ramaraj posted a comment on discussion PBJelly Tickets
Dear PBJELLY2 Users: We have a genome assembled using PacBio -> BioNano -> HiC The genome assembled is 1.5Gb with the following Gap metrics, Captured Gaps | 78,205 Max Gap | 59,257 Mean Gap | 4,371 Gap N50 | 6,221 Total Gap Length | 341,861,624 We ran PBJELLY2 using close to 50X PacBio data. It only filled 1,754 gaps and the Total gap length went down from 341,861,624 to 335,564,895(resolving only 6,296,729 N's) This is assembly is a prime candidate for gap filling and we were expecting PBJELLY2...
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Amit Rai posted a comment on discussion PBJelly Tickets
Hi, Could you please help me to know how to remove RQ. I have encountered exactly the same problem and will really appreciate your help or suggestion. Thank you so much
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Qincai Li posted a comment on discussion PBHoney Tickets
2018-05-23 16:15:42,907 [ERROR] Exception raised in task NC_008401.2:ErrorCounter - exit 2018-05-23 16:15:42,928 [ERROR] Dumping Traceback: Traceback (most recent call last): File "/xxxx/PBSuite_15.8.24/pbsuite/honey/HSpots.py", line 500, in run next_task(self.bam, self.reference, self.honH5) File "/xxxx/PBSuite_15.8.24/pbsuite/honey/HSpots.py", line 597, in call with honH5.acquireH5('a') as h5dat: File "/xxxx/Python/2.7.8/lib/python2.7/contextlib.py", line 17, in enter return self.gen.next() File...
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Ch Cu posted a comment on discussion PBHoney Tickets
Ostensibly this is because I'm using the wrong version of blasr. I've asked how to install the right version here.
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Where can I install blasr 1.3.1.127046 from? It's not available through conda, it doesn't seem to be available on Github, and I can't run PBHoney without it. Thanks for your help.
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At the first step of the PBHoney example, Honey.py pie $inputReads $reference, I'm hitting the error -nproc is not a valid option. The full output is /home/users/ccurnin/miniconda3/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters Please Cite: English, Adam C.,...
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Rodrigo Baptista modified a comment on a wiki page
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Hi Adam, I'm currently using PBJelly to extend/fill gaps in my assembly but here is a problem, most of my gaps were generated with unknown sizes, (1000 bp). My main idea is to extend the "contig region" and in some cases better recover the telomere information of some chromosomes. The problem is that some of the unknown size gaps were filled and I believe that they are not "real" fills, it is maybe happening because of the unknown size gap length issue of my current assembly. There is any parameter...
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biod posted a comment on ticket #4
Hi Adam, I am facing problem in the output stage wherein I attempt to run PBJelly to fill gaps in my draft genome using pacbio data. All the steps/ stages leading to the output stage run without any discernible error but the output stage does not produce the "3" files, viz, <outputDir>/pbjelly.out.fasta <outputDir>/pbjelly.out.qual <outputDir>/liftOverTable.json which are expected on successful completion of the process. However, I do end with output.err file and "gap_fill_status.txt" but the files...
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Hi, I am facing similar problem wherein I attempt to run PBJelly to fill gaps in my draft genome using pacbio data. I do end with output.err file and "gap_fill_status.txt" but the files have not been helpful in debugging the error. Could you be kind enough to help understand the error. I have provided the following snippets below: snippet of output.err file: I am providing the first and last 15 lines of the output.err file $ cat out.err | head -15 2018-03-12 12:20:33,910 [INFO] Running /opt/packages/pbjelly/PBSuite_15.8.24/bin/Collection.py...
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Jose G. Pérez-Silva posted a comment on discussion PBJelly Tickets
Hi! I was just wondering if there is a way to know, from the standard output of the software, the genome coordinates at which the pacbio reads mapped. Thanks!
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Hi Adam, I have contigs from CLC workbench and LorDEC corrected Pacbio reads. I was wondering if PBJelly can fill gaps for the said reads? If yes, what are the computational requirements, viz, RAM needed and storage needed. I am working with a reptile Genome of 2.5 Gbp size (six corrected pacbio files of size 16 GB ). I have access to 2 TB RAM and 3 TB disk storage but I cannot use all of the disk storage maybe 2TB. Is that enough? Also what is the approximate walltime that I should ask when submitting...
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George Wang posted a comment on discussion General Discussion
Hi there, I am just wondering how to interpret the pbhoney tail result? For example, for a deletion what is the start and end coordinates, and what size the deletion is? There are uBreak and dBreak columns as well as remainSeq column, but I do not know how to interpret it. Thanks. George
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Faraz Khan posted a comment on discussion General Discussion
Is it ok to keep the sequence in reverse complement mode in the new output.fasta or not?. How to deal with this behaviour? Is there a way to order the sequence as the original.fasta file?
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Sergey Kolchenko posted a comment on discussion General Discussion
Hi! How can I extract positions of filled regions relative to corrected assembly? What I mean is that suppose I have a gap in my initial assembly, e.g from 1282 to 3157 and I want to know coordinates of sequence, inserted in my corrected assembly in stead of this gap. This sequences can be bigger or smaller than predicted gap size + corrdinates will be shifted because of other filled gaps. For example, In my case it can be sequence of length 200 and its new coordinates can be 1800-2000 How can I...
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Jeremie Vidal-Dupiol posted a comment on discussion PBJelly Tickets
Hello, additionnal information such an image of dockers can be found here. https://github.com/pgdurand/pbsuite-docker/issues/1 Regards, Jeremie
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Dear all, I'm trying to run PBjelly to close the gap with a 15X Pacbio run in a 1.3Gb genome scaffolded with platanus. I try to do this on a cluster where the sheduler is PBSpro and where programms are installed in a docker image with all its associated program. We manage to install the soft and try it on the test data. Here is the xml <jellyProtocol> <reference>/home/genome/script/assembly/PBjelly/test_jelly/reference/lambda.fasta</reference> <outputDir>/home/genome/script/assembly/PBjelly/test_jelly/test_results/</outputDir>...
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Can we use illumina paired-end assembled reference genome for integrating long reads to improve the assembly? I heard it's only for mate-pair end assembled reference genome?
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medhat modified a comment on discussion PBHoney Tickets
Hi, I'm using PBSuite version 15.8.24 Honey.py spots was used to identify structure variations. one line from the output: 1 1211650 1211854 INS 353 zscore=-11.943;szMean=353.000;sz3rdQ=550.000;szCount=5.000;strandCnt=2,3;szMedian=547.000;groupName=1;coverage=14.000;sz1stQ=60.000;mqfilt=0.000 this means that the start of the insertion in the genome is 1211650 and the end 1211854?! is not the insertion should happen in one point in the genome (so the start and the end should be the same as in https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/9b263cf1/),...
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Hi, I'm using PBSuite version 15.8.24 Honey.py spots was used to identify structure variations. one line from the output: 1 1211650 1211854 INS 353 zscore=-11.943;szMean=353.000;sz3rdQ=550.000;szCount=5.000;strandCnt=2,3;szMedian=547.000;groupName=1;coverage=14.000;sz1stQ=60.000;mqfilt=0.000 this means that the start of the insertion in the genome is 1211650 and the end 1211854?! is not the insertion should happen in one point in the genome (so the start and the end should be the same as in https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/9b263cf1/),...
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Hi, I'm using PBSuite version 15.8.24 Honey.py spots was used to identify structure variations. one line from the output 1 1211650 1211854 INS 353 zscore=-11.943;szMean=353.000;sz3rdQ=550.000;szCount=5.000;strandCnt=2,3;szMedian=547.000;groupName=1;coverage=14.000;sz1stQ=60.000;mqfilt=0.000 this means that the start of the insertion in the genome is 1211650 and the end 1211854?! is not the insertion should happen in one point in the genome (so the start and the end should be the same as in https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/9b263cf1/),...
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Michael Bronski posted a comment on discussion PBJelly Tickets
Hi, I'm using PBJelly 15.8.24 with networkx 1.7, and attempting to fill gaps in an ~ 1.3 Gb 10X assembly. My PBJelly installation runs without error on the test data, and as far as I can tell, there are no problems with my genome up until the output stage. The output stage fails to generate the files output.err and output.out. All of the other output files are present, and seem to have reasonable results. Any idea what the problem might be? Thanks for your help.
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Hi, I am running Honey.py spots with 10 threads and I have this error: 2017-10-11 14:46:53,098 [INFO] |6:SpotCaller|RateMean 0.060716 -- RateStd 0.238808 [e0129:31253] *** Process received signal *** [e0129:31253] Signal: Segmentation fault (11) [e0129:31253] Signal code: Address not mapped (1) [e0129:31253] Failing at address: 0x1581078 [e0129:31254] *** Process received signal *** [e0129:31254] Signal: Segmentation fault (11) [e0129:31254] Signal code: Address not mapped (1) [e0129:31254] Failing...
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Adam English created ticket #8
FASTA/Q name space handling
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Thanks Related: https://sourceforge.net/p/pb-jelly/tickets/7/
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Clean UI
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I can't help you estimate how long it'll take. Hopefully it's done by now? Related: https://sourceforge.net/p/pb-jelly/tickets/6/
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better progress tracking
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--minIndelErr, and insertion/deletion in the alignment needs to be over -m basepairs before we consider it for potential SV evaluation. This helps get rid of most of the sequencing errors since pacbio reads' main mistakes are single base pair insertions or deletions. --threshold, is the minimum number of reads needed to support a varaint before it's considered for SV evaluation --spanMax, if there's a region longer than this threshold where we have a signal of an SV, we ignore it. This helps filter...
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Not all reads are mapped in an orientation that allows them to confidently span the region of interest. Additionally, sometimes, alignment of the long-noisy reads using blasr can 'hide' the variant (e.g. supurious matches to bases that have been deleted in order to gain a better alignment score). Alternate supporting reads those supporting the variant and are fed into the assembly process for refinement. Reference reads are those that confidently span the region of interest.
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Melanie Lou posted a comment on discussion PBHoney Tickets
Hi Adam, For each call, coverage is reported. However I notice that there tend to be more reads shown in IGV than what is reported as coverage for a region in a VCF. How do you calculate coverage (or which reads do you not include and why)? Best, Melanie
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Hi Adam, I checked the documentation (HoneyReadme.txt and the url https://hgsc-vmweb-08.hgsc.bcm.edu/software/honey is down); please let me know if I should have looked elsewhere. What do the following parameters mean? -m MININDELERR, --minIndelErr MININDELERR Minimum size of an indel error to be counted (5) -e THRESHOLD, --threshold THRESHOLD Minimum Spot Threshold (3) --spanMax SPANMAX Maximum Size of spot to be called (3000) For the following parameters, I believe -q uses MAPQ and -i uses szMean....
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RAKESH posted a comment on discussion PBJelly Tickets
I am trying to assemble a 2.5GB genome. I was able to complete Steps setup, mapping, support, extraction and assemble steps in about 4 days using about 10 nodes - 300 Cores. I started running PBJelly output step , It seems to be running on a single Node with 70 cores and 1 TB RAM, althought the load is little low. the output log hasnt got updated from yesterday. I think they are about 1600K Folders in the assembly folder. Is there an estimate time it would take to complete the output stage? Below...
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Afif Elghraoui posted a comment on discussion PBJelly Tickets
looks like this file was supposed to be a symlink. I guess mine got converted to a regular file somehow.
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I just had one of our users experience this problem. He traced it to spaces in the headers of the reads fasta file, where "header1 additional_info" wouldn't match the string as appears in the blasr output ("header1"). I made the following patch to address the problem: --- /usr/local/apps/pbsuite/15.8.24/pbsuite/utils/FileHandlers.py~ 2015-08-24 13:42:15.000000000 -0400 +++ /usr/local/apps/pbsuite/15.8.24/pbsuite/utils/FileHandlers.py 2017-07-27 16:39:12.591370000 -0400 @@ -33,7 +33,7 @@ def __parse(self):...
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One of our users ran into an error with fakeQuals.py: $ fakeQuals.py --help Traceback (most recent call last): File "/usr/local/apps/pbsuite/15.8.24/bin/fakeQuals.py", line 4, in <module> from FileHandlers import FastaFile ImportError: No module named FileHandlers It looks like the import statement is off. The following change fixes it. --- /usr/local/apps/pbsuite/15.8.24/bin/fakeQuals.py~ 2017-07-21 18:27:28.697420000 -0400 +++ /usr/local/apps/pbsuite/15.8.24/bin/fakeQuals.py 2017-07-27 11:22:01.864624000...
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Chad Tomlinson posted a comment on discussion PBJelly Tickets
Hi Adam, I ran the most recent version of PBJelly (15.8.24) to gapfill scaffolds from a chicken Supernova assembly (10x Genomics) using 20X of chicken pacbio data. All of the steps went smoothly with no errors up until the point of the final output stage. I verified that all jobs from all previous stages completed successfully. The output stage is failing at one particular point and I cannot seem to figure out how to get it to work correctly. I have used this same installation of PBJelly and sourced...
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just found that old blasr5 ticket again and re-read your post https://sourceforge.net/p/pb-jelly/tickets/5/#8255 Since the additional changes you talked about got delayed, would you mind just making a release with the current feature-set as a hold-over?
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just found that old blasr5 ticket again and re-read your post https://sourceforge.net/p/pb-jelly/tickets/5/#8255 Since the additional changes you talked about got delayed, would you mind just making a release with the current status as a hold-over?
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We received a request to install pbsuite on our cluster, but I'd like to get a version that's compatible with the latest blasr version. When do you think you could finalize the next release, which would include those changes?
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Andrey Yurchenko posted a comment on discussion PBJelly Tickets
Hello, I use the last version of PBJelly and tried it on the example datset. I have got the error: 2017-06-30 15:34:53,048 [INFO] Running /export/home/aay2c/app2/PBSuite_15.8.24/bin/m4pie.py /export/home/aay2c/PROJECTS/zootoka/PBjelly/mapping/filtered_subreads.fastq.m4 /export/home/aay2c/PROJECTS/zootoka/PBjelly/reads/filtered_subreads.fastq /export/home/aay2c/PROJECTS/zootoka/PBjelly/lambda.fasta --nproc 23 -i 2017-06-30 15:34:53,107 [INFO] Extracting tails Traceback (most recent call last): File...
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Ankit Gupta posted a comment on discussion PBJelly Tickets
Hello , After succesfully running the setup, mapping and suport steps, the extraction step is giving the follwong output: 2017-06-20 14:54:09,258 [INFO] Running /home/ankitg/Software/PBSuite15.8.24/bin/Extraction.py /mnt/hdd2/Work/PCGenome/Improvinggenoassembly/blasr/Protocol.xml 2017-06-20 14:54:09,261 [INFO] Opening GML Files 2017-06-20 14:54:09,336 [INFO] Loading Reference Sequence 2017-06-20 14:54:10,245 [INFO] Extracting Reads 2017-06-20 14:54:10,245 [INFO] Parsing /mnt/hdd2/Work/PCGenome/Improvinggenoassembly/blasr/PCpacbiocontigs.fasta...
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Hello Urmi, Could you also look in the folder for the assembly/ ref0004924.2e3_ref0004924.3e5 and see what's there? Should maybe be some logs or sequence files or jsons. Something about that particular assembly is breaking the pipeline. On Tue, May 16, 2017 at 1:46 AM, Urmi Trivedi urmi208@users.sf.net wrote: Hello Chris and Adam, I am facing same error. 2017-05-09 11:18:44,904 [DEBUG] Getting fill sequence for ref0004924.2e3_ref0004924.3e5 2017-05-09 11:18:44,904 [DEBUG] No predicted gap size Traceback...
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Hello, --nproc=24 helps speed up the mapping step by taking advantage of multi-threading, but the assembly step is single-threaded. Inside the Readme, there are instructions on how to use the njobs of the protocol.xml so that you can run split the single-threaded jobs. """ If you have a single, large machine and not a cluster, use the following command to submit all of your jobs in the background and parallelize operations. Just be careful the number of jobs/resources you execute or you can freeze...
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miquelgralo posted a comment on discussion PBJelly Tickets
Hi all, I am using pb-jelly with an Illumina assembly (350Mb, ~ 370Mbp, average scaffold length ~ 250kbp) and corrected PacBio reads (40Gb, ~30x coverage, avg length read 200kbp, ~3Million reads). In order to run the assembly step, I used -x "--nproc=24" but it is working for two weeks without finish. There is any way to check the overall progress? How can it be speed up? What is the expected runtime in these conditions? Thanks! MG
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Urmi Trivedi posted a comment on discussion PBJelly Tickets
Hello Chris and Adam, I am facing same error. 2017-05-09 11:18:44,904 [DEBUG] Getting fill sequence for ref0004924.2e3_ref0004924.3e5 2017-05-09 11:18:44,904 [DEBUG] No predicted gap size Traceback (most recent call last): File "/lustre/software/PBSuite_15.8.24/bin/Collection.py", line 963, in <module> c.run() File "/lustre/software/PBSuite_15.8.24/bin/Collection.py", line 923, in run self.outputContigs() File "/lustre/software/PBSuite_15.8.24/bin/Collection.py", line 818, in outputContigs liftTracker.append((name,...
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chengjun zhang posted a comment on discussion PBJelly Tickets
Dear team members, I had read the topics and yet seems no one offer an final way to let people estimate how long it will take at the final stage. So i try to read the code and think may be the "cleanGraph" part is the very time-consuming section. So i want to suggest, is that possible to print out the document_name periodically. for example, print out "now is working with the 10000th document: ref10000008.e2-ref20000000e5", and let it show on the screen or file without delay! Many Thanks, best regards,...
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Seyhan Yazar posted a comment on discussion PBJelly Tickets
Dear Adam, I am getting the following error message when running the Collection.py. Everything else has worked fine until this stage. I cannot see any error message in the outputs. Any help will be appreciated. Thanks, Seyhan 2017-05-05 10:22:22,255 [DEBUG] Breaking ref1377171.7e3_ref1377171.8e5 due to assembly failure 2017-05-05 10:23:45,461 [DEBUG] Breaking ref1329073.10e5_ref1329073.9e3 due to assembly failure 2017-05-05 10:25:15,016 [DEBUG] Getting fill sequence for ref3130664e3_ref3681251e5...
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hui-jou chou posted a comment on discussion PBHoney Tickets
Adam do you have any idea about the data?
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I used the follow comment to output partial content: samtools view -h merged_NA12878_sorted.bam...
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Unfortunately no. It looks like you've run everything correctly, but tails isn't...
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because I have about 80 fastq files need to be aligned, which are total 420gb, I...
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It was generated when you ran Honey.py pie to align the reads. On Wed, Mar 29, 2017...
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where can i find bampie.py log?
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How about your bampie.py log?
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there was no error shown when I ran tails. following is the log that shown in the...
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PG notes the program that was run on the bam. Try looking at the tails log output...
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Hi Adam following is the @PG tags in header of my bam file @RG ID:9f749cc6 PU:/g4/scratch/tmp/tmpLNtYTO.fastq...
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what does the @PG bampie.py do? the last path looks weird...
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Could you post the @PG entries in the header of your bam? Specifically, we're looking...
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Hi Adam I was running PBHoney tails with a human genome dataset. But after the program...
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I am not saying the insertion's coordinates are [29999, 30085). The new 86bp sequence...
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Let me reiterate what you're saying. As long as I have reference coordinate (i.e.,...
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Starts and end are built so that you can edit the reference sequence easily for deletions...
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Hi Adam, I'm confused regarding the spots output with respect to insertions. In honeyExample,...
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Cristina Osuna posted a comment on discussion PBJelly Tickets
Hi Edi, How much memory are you using? What is the size of your input read files?...
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Edi Sudianto posted a comment on discussion PBJelly Tickets
Dear PBJelly users, I am encountering a problem with the mapping process of PBJelly....
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Brad Langhorst posted a comment on discussion PBJelly Tickets
I also tried checking out the trunk... I see a commit from a while ago that's looks...
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Hi Neal, I am struggling the same issue that you posted last year... Would you mind...
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Hi Neal, I am struggling the same issue that you posted last year... Would you mind...
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Hi Neal, I am struggleing the same issue that you posted last year... Would you mind...
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Takako Mochizuki posted a comment on discussion PBJelly Tickets
Hello, I have the error message at the support stage. ./RESULT/support/PacBio.fastq.err...
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