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ccgd-profile / BreaKmer

A method to identify structural variation from sequencing data in target regions
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How to fix the 15min gServer issue #25

Open radaniba opened 8 years ago

radaniba commented 8 years ago

I am trying to run breakmer on a 5k bed regions file but I am having the same error

breakmer.params - ERROR - gfServer wait time exceeded ~15 minutes, exiting Any idea on how to fix this ? should I manually edit the code to increase the wait time ? would that fix the issue ?

Thanks

signy-chow commented 8 years ago

I am having the same issue. I wonder if it's not recognizing the .2bit generated from the reference genome fasta sequence, but it doesn't work even after regenerating the file.

Was this resolved?

SemiQuant commented 8 years ago

I found that if plac a .2bit version in the same folder as the dir with the fasta it works, i assume that it doesn't include the entire path to the fasta file and that is causing the issue.

Shruti-Desai commented 7 years ago

I have same issue, T have prepared the reference data in folder named "BreaKmer" stated in config file. But I am getting the above error continuously. Is there a way if I can really find out whether I was able to generate connection with the server, since I checked the script, and I did not find any command which enables printing of successful test run. below is my command : python ~/BreaKmer/breakmer.py run --generate_image --indel_size 20 --gene_list ~/Reference_files/geneList350.txt --nprocessors 10 --port_number 9000 -c ~BreaKmer/breakmer.cfg

rmurphy49 commented 7 years ago

I also have the same issue. I am running the following command:

python breakmer.py kmer_region.config

My configuration file contains the following paths:

analysis_name=04-0309 targets_bed_file=/mnt/scratch/users/40057929/svaba/Manifest_regionsUsed.bed sample_bam_file=/mnt/scratch/users/40057929/MCLHighNov2016/Batch1/04-0309*/04-0309-01_S2.bam analysis_dir=/users/40057929 reference_data_dir=/users/40057929/BreaKmer-0.0.6/test cutadapt=/opt/gridware/etc/el6/modules/apps/cutadapt/1.8 cutadapt_config_file=/ifs/rcgroups/ccgd/rpa4/scripts/sv/kmer_sv/cutadapt.conf jellyfish=/opt/apps/etc/modules/jellyfish/2.2.6 assembler=/ifs/rcgroups/ccgd/rpa4/software/newbler/install2.6/bin/runAssembly blat=/opt/apps/blat/userApps/bin/gfServer reference_fasta=/mnt/scratch/users/40057929/BWA/Homo_sapiens/NCBI/GRCh38Decoy/Sequence/BWAIndex/genome.fa gene_annotation_file=/users/40057929/refGene.txt kmer_size=15

Checking the relevant log file for the run, it keeps repeating the following output:

08/07/2017 02:08:22 PM - root - INFO - Waiting for log file /users/40057929/output/gfserver_8489.log

This is after it has created the 2bit from the reference genome fasta and attempts to start the gfServer.

08/07/2017 02:07:39 PM - root - INFO - Creating 2bit from genome reference fasta.fa 08/07/2017 02:08:22 PM - root - INFO - Starting gfServer /opt/apps/blat/userApps/bin/gfServer -canStop -log=/users/40057929/output/gfserver_8489.log -stepSize=5 start localhost 8489 genome.2bit &

I tried @sciencebuff resolution but it did not fix the issue unfortunately. Any help or advice?

ryanabo commented 6 years ago

Sorry for the late reply to this. There could be a number of issues going on here. I have done updates recently to the code, but it is a branched version: https://github.com/ryanabo/BreaKmer

You can email me directly with issues and help in the future.