Question: Error with pb-assembly using falcon
0
gravatar for aditi.thakare.14
7 months ago by
aditi.thakare.140 wrote:

I am trying to run Falcon assembly on "local". I have a .cfg file with reference to https://github.com/PacificBiosciences/pbassembly/blob/master/cfgs/fc_run_mosquito.cfg for certain parameters. However, I am getting an error during the "1-preads-ovl" step.

The error in the log file was as follows :

[ERROR]Task Node(1-preads_ovl/daligner-runs/j_0008) failed with exit-code=1
[ERROR]Task Node(1-preads_ovl/daligner-runs/j_0004) failed with exit-code=1
[ERROR]Task Node(1-preads_ovl/daligner-runs/j_0000) failed with exit-code=1

I tried checking the .stderr in the 1-preads_ovl/daligner-runs/j_0008 to find :

Exception: Call 'bash -vex run_daligner.sh' returned 256.
WARNING:root:Call '/bin/bash user_script.sh' returned 256.
INFO:root:CD: 'uow-00' -> '/path_to_dir/1-preads_ovl/daligner-runs/j_0008'
ERROR:root:failed multiprocessing

I am not able to find a solution to fix this error. Can someone please help understand this ?

The .cfg file is as follows :

[General]
input_type = raw

input_fofn = fasta.fofn

genome_size = 231000000

seed_coverage = 20

length_cutoff = -1

length_cutoff_pr = 1000

pa_daligner_option = -e0.76 -l1200 -k18 -h70 -w8 -s100

ovlp_daligner_option = -k24 -h1024 -e.95 -l1800 -s100

pa_HPCdaligner_option = -v -B128 -M24

ovlp_HPCdaligner_option = -v -B128 -M24

pa_HPCTANmask_option = -k18 -h480 -w8 -e.8 -s100

pa_HPCREPmask_option = -k18 -h480 -w8 -e.8 -s100

pa_DBsplit_option = -x1000 -s400

ovlp_DBsplit_option = -s400

falcon_sense_option = --output-multi --min-idt 0.70 --min-cov 3 --max-n-read 400 --n-core 4

overlap_filtering_setting = --max-diff 100 --max-cov 150 --min-cov 3 --n-core 4

[job.defaults]
use_tmpdir = /home/ssubha/Aditi/hap_phase/tmpdir

job_type=local

pwatcher_type=blocking

JOB_QUEUE=default

MB=32768

NPROC=32

submit = bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}
pacbio falcon assembly • 288 views
ADD COMMENTlink modified 7 months ago by h.mon32k • written 7 months ago by aditi.thakare.140
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