[Breakdancer-help] Problems with bam2cfg

[Adriana Di B. <adr...@un...>]

Hi!

I'm facing problems to generate the cfgfile with bam2cfg option from breakdancer.

First I thought it was just the RG header that was wrong in my bam file, but now I already fixed it and still, it is not generating. Before it was creating an empty cfgfile, as I saw in other issues, but now it's not creating a cfg file at all.

Is this bam2cfg still working in the latest version? Because I don't see many pieces of information about it.

And when I launch the command, it finishes saying to me that the job was successfully completed (?)
Here follows my command line and my output file:

COMMAND:

#!/usr/bin/env
module add /breakdancer/1.4.5
bam2cfg.pl -g -h sample.sorted.bam > sample.cfg

OUTPUT:

SBD_KRB5CCNAME_VAL=
LSF_VERSION=27
LOGNAME=adibatti
LSB_UNIXGROUP_INT=cig_reym
LSB_BATCH_NEW_SESSION=y
HOSTTYPE=X86_64
LSB_BATCH_JID=992776
LSB_JOBRES_PID=25148
LSB_JOBID=992776
LSB_JOBINDEX=0
LSB_JOBFILENAME=/home/adibatti/.lsbatch/1534151815.992776
LSB_CHKFILENAME=/home/adibatti/.lsbatch/1534151815.992776
LSB_TRAPSIGS=trap # 15 10 12 2
LSB_HOSTS=cpt133 cpt133
LSB_MCPU_HOSTS=cpt133 2
LSB_QUEUE=normal
LSB_JOBNAME=cfgfile
LSFUSER=adibatti
USER=adibatti
LSB_JOB_EXECUSER=adibatti
LSB_EXIT_PRE_ABORT=99
LS_EXEC_T=START
BSUB_BLOCK_EXEC_HOST=
PATH=/bin:/usr/bin/:/usr/mbin:/local/bin:/usr/local:/usr/ucb
LS_JOBPID=25148
LS_SUBCWD=/scratch/cluster/monthly/adibatti/WGS
LSB_SUB_HOST=frt
LSB_SUB_USER=adibatti
LSB_SUB_RES_REQ= rusage[mem=1000] span[hosts=1]
LSB_MAX_NUM_PROCESSORS=2
LSB_EXEC_HOSTTYPE=X86_64
LSF_ENVDIR=/mnt/common/lsf/conf
LSF_EGO_ENVDIR=/mnt/common/lsf/conf/ego/prdclst/kernel
LSF_SERVERDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/etc
LSF_BINDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/bin
LSF_LOGDIR=/mnt/common/lsf/log
LSF_LIBDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
LD_LIBRARY_PATH=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
LSB_JOBEXIT_STAT=0
LSB_EXEC_CLUSTER=prdclst
LSB_EEXEC_REAL_UID=
LSB_EEXEC_REAL_GID=
LSB_EFFECTIVE_RSRCREQ=select[ (((type == any)&&(tmp>1024)))] order[r1m:ut] rusage[mem=1000.00] span[hosts=1] same[model]
LSB_DJOB_NUMPROC=2
LSF_LIC_FEATURES_NEEDED=543682721
LSF_CGROUP_TOPDIR_KEY=prdclst
LSF_JOB_TIMESTAMP_VALUE=1534151816
PWD=/scratch/cluster/monthly/adibatti/WGS
HOME=/home/adibatti
LSF_JOB_TMPDIR=/tmp/992776.tmpdir
LSB_DJOB_HOSTFILE=/home/adibatti/.lsbatch/1534151815.992776.hostfile
SHELL=/bin/env

Thank you!?