liufy11
commented
5 years ago when I run bam2cfg.pl test.bam
the screen says: Use of uninitialized value $lib in hash element at ../soft/breakdancer/perl/bam2cfg.pl line 195, and get no result.
but the error didn't occur when I run bam2 cfg.pl with another file named sort.bam. and get the expected result. the two bam file derived from difference resources.
I compare the format between two bam file. but find no difference. can anybody tell me why?
the two bam file have already upload to baidu network disk with the linker : https://pan.baidu.com/s/1PJSD6eqo9jxUH3NbHiCtVA
and password: 4n64
JohnMCMa
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. Does anybody know if this bam2cfg is still working? 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:
!/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!