monitor_process fails to kill process halfway

[jayaramanp]

Hello @yunfeiguo

I'm trying to replicate the generation of fastqs using varsim_multi.py and i keep getting stuck towards the end:

here is the command i used:

python /Public/varsim/master/varsim/varsim_multi.py --regions /DGD/Research/ConsPanel_RD/SIM/CONS.bed --reference /DGD/clin-air/references/GRCh37/human_g1k_v37.fasta --sampling_vcf /Public/varsim/0.8.3/All.vcf.gz --sv_insert_seq /Public/varsim/0.8.3/insert_seq.txt --disable_rand_dgv --vc_num_snp 1500 --vc_num_ins 160 --vc_num_del 160 --vc_num_mnp 0 --vc_num_complex 0 --vc_percent_novel 0.01 --vc_min_length_lim 0 --vc_max_length_lim 49 --nlanes 1 --total_coverage 600 --simulator_executable /Public/varsim/master/varsim/opt/ART/art_bin_VanillaIceCream/art_illumina --out_dir out_05072019 --simulator art --simulator_options "-p -l 200 -m 350 -s 50" --samples_random 1 --loglevel debug

I was able to disable DGV by using the argument: --disable_rand_dgv yet I see that I haven't been able to replicate the generation of fastqs completely after that first time... what am I doing wrong?

the varsim.log reads like this

INFO 2019-05-07 13:57:31,994 run_vcfstats Executing command java -Xmx10g -jar /resnfs03/DGD/public/varsim/master/varsim/VarSim.jar vcfstats -vcf out_05072019/VarSim0/out/VarSim0.truth.vcf INFO 2019-05-07 13:57:33,033 varsim_main vcf2diploid done INFO 2019-05-07 13:57:33,060 varsim_main Executing command cat out_05072019/VarSim0/out/simulated.lane0.read1.fq | gzip -2 > out_05072019/VarSim0/out/simulated.lane0.read1.fq.gz INFO 2019-05-07 13:57:33,160 varsim_main with pid 66373 INFO 2019-05-07 13:57:33,165 varsim_main Executing command cat out_05072019/VarSim0/out/simulated.lane0.read1.aln | gzip -2 > out_05072019/VarSim0/out/simulated.lane0.read1.aln.gz INFO 2019-05-07 13:57:33,266 varsim_main with pid 66376 INFO 2019-05-07 13:57:33,272 varsim_main Executing command cat out_05072019/VarSim0/out/simulated.lane0.read2.fq | gzip -2 > out_05072019/VarSim0/out/simulated.lane0.read2.fq.gz INFO 2019-05-07 13:57:33,373 varsim_main with pid 66379 INFO 2019-05-07 13:57:33,378 varsim_main Executing command cat out_05072019/VarSim0/out/simulated.lane0.read2.aln | gzip -2 > out_05072019/VarSim0/out/simulated.lane0.read2.aln.gz INFO 2019-05-07 13:57:33,477 varsim_main with pid 66382 INFO 2019-05-07 13:57:33,578 varsim_main Executing command /Public/varsim/master/varsim/opt/ART/art_bin_VanillaIceCream/art_illumina -p -l 250 -m 350 -s 50 -i out_05072019/VarSim0/out/VarSim0.fa -f 300.0 -rs 0 -o out_05072019/VarSim0/out/simulated.lane0.read with pid 66385 INFO 2019-05-07 13:57:47,595 monitor_processes Process 66376 exited with code 0 INFO 2019-05-07 13:57:47,595 monitor_processes Process 66382 exited with code 0 INFO 2019-05-07 13:57:47,595 monitor_processes Process 66385 exited with code 1 ERROR 2019-05-07 13:57:47,595 monitor_processes Process 66385 failed. Will kill the remaining processes. ERROR 2019-05-07 13:57:47,596 monitor_processes Could not kill the process 66373 ERROR 2019-05-07 13:57:47,596 monitor_processes Could not kill the process 66379

[yunfeiguo]

Hi @jayaramanp looks like ART failed. In the log folder, you should find logs for ART: art.lane*.err or art.lane*.out, could you post the contents of these files? You can also try manually run ART commands, e.g. /Public/varsim/master/varsim/opt/ART/art_bin_VanillaIceCream/art_illumina -p -l 250 -m 350 -s 50 -i out_05072019/VarSim0/out/VarSim0.fa -f 300.0 -rs 0 -o out_05072019/VarSim0/out/simulated.lane0.read to see what is causing the problem.