Exception: Aborting... Please check log for details.

[haoziyeung]

Hello ,sorry for bother your again,i'm using varsim_multi.py to get simulated data,here is my command:

python /gpfs/users/yanghao/software/varsim/varsim_multi.py --regions ../Euler_MSKCC_actionable_cancer_original.sort.bed --sv_insert_seq /gpfs/users/yanghao/software/varsim_run/insert_seq.txt --sv_dgv /gpfs/users/yanghao/software/varsim_run/GRCh37_hg19_supportingvariants_2013-07-23.txt --reference /gpfs/users/yanghao/database/ref/b37/human_g1k_v37_decoy.fasta --vc_num_snp 3000000 --vc_num_ins 100000 --vc_num_del 100000 --vc_num_mnp 0 --vc_num_complex 0 --sv_num_ins 0 --sv_num_del 0 --sv_num_dup 0 --sv_num_inv 0 --sv_percent_novel 0 --vc_percent_novel 0 --vc_min_length_lim 0 --vc_max_length_lim 49 --sv_min_length_lim 50 --sv_max_length_lim 1000000 --nlanes 10 --total_coverage 10 --simulator_executable /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina --out_dir . --simulator art --log_to_stderr --loglevel debug --sampling_vcf /gpfs/users/yanghao/database/ncbi/dbsnp/All_20170710.vcf.gz --samples region-specific-simulation --samples_random 1

and i get ERROR:

INFO 2018-02-08 16:18:33,278 concatenate_files Removing ./region-specific-simulation/out/X_123224425_123224614_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,279 concatenate_files Removing ./region-specific-simulation/out/X_123224704_123224814_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,281 concatenate_files Removing ./region-specific-simulation/out/X_123227868_123227994_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,284 concatenate_files Removing ./region-specific-simulation/out/X_123229222_123229299_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,286 concatenate_files Removing ./region-specific-simulation/out/X_123234424_123234447_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,288 concatenate_files Removing ./region-specific-simulation/out/X_123480493_123480629_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,290 concatenate_files Removing ./region-specific-simulation/out/X_123499611_123499674_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,291 concatenate_files Removing ./region-specific-simulation/out/X_123504026_123504170_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,293 concatenate_files Removing ./region-specific-simulation/out/X_123505201_123505241_region-specific-simulation.vcf INFO 2018-02-08 16:18:33,295 run_vcfstats Executing command java -Xmx1g -Xms1g -jar /gpfs/users/yanghao/software/varsim_run/VarSim.jar vcfstats -vcf ./region-specific-simulation/out/region-specific-simulation.truth.vcf INFO 2018-02-08 16:18:33,360 run_vcfstats with pid 108965 INFO 2018-02-08 16:18:36,363 monitor_processes Process 108965 exited with code 0 INFO 2018-02-08 16:18:36,367 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane0.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane0.read1.fq.gz INFO 2018-02-08 16:18:36,388 varsim_main with pid 108987 INFO 2018-02-08 16:18:36,389 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane0.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane0.read1.aln.gz INFO 2018-02-08 16:18:36,410 varsim_main with pid 108990 INFO 2018-02-08 16:18:36,411 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane0.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane0.read2.fq.gz INFO 2018-02-08 16:18:36,432 varsim_main with pid 108993 INFO 2018-02-08 16:18:36,432 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane0.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane0.read2.aln.gz INFO 2018-02-08 16:18:36,450 varsim_main with pid 108996 INFO 2018-02-08 16:18:36,451 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane1.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane1.read1.fq.gz INFO 2018-02-08 16:18:36,468 varsim_main with pid 108999 INFO 2018-02-08 16:18:36,469 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane1.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane1.read1.aln.gz INFO 2018-02-08 16:18:36,485 varsim_main with pid 109002 INFO 2018-02-08 16:18:36,486 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane1.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane1.read2.fq.gz INFO 2018-02-08 16:18:36,505 varsim_main with pid 109005 INFO 2018-02-08 16:18:36,505 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane1.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane1.read2.aln.gz INFO 2018-02-08 16:18:36,523 varsim_main with pid 109008 INFO 2018-02-08 16:18:36,524 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane2.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane2.read1.fq.gz INFO 2018-02-08 16:18:36,541 varsim_main with pid 109011 INFO 2018-02-08 16:18:36,541 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane2.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane2.read1.aln.gz INFO 2018-02-08 16:18:36,557 varsim_main with pid 109014 INFO 2018-02-08 16:18:36,558 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane2.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane2.read2.fq.gz INFO 2018-02-08 16:18:36,573 varsim_main with pid 109017 INFO 2018-02-08 16:18:36,574 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane2.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane2.read2.aln.gz INFO 2018-02-08 16:18:36,589 varsim_main with pid 109020 INFO 2018-02-08 16:18:36,590 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane3.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane3.read1.fq.gz INFO 2018-02-08 16:18:36,605 varsim_main with pid 109023 INFO 2018-02-08 16:18:36,606 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane3.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane3.read1.aln.gz INFO 2018-02-08 16:18:36,621 varsim_main with pid 109026 INFO 2018-02-08 16:18:36,622 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane3.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane3.read2.fq.gz INFO 2018-02-08 16:18:36,642 varsim_main with pid 109029 INFO 2018-02-08 16:18:36,643 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane3.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane3.read2.aln.gz INFO 2018-02-08 16:18:36,661 varsim_main with pid 109032 INFO 2018-02-08 16:18:36,662 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane4.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane4.read1.fq.gz INFO 2018-02-08 16:18:36,680 varsim_main with pid 109035 INFO 2018-02-08 16:18:36,680 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane4.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane4.read1.aln.gz INFO 2018-02-08 16:18:36,697 varsim_main with pid 109038 INFO 2018-02-08 16:18:36,698 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane4.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane4.read2.fq.gz INFO 2018-02-08 16:18:36,713 varsim_main with pid 109041 INFO 2018-02-08 16:18:36,714 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane4.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane4.read2.aln.gz INFO 2018-02-08 16:18:36,729 varsim_main with pid 109044 INFO 2018-02-08 16:18:36,730 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane5.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane5.read1.fq.gz INFO 2018-02-08 16:18:36,745 varsim_main with pid 109047 INFO 2018-02-08 16:18:36,745 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane5.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane5.read1.aln.gz INFO 2018-02-08 16:18:36,760 varsim_main with pid 109050 INFO 2018-02-08 16:18:36,760 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane5.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane5.read2.fq.gz INFO 2018-02-08 16:18:36,775 varsim_main with pid 109053 INFO 2018-02-08 16:18:36,776 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane5.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane5.read2.aln.gz INFO 2018-02-08 16:18:36,789 varsim_main with pid 109056 INFO 2018-02-08 16:18:36,790 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane6.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane6.read1.fq.gz INFO 2018-02-08 16:18:36,803 varsim_main with pid 109059 INFO 2018-02-08 16:18:36,803 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane6.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane6.read1.aln.gz INFO 2018-02-08 16:18:36,816 varsim_main with pid 109062 INFO 2018-02-08 16:18:36,817 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane6.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane6.read2.fq.gz INFO 2018-02-08 16:18:36,829 varsim_main with pid 109065 INFO 2018-02-08 16:18:36,830 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane6.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane6.read2.aln.gz INFO 2018-02-08 16:18:36,842 varsim_main with pid 109068 INFO 2018-02-08 16:18:36,843 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane7.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane7.read1.fq.gz INFO 2018-02-08 16:18:36,855 varsim_main with pid 109071 INFO 2018-02-08 16:18:36,855 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane7.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane7.read1.aln.gz INFO 2018-02-08 16:18:36,867 varsim_main with pid 109074 INFO 2018-02-08 16:18:36,868 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane7.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane7.read2.fq.gz INFO 2018-02-08 16:18:36,879 varsim_main with pid 109077 INFO 2018-02-08 16:18:36,880 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane7.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane7.read2.aln.gz INFO 2018-02-08 16:18:36,891 varsim_main with pid 109080 INFO 2018-02-08 16:18:36,891 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane8.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane8.read1.fq.gz INFO 2018-02-08 16:18:36,902 varsim_main with pid 109083 INFO 2018-02-08 16:18:36,903 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane8.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane8.read1.aln.gz INFO 2018-02-08 16:18:36,914 varsim_main with pid 109086 INFO 2018-02-08 16:18:36,914 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane8.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane8.read2.fq.gz INFO 2018-02-08 16:18:36,925 varsim_main with pid 109089 INFO 2018-02-08 16:18:36,926 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane8.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane8.read2.aln.gz INFO 2018-02-08 16:18:36,936 varsim_main with pid 109092 INFO 2018-02-08 16:18:36,937 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane9.read1.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane9.read1.fq.gz INFO 2018-02-08 16:18:36,947 varsim_main with pid 109095 INFO 2018-02-08 16:18:36,947 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane9.read1.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane9.read1.aln.gz INFO 2018-02-08 16:18:36,958 varsim_main with pid 109098 INFO 2018-02-08 16:18:36,958 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane9.read2.fq | gzip -2 > ./region-specific-simulation/out/simulated.lane9.read2.fq.gz INFO 2018-02-08 16:18:36,968 varsim_main with pid 109101 INFO 2018-02-08 16:18:36,969 varsim_main Executing command cat ./region-specific-simulation/out/simulated.lane9.read2.aln | gzip -2 > ./region-specific-simulation/out/simulated.lane9.read2.aln.gz INFO 2018-02-08 16:18:36,979 varsim_main with pid 109104 INFO 2018-02-08 16:18:36,990 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 0 -o ./region-specific-simulation/out/simulated.lane0.read with pid 109107 INFO 2018-02-08 16:18:37,000 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 1 -o ./region-specific-simulation/out/simulated.lane1.read with pid 109108 INFO 2018-02-08 16:18:37,011 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 2 -o ./region-specific-simulation/out/simulated.lane2.read with pid 109109 INFO 2018-02-08 16:18:37,026 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 3 -o ./region-specific-simulation/out/simulated.lane3.read with pid 109110 INFO 2018-02-08 16:18:37,039 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 4 -o ./region-specific-simulation/out/simulated.lane4.read with pid 109111 INFO 2018-02-08 16:18:37,052 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 5 -o ./region-specific-simulation/out/simulated.lane5.read with pid 109112 INFO 2018-02-08 16:18:37,065 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 6 -o ./region-specific-simulation/out/simulated.lane6.read with pid 109113 INFO 2018-02-08 16:18:37,078 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 7 -o ./region-specific-simulation/out/simulated.lane7.read with pid 109114 INFO 2018-02-08 16:18:37,091 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 8 -o ./region-specific-simulation/out/simulated.lane8.read with pid 109115 INFO 2018-02-08 16:18:37,103 varsim_main Executing command /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina -i ./region-specific-simulation/out/region-specific-simulation.fa -f 0.5 -rs 9 -o ./region-specific-simulation/out/simulated.lane9.read with pid 109116 INFO 2018-02-08 16:18:38,107 monitor_processes Process 109107 exited with code 1 ERROR 2018-02-08 16:18:38,107 monitor_processes Process 109107 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,107 monitor_processes Process 109108 exited with code 1 ERROR 2018-02-08 16:18:38,107 monitor_processes Process 109108 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,107 monitor_processes Process 109109 exited with code 1 ERROR 2018-02-08 16:18:38,108 monitor_processes Process 109109 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,108 monitor_processes Process 109110 exited with code 1 ERROR 2018-02-08 16:18:38,108 monitor_processes Process 109110 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,108 monitor_processes Process 109111 exited with code 1 ERROR 2018-02-08 16:18:38,108 monitor_processes Process 109111 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,108 monitor_processes Process 109112 exited with code 1 ERROR 2018-02-08 16:18:38,108 monitor_processes Process 109112 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,108 monitor_processes Process 109113 exited with code 1 ERROR 2018-02-08 16:18:38,108 monitor_processes Process 109113 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,109 monitor_processes Process 109114 exited with code 1 ERROR 2018-02-08 16:18:38,109 monitor_processes Process 109114 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,109 monitor_processes Process 109115 exited with code 1 ERROR 2018-02-08 16:18:38,109 monitor_processes Process 109115 failed. Will kill the remaining processes. INFO 2018-02-08 16:18:38,109 monitor_processes Process 109116 exited with code 1 ERROR 2018-02-08 16:18:38,109 monitor_processes Process 109116 failed. Will kill the remaining processes. ERROR 2018-02-08 16:18:38,109 monitor_processes Could not kill the process 108987 ERROR 2018-02-08 16:18:38,109 monitor_processes Could not kill the process 108990 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 108993 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 108996 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 108999 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 109002 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 109005 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 109008 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 109011 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 109014 ERROR 2018-02-08 16:18:38,110 monitor_processes Could not kill the process 109017 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109020 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109023 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109026 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109029 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109032 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109035 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109038 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109041 ERROR 2018-02-08 16:18:38,111 monitor_processes Could not kill the process 109044 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109047 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109050 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109053 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109056 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109059 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109062 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109065 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109068 ERROR 2018-02-08 16:18:38,112 monitor_processes Could not kill the process 109071 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109074 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109077 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109080 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109083 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109086 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109089 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109092 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109095 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109098 ERROR 2018-02-08 16:18:38,113 monitor_processes Could not kill the process 109101 ERROR 2018-02-08 16:18:38,114 monitor_processes Could not kill the process 109104 Traceback (most recent call last): File "/gpfs/users/yanghao/software/varsim/varsim_multi.py", line 256, in <module> samples_random=args.samples_random) File "/gpfs/users/yanghao/software/varsim/varsim_multi.py", line 111, in varsim_multi disable_vcf2diploid) File "/gpfs/users/yanghao/software/varsim/varsim.py", line 472, in varsim_main monitor_processes(processes) File "/gpfs/users/yanghao/software/varsim/varsim.py", line 141, in monitor_processes raise Exception('Aborting... Please check log for details.') Exception: Aborting... Please check log for details. i don't know what happend? and i'm wondering,this command is for germline data within certain interval but how can i get tumor data in a certain interval too?

Thanks a lot.

[haoziyeung]

@marghoob

[marghoob]

@haoziyeung Could you please attach your log directory as a tar-gzipped archive and we will have a look. It looks like one of the processes failed for some reason and we are hoping the log files would have information about it.

[zz-huang]

Hello @marghoob , I am having the same issue as well (pulled the new master because I was having the Logger attribute 'write' problem and now "Exception (Aborting...")).

Attached is my log achieve. Thank you!
varsim_log.tar.gz

[yunfeiguo]

@zhuang96 apparently the command is different from the 1st user, could you post it here?

[zz-huang]

Hello @yunfeiguo , this is my command input for testing

./varsim-master/varsim.py --vc_in_vcf All.20170710.vcf.gz --sv_insert_seq insert_seq.txt \ --sv_dgv GRCh38_hg38_supportingvariants_2016-08-31.txt\ --reference /project/vntrseek/share/GRCh38/GRCh38.fa --id simu --read_length 100 --vc_num_snp 3000000 --vc_num_ins 100000 \ --vc_num_del 100000 --vc_num_mnp 50000 --vc_num_complex 50000 --sv_num_ins 2000 \ --sv_num_del 2000 --sv_num_dup 200 --sv_num_inv 1000 --sv_percent_novel 0.01 \ --vc_percent_novel 0.01 --mean_fragment_size 350 --sd_fragment_size 50 \ --vc_min_length_lim 0 --vc_max_length_lim 49 --sv_min_length_lim 50 \ --sv_max_length_lim 1000000 --nlanes 5 --total_coverage 1 \ --simulator_executable ART/art_bin_VanillaIceCream/art_illumina --out_dir out --log_dir log --work_dir work \ --simulator art \

Thank you.

[yunfeiguo]

Thanks, @zhuang96 @haoziyeung

We are working on this issue.

[haoziyeung]

Hello, @yunfeiguo ,here is my cmd: python /gpfs/users/yanghao/software/varsim/varsim_multi.py --regions ../Euler_MSKCC_actionable_cancer_original.sort.bed --sv_insert_seq /gpfs/users/yanghao/software/varsim_run/insert_seq.txt --sv_dgv /gpfs/users/yanghao/software/varsim_run/GRCh37_hg19_supportingvariants_2013-07-23.txt --reference /gpfs/users/yanghao/database/ref/b37/human_g1k_v37_decoy.fasta --vc_num_snp 3000000 --vc_num_ins 100000 --vc_num_del 100000 --vc_num_mnp 0 --vc_num_complex 0 --sv_num_ins 0 --sv_num_del 0 --sv_num_dup 0 --sv_num_inv 0 --sv_percent_novel 0 --vc_percent_novel 0 --vc_min_length_lim 0 --vc_max_length_lim 49 --sv_min_length_lim 50 --sv_max_length_lim 1000000 --nlanes 10 --total_coverage 10 --simulator_executable /gpfs/users/yanghao/software/varsim_run/ART/art_bin_MountRainier/art_illumina --out_dir . --simulator art --loglevel debug --sampling_vcf /gpfs/users/yanghao/database/ncbi/dbsnp/All_20170710.vcf.gz --samples region-specific-simulation --samples_random 1

Traceback (most recent call last): File "/gpfs/users/yanghao/software/varsim/varsim_multi.py", line 256, in <module> samples_random=args.samples_random) File "/gpfs/users/yanghao/software/varsim/varsim_multi.py", line 111, in varsim_multi disable_vcf2diploid) File "/gpfs/users/yanghao/software/varsim/varsim.py", line 472, in varsim_main monitor_processes(processes) File "/gpfs/users/yanghao/software/varsim/varsim.py", line 141, in monitor_processes raise Exception('Aborting... Please check log for details.') Exception: Aborting... Please check log for details.

Attached is my log achieve. Thank you! varsim.log.tar.gz

[yunfeiguo]

@haoziyeung thanks, I suspect this is still caused by attempt to restrict dgv in some region (which is not supported yet). We will work on this (and maybe additional information is needed later). Thanks.