search

bioinform / varsim

VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
http://bioinform.github.io/varsim/
BSD 2-Clause "Simplified" License
79 stars 31 forks source link

AttributeError: 'Logger' object has no attribute 'write' #144

Open haoziyeung opened 6 years ago

haoziyeung commented 6 years ago

Hi,there,i'm using varsim to create a simulated somatic data,and i hava a error message,like below: python varsim_somatic.py --reference /gpfs/users/yanghao/database/ref/b37/human_g1k_v37_decoy.fasta --id cosmic --som_num_snp 10000 --som_num_ins 2000 --som_num_del 2000 --som_num_mnp 200 --som_num_complex 200 --cosmic_vcf cosmic.vcf.gz --normal_vcf somatic_sim_data/simu.truth.vcf --nlanes 1 --total_coverage 2000 --simulator art --simulator_executable ART/art_bin_MountRainier/art_illumina --out_dir som_out --log_dir som_log --work_dir som_work --sv_insert_seq insert_seq.txt

Traceback (most recent call last): File "varsim_somatic.py", line 227, in <module> varsim_somatic_main() File "varsim_somatic.py", line 202, in varsim_somatic_main processes = monitor_processes(processes) File "/gpfs/users/yanghao/software/varsim_run/varsim.py", line 140, in monitor_processes logger.write("Could not kill the process " + str(p.pid)) AttributeError: 'Logger' object has no attribute 'write' can anybody tell me how to fix it? thanks a lot!

yunfeiguo commented 6 years ago

Hi @haoziyeung

Please pull from master branch and try again. Thanks!