yunfeiguo
commented
3 years ago Hi George,
Are you using master branch? And when you built varsim, did you have your own python virtual environment or conda environment? Such environments must be cleared (with re-login) before installation.
Best, Yunfei
George Tollefson @.***>于2021年9月2日 周四下午1:54写道：
Hi,
I've downloaded and built VarSim following the instructions on the documentation page. However, when I run the following code on my reference genome (I am using the hg38 reference genome, not the fasta included in VarSim), I get an error message stating that certain python modules are not installed. Since there were no errors during the build step, I'm concerned that there is an issue with the installation of the python dependencies which is not reported as a failure in the build step. Can you help me to troubleshoot this issue?
The error message I see in the somatic output log:
Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/varsim/varsim/varsim_somatic.py", line 13, in from varsim import monitor_processes, check_executable, run_vcfstats, run_randvcf, RandVCFOptions File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/varsim/varsim/varsim.py", line 17, in from liftover_restricted_vcf_map import lift_vcfs, lift_maps File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/varsim/varsim/liftover_restricted_vcf_map.py", line 6, in import vcf ImportError: No module named vcf
My command:
varsim_somatic.py --reference hg38.fa --id cosmic --som_num_snp 10 \ --som_num_ins 5 --som_num_del 5 \ --som_num_mnp 0 \ --som_num_complex 1 \ --cosmic_vcf CosmicCodingMuts.vcf \ --normal_vcf out/simu.truth.vcf \ --nlanes 5 --total_coverage 30 \ --simulator art \ --simulator_executable /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/indel_detection_project/simulated_sequence_data/ART/art_src_MountRainier_Linux/art_illumina \ --out_dir /som_out --log_dir som_log --work_dir som_work &> somatic.log
based off of the somatic simulation in the docs:
varsim_somatic.py --reference hs37d5.fa --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 out/simu.truth.vcf \ --nlanes 5 --total_coverage 1 \ --simulator art \ --simulator_executable ART/art_bin_VanillaIceCream/art_illumina \ --out_dir som_out --log_dir som_log --work_dir som_work &> somatic.log
Thank you very much. George Tollefson
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-- Best, Yunfei Bioinformatics Research and Early Development (bRED) Roche Sequencing Solutions, based in Massachusetts, USA
gtollefson
Hi,
I've downloaded and built VarSim following the instructions on the documentation page. However, when I run the following code on my reference genome (I am using the hg38 reference genome, not the fasta included in VarSim), I get an error message stating that certain python modules are not installed. Since there were no errors during the build step, I'm concerned that there is an issue with the installation of the python dependencies which is not reported as a failure in the build step. Can you help me to troubleshoot this issue?
The error message I see in the somatic output log:
My command:
based off of the somatic simulation in the docs:
Thank you very much. George Tollefson