biosunsci
commented
2 years ago @bingzhang16 Could you please help me?
Open biosunsci opened 2 years ago
biosunsci
commented
2 years ago @bingzhang16 Could you please help me?
wenbostar
commented
2 years ago Could you send me the second vcf file (7191 records)?
biosunsci
commented
2 years ago Could you send me the second vcf file (7191 records)?
sample7796.vcf.zip please unzip it then you'll get the vcf file I listed. I'm sorry about the wrong number of lines I counted, but it still can trigger the error I mentioned.
I've tried to sample the data to different number of rows from 500 ~ 10000, all the same error. @wenbostar
wenbostar
commented
2 years ago Could you share with me the command line you used for both step 1 and step 2?
biosunsci
commented
2 years ago Could you share with me the command line you used for both step 1 and step 2?
I'm using the sh test_cmd.sh to test step 1 and step2
and the content of the test_cmd.sh is
docker run --rm -it -w neoantigen2 --user root -v /seq:/seq -v /var/run/docker.sock:/var/run/docker.sock bzhanglab/neoflow:1.0 ./nextflow run ./neoflow_db.nf --ref_dir ./annovar/humandb_hg19/ --vcf_file ./input/test_vcf_files.tsv --annovar_dir ./annovar/ --ref_ver hg19 --out_dir output --cpu 30 &&
echo crc_test && docker run --rm -it -w neoantigen2 --user root -v /seq:/seq -v /var/run/docker.sock:/var/run/docker.sock bzhanglab/neoflow:1.0 ./nextflow run ./neoflow_msms.nf --ms refs/mgf/ --msms_para_file refs/comet_parameter.txt --search_engine comet --db output/customized_database/crc_test_target_decoy.fasta --out_dir output_crc_test/ --pv_refdb output/customized_database/ref.fasta --pv_tol 20 --pv_itol 0.05 --prefix crc_test && echo done!The other dir structures or file contents are listed below in case to help.
ls -la /seq/neoantigen2drwxr-xr-x 1 1024 983 33 Jan 12 11:35 ./ drwxrwxr-x 1 1024 1026 17 Jan 5 05:20 ../ drwxr-xr-x 1 1024 983 7 Jan 4 01:27 annovar/ drwxr-xr-x 1 1024 983 8 Jan 4 01:27 bin/ drwxr-xr-x 1 1024 983 1 Jan 4 01:27 database/ drwxr-xr-x 1 1024 983 11 Jan 12 09:16 input/ -rwxr-xr-x 1 1024 983 6636 Jan 4 01:27 neoflow_db.nf -rwxr-xr-x 1 1024 983 3193 Jan 4 01:27 neoflow_hlatyping.nf -rwxr-xr-x 1 1024 983 10976 Jan 4 01:27 neoflow_msms.nf -rwxr-x--- 1 1024 983 8774 Jan 4 01:27 neoflow_neoantigen.nf drwxr-xr-x 1 1024 983 6 Jan 4 01:27 netMHCpan-4.0/ drwxr-xr-x 1 root root 3 Jan 12 12:12 .nextflow/ -rwxr-xr-x 1 1024 983 56633890 Jan 4 01:27 nextflow -rwxr-xr-x 1 1024 983 142 Jan 4 01:27 nextflow.config drwxr-xr-x 1 root root 3 Jan 12 10:25 output/ drwxr-xr-x 1 root root 3 Jan 12 11:03 output_crc_test/ **drwxr-xr-x 1 1024 983 2 Jan 4 01:27 refs/ -rw-r--r-- 1 root root 911 Jan 13 01:55 test_cmd.sh drwxr-xr-x 1 root root 190 Jan 12 12:12 work/
ls -la ./input/drwxr-xr-x 1 1024 983 11 Jan 12 09:16 ./ drwxr-xr-x 1 1024 983 33 Jan 12 11:35 ../ -rw-r--r-- 1 root root 55571 Jan 12 08:04 500.txt -rw-r--r-- 1 root root 46592 Jan 12 08:04 noGQ-PL-500.txt -rw-r--r-- 1 root root 5115845 Jan 12 07:55 noGQ-PL.txt -rw-r--r-- 1 root root 6068515 Jan 11 10:03 noGQ.txt -rw-r--r-- 1 root root 5573011 Jan 11 10:04 noPL.txt -rw-r--r-- 1 root root 6557121 Jan 13 01:57 sample1.txt -rw-r--r-- 1 1024 983 6557121 Jan 13 01:58 sample1.vcf -rw-r--r-- 1 1024 983 127 Jan 13 03:01 test_vcf_files.tsv
less ./input/test_vcf_files.tsvexperiment sample file file_type crc_test sample1 /seq/neoantigen2/input/500.txt somatic
tree ./refs
./refs
├── ./comet_parameter.txt
└── ./mgf/
├── spec-00030.mgf
├── spec-00139.mgf
├── spec-00279.mgf
├── spec-00364.mgf
├── spec-00560.mgf
├── spec-00037.mgf
├── spec-00208.mgf
├── spec-00285.mgf
├── spec-00373.mgf
├── spec-00565.mgf
├── spec-00129.mgf
├── spec-00219.mgf
├── spec-00351.mgf
├── spec-00465.mgf
└── spec-00622.mgf
biosunsci
commented
2 years ago @wenbostar I've pasted the relative information, Could you find any clues about the error I met?
Sawakotx
commented
1 year ago Hello, @biosunsci Unlike the command you executed, I am not using docker to run the script, just locally, and all the required software and docker in NeoFlow have been successfully installed locally. But I never managed to run step 2, and I got the error #9. So I was very excited when I saw that you were able to run step 2. According to your above description in #3 , I guess maybe I should use docker to run example. However, I am not clear whether I need to create a docker and install software such as an novar and nextflow in it? I have never used docker before😶🌫️, and I really hope you can give me some advice, please~
I copied test data from example_data folder provided by the neoflow. the input_vcf_list.txt file looks like:
the copied sample1.vcf looks like:
I can run through STEP2 using these 2 files.
but when I randomly sample 7191 vcf records from sample1.vcf before running the same pipeline, it is exactly the same as the last one except for the number of rows. this time the input vcf file looks like:
I got an fatal Error when running the last procedure of STEP2 whose Error message is :
I think it is caused by the empty of the intermediate file: /neoantigen2/work/7d/3269b5449820da00611a534f20e697/novel_peptides_psm.tsv and the novel_peptides_psm.tsv looks like:
I don't understand why the number of rows affect the pipeline's execution.
Could you help me out ?