missing coverage_ps.csv file

[Larrycpan]

When I ran wakhan.py cna, I encountered the error FileNotFoundError: [Errno 2] No such file or directory: '/output/wakhan/coverage_data/coverage_ps.csv'. All input files have been created successfully. The code I used listed below

python /App/Wakhan/wakhan.py cna \
--threads 16 \
--reference  ${REF} \
--target-bam ${OUTPUT_DIR}/${SAMPLE}.haplotagged.bam \
--tumor-phased-vcf ${VCF_REPHASING} \
--genome-name ${SAMPLE} \
--breakpoints ${OUTPUT_DIR}/severus_out/somatic_SVs/severus_somatic.vcf \
--purity-range 0.01-1.0 \
--out-dir-plots ${OUTPUT_DIR}/wakhan \
--use-sv-haplotypes

[tahashmi]

Hi @Larrycpan , sorry for late reply. I can help you in resoving this issue. Could you please let me know the version you are using and a bit more actual log where this is being happend.

[Larrycpan]

Hi, I used the latest version. Actually, I found this error coming from the relative path of the coverage_ps.csv. The directory coverage_data was generated by Severus separately, and it was not in the /output/wakhan. I could resolve this by using standalone mode. However, I encountered another error

Traceback (most recent call last):
  File "/App/Wakhan/wakhan.py", line 28, in <module>
    main()
  File "/App/Wakhan/wakhan.py", line 24, in main
    sys.exit(main())
  File "/App/Wakhan/src/main.py", line 428, in main
    wakhan_all(args) #hapcorrect + cna
  File "/App/Wakhan/src/main.py", line 444, in wakhan_all
    cna_process(args) #cna
  File "/App/Wakhan/src/main.py", line 666, in cna_process
    copy_numbers_assignment_haplotypes(args, tumor_cov, max_limit, single_copy_cov, centers, subclonals, df_hp1, df_hp2, df_segs_hp1, df_segs_hp2, snps_cpd_means_df, csv_df_snps_mean, df_snps_in_csv, df_unphased, x_axi
  File "/App/Wakhan/src/main.py", line 116, in copy_numbers_assignment_haplotypes
    plot_ploidy_purity_p_values(args, [data[n][0] for n in range(len(data))], [data[n][1] for n in range(len(data))], [data[n][3] for n in range(len(data))])
  File "/App/Wakhan/src/plots/plots_main.py", line 5251, in plot_ploidy_purity_p_values
    if (purity_values[0] < float(args.purity_range.split('-')[0]) or purity_values[0] > float(args.purity_range.split('-')[1])) or (
IndexError: list index out of range

[tahashmi]

Could you try with the latest commit?

[manascripts]

This issue still persists in the latest release.
The cna module expects coverage data from the hapcorrect, but when cna is invoked after severus (as shown in the README), the process fails since the coverage_ps.csv file (along with others) hasn't been generated.

The cna module works only when hapcorrect is executed first.

[mikolmogorov]

@manascripts this is expected - in the mode 2, one needs to run hapcorrect first, then Severus, then cna modules. Or alternatively mode 1 does everything in a single run and from the resulting CNA reconstruction results are very similar for the most datasets.

[manascripts]

Alright, thanks for the clarification about the expected behavior. I was a bit confused by the contents of this thread.