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intvi_other-tools's Issues

vifi input files

@szsctt I have some issues getting all the input files for vifi and the HG37:

mappability: "../vifi-test/data_repo/GRCh38/hg38full_k35_noMM.mappability.bedgraph"
mappability_exclude: "../data/references/GRCh38/ENCFF356LFX.bed"
genes: "../data/references/GRCh38/hg38.gencode.v35.annotation.genes.gff3"
exons: "../data/references/GRCh38/hg38.gencode.v35.annotation.exons.gff3"
oncogenes: "../data/references/GRCh38/hg38.gencode.v35.annotation.genes.gff3"
centromeres: "../data/references/GRCh38/centromeres.bed"
conserved_regions: "../data/references/GRCh38/exclude.cnvnator_100bp.GRCh38.20170403.bed"
segdup: "../data/references/GRCh38/genomicSuperDups.bed"

Did you already use the HG37 for this?

Can't access references with --use-singularity flag

The singularity env seems to only have access to the directory of execution.

shell:
	"""
	pwd
        ls
	ls ../..
	echo {input}
	head {input}
	bowtie2-build {input} {params.prefix}
	"""

Without singularity:

/home/<user>/scratch/intvi_other-tools
data  docker  scripts  Snakefile  snakemake_rules  test
intvi_other-tools  intvi_pipeline  intvi_pipeline_old  lau_hbv  nelson_aav  references  scripts  sung_hbv
/home/<user>/scratch/references/GRCm39_genomic.fna
>NC_000067.7 Mus musculus strain C57BL/6J chromosome 1, GRCm39
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
/usr/bin/bash: line 5: bowtie2-build: command not found

With singularity:

/scratch/<user>/intvi_other-tools
Snakefile  data  docker  scripts  snakemake_rules  test
intvi_other-tools
/home/<user>/scratch/references/GRCm39_genomic.fna
head: cannot open '/home/<user>/scratch/references/GRCm39_genomic.fna' for reading: No such file or directory

Error in rule verse

It seems that there is something wrong with the rule verse.
@szsctt Do you know that issue?

verse_references/human/human.nhr, test/out/verse_references/human/human.nin, test/out/verse_references/human/human.nsq
    output: test/out/test/verse/cond0.rep0.human.AAV/integration-sites.txt, test/out/test/verse/cond0.rep0.human.AAV/config.txt
    log: test/out/logs/test_verse_cond0.rep0_human_AAV.log
    jobid: 1
    wildcards: outpath=test/out, dset=test, samp=cond0.rep0, host=human, virus=AAV
    resources: mem_mb=100000, time=2:00:00, nodes=1

InputFunctionException in line 60 of /home/hartkopff/scratch/intvi_other-tools/snakemake_rules/verse.smk:
Error:
  ValueError: cannot convert float NaN to integer
Wildcards:
  outpath=test/out
  dset=test
  samp=cond0.rep0
  host=human
  virus=AAV
Traceback:
  File "/home/<user>/scratch/intvi_other-tools/snakemake_rules/verse.smk", line 85, in <lambda>
  File "/home/<user>/miniconda3/envs/snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 131, in run_jobs
  File "/home/<user>/miniconda3/envs/snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 140, in run
  File "/home/<user>/miniconda3/envs/snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 151, in _run
  File "/home/<user>/miniconda3/envs/snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 171, in printjob
  File "/home/<user>/miniconda3/envs/snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 157, in printjob

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