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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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cannot find coverage.stats in data repo #110

Open najoshi opened 3 years ago

najoshi commented 3 years ago

So I've downloaded the GRCh38 repo and I am using the docker image. When I run my command I get the error below:

root@chimera:/home/joshi/sandbox# $AA --bed /home/joshi/sandbox/seed.bed --bam /home/joshi/sandbox/ANZC8_17.ALL.bam --out /home/joshi/sandbox/aa_try --ref GRCh38

[root:INFO] Commandline: programs/AmpliconArchitect-master/src/AmpliconArchitect.py --bed /home/bed_dir/seed.bed --bam /home/bam_dir/ANZC8_17.ALL.bam --out /home/output/aa_try --ref GRCh38
[root:INFO] AmpliconArchitect version 1.2

[root:INFO] #TIME 1.093 Loading libraries and reference annotations for: GRCh38 Global ref name is GRCh38 [root:INFO] #TIME 4.020 Initiating bam_to_breakpoint object for: /home/bam_dir/ANZC8_17.ALL.bam Traceback (most recent call last): File "programs/AmpliconArchitect-master/src/AmpliconArchitect.py", line 159, in coverage_stats_file = open(hg.DATA_REPO + "/coverage.stats") IOError: [Errno 2] No such file or directory: '/home/data_repo/coverage.stats'

Should this file already be in the data repo?

virajbdeshpande commented 3 years ago

This file is created by AA if it was not already created during a previous run. Is the data_repo directory set to be a read-only directory?

On Thu, Oct 14, 2021 at 3:00 AM najoshi @.***> wrote:

So I've downloaded the GRCh38 repo and I am using the docker image. When I run my command I get the error below:

@.***:/home/joshi/sandbox# $AA --bed /home/joshi/sandbox/seed.bed --bam /home/joshi/sandbox/ANZC8_17.ALL.bam --out /home/joshi/sandbox/aa_try --ref GRCh38 i: /home/joshi/sandbox/ANZC8_17.ALL.bam bam_file: /home/joshi/sandbox/ANZC8_17.ALL.bam argstring: --bed /home/bed_dir/seed.bed --bam /home/bam_dir/ANZC8_17.ALL.bam --out /home/output/aa_try --ref GRCh38 aa_data_repo: /home/joshi/sandbox/aa_data_repo/ bam_dir: /home/joshi/sandbox bed_dir: /home/joshi/sandbox license_file: /home/joshi/sandbox/mosek/8/ [root:INFO] Commandline: programs/AmpliconArchitect-master/src/AmpliconArchitect.py --bed /home/bed_dir/seed.bed --bam /home/bam_dir/ANZC8_17.ALL.bam --out /home/output/aa_try --ref GRCh38 [root:INFO] AmpliconArchitect version 1.2

[root:INFO] #TIME 1.093 Loading libraries and reference annotations for: GRCh38 Global ref name is GRCh38 [root:INFO] #TIME 4.020 Initiating bam_to_breakpoint object for: /home/bam_dir/ANZC8_17.ALL.bam Traceback (most recent call last): File "programs/AmpliconArchitect-master/src/AmpliconArchitect.py", line 159, in coverage_stats_file = open(hg.DATA_REPO + "/coverage.stats") IOError: [Errno 2] No such file or directory: '/home/data_repo/coverage.stats'

Should this file already be in the data repo?

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