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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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Unable to run after pulling latest image #101

Open lindakohn opened 3 years ago

lindakohn commented 3 years ago

I can't seem to get AA running after pulling the latest image and cloning from github, AA_DATA_REPO is set as:

$echo $AA_DATA_REPO /home/Genomes/aa_data_repo

Output after execution command:

[root:INFO] Commandline: programs/AmpliconArchitect-master/src/AmpliconArchitect.py  --bam  /home/bam_dir/1010.bam  --bed  /home/bed_dir/1010_CN3_100kb.bed  --out  /home/output/1010  --ref  GRCh38  
[root:INFO] AmpliconArchitect version 1.2

[root:INFO] #TIME 2.970 Loading libraries and reference annotations for: GRCh38
Global ref name is GRCh38
[root:WARNING]  #TIME 2.995  Unable to find reference in $AA_DATA_REPO/REF/file_list.txt. Setting to empty.
[root:WARNING]  #TIME 2.995  Unable to open fasta file: "/home/data_repo/GRCh38/". Reference sequences will be set to N.
[root:WARNING]  #TIME 2.995  Unable to open chromosome lengths file: "/home/data_repo/GRCh38/"
[root:WARNING]  #TIME 2.995  interval_list: Unable to open interval file "/home/data_repo/GRCh38/".
[root:WARNING]  #TIME 2.995  interval_list: Unable to open interval file "/home/data_repo/GRCh38/".
[root:WARNING]  #TIME 2.995  interval_list: Unable to open interval file "/home/data_repo/GRCh38/".
[root:WARNING]  #TIME 2.995  interval_list: Unable to open interval file "/home/data_repo/GRCh38/".
[root:WARNING]  #TIME 2.996  interval_list: Unable to open interval file "/home/data_repo/GRCh38/".
[root:WARNING]  #TIME 2.996  interval_list: Unable to open interval file "/home/data_repo/GRCh38/".
[root:INFO] #TIME 5.449 Initiating bam_to_breakpoint object for: /home/bam_dir/1010.bam
Traceback (most recent call last):
  File "programs/AmpliconArchitect-master/src/AmpliconArchitect.py", line 159, in <module>
    coverage_stats_file = open(hg.DATA_REPO + "/coverage.stats")
IOError: [Errno 2] No such file or directory: '/home/data_repo/coverage.stats'

As recommended in other issues I've created an empty coverage.stats with rw permissions within/home/Genomes/aa_data_repo/. Files listed within/home/Genomes/aa_data_repo/GRCh38/ are:

annotations                                     
cancer                                            
chrom_list.txt                                    
conserved_gain5_hg38.bed               
dummy_ploidy.vcf                             
exclude.cnvnator_100bp.GRCh38.20170403.bed       
file_list.txt                                         
file_sources.txt                                  
GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai
Genes_hg38.gff
GRCh38_centromere.bed
GRCh38_cnvkit_filtered_ref.cnn
GRCh38_merged_centromeres_conserved_sorted.bed
GRCh38_noAlt.fa.fai
hg38full_k35_noMM.mappability.bedgraph
refGene.txt

Any suggestions are very welcome!

jluebeck commented 3 years ago

Duplicate of #97 - we will correct this bug soon when we next update the docker image. Can be fixed by creating an empty file inside $AA_DATA_REPO called 'coverage.stats' with read and write permissions enabled.

Best, Jens