Open kbarrr opened 8 months ago
Hi Karla, Is there any chance that the input bam file is empty?
On Sun, Mar 10, 2024, 7:12 PM Karla Guzmán @.***> wrote:
code: python ncm.py -B -f -l M1M2.txt -O M1M2_results -N outputfile_prefix -bed SNP_GRCh38_hg38_wChr.bed
WARNNING : NCM_HOME is not defined yet. Therefore, program will try to search ncm.conf file from the current directory 1.6 /home/seisbio/mambaforge/envs/ngscheckmate-env/bin/samtools mpileup -uf GCA_000001405.29_GRCh38.p14_genomic.fna -l SNP_GRCh38_hg38_wChr.bed M1_dedup_filtrado_sorted.bam | /home/seisbio/mambaforge/envs/ngscheckmate-env/bin/bcftools call -c > M1M2_results/M1_dedup_filtrado_sorted.vcf [mpileup] 1 samples in 1 input files Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid Set max per-file depth to 8000 /home/seisbio/mambaforge/envs/ngscheckmate-env/bin/samtools mpileup -uf GCA_000001405.29_GRCh38.p14_genomic.fna -l SNP_GRCh38_hg38_wChr.bed M2_dedup_filtrado_sorted.bam | /home/seisbio/mambaforge/envs/ngscheckmate-env/bin/bcftools call -c > M1M2_results/M2_dedup_filtrado_sorted.vcf [mpileup] 1 samples in 1 input files Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid Set max per-file depth to 8000 Generate Data Set from M1M2_results using this bed file : SNP_GRCh38_hg38_wChr.bed Traceback (most recent call last): File "ncm.py", line 1453, in createDataSetFromDir(base_dir,bedFile) File "ncm.py", line 222, in createDataSetFromDir real_depth[file] = depth[file] / float(real_count[file]) ZeroDivisionError: float division by zero
someone can help?
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Hello. No, the bam file is not empty. However i tried with fastq files and worked perfectly!!!
Same error here!!!!
Any solutions will be deeply appreciated
first time around it ran without hiccups though
or possibly the chromosomes names don't match between the bed and the bam? e.g with or without 'chr'
On Thu, Apr 18, 2024, 5:42 PM Shashwat Sahay @.***> wrote:
Same error here!!!!
Any solutions will be deeply appreciated
first time around it ran without hiccups though
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nope that wasn't the case interestingly if i just re-ran it it worked fine which confuses me even further
dear author, thanks for sharing this useful utility.
I noticed that for some shallow BAM files, your utility generate the following error:
NGSCheckMate/ncm.py", line 220, in createDataSetFromDir real_depth[file] = depth[file] / float(real_count[file]) ZeroDivisionError: float division by zero
Would it be possible to validate the BAM file in the preflight so that your utility can be integrated into larger pipelines without risking to fail the larger run?
code: python ncm.py -B -f -l M1M2.txt -O M1M2_results -N outputfile_prefix -bed SNP_GRCh38_hg38_wChr.bed
WARNNING : NCM_HOME is not defined yet. Therefore, program will try to search ncm.conf file from the current directory 1.6 /home/seisbio/mambaforge/envs/ngscheckmate-env/bin/samtools mpileup -uf GCA_000001405.29_GRCh38.p14_genomic.fna -l SNP_GRCh38_hg38_wChr.bed M1_dedup_filtrado_sorted.bam | /home/seisbio/mambaforge/envs/ngscheckmate-env/bin/bcftools call -c > M1M2_results/M1_dedup_filtrado_sorted.vcf [mpileup] 1 samples in 1 input files Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid