File "ncm.py", line 1453, in <module> File "ncm.py", line 222, in createDataSetFromDir ZeroDivisionError: float division by zero

Question

File "ncm.py", line 1453, in <module> File "ncm.py", line 222, in createDataSetFromDir ZeroDivisionError: float division by zero

kbarrr opened this issue 6 months ago · comments

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?

Soo Lee · Answer 1 · Mon Mar 11 2024 21:25:16 GMT+0800 (China Standard Time)

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? — Reply to this email directly, view it on GitHub <#51>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHLO3BML75MLO75QFT2U73YXTSEBAVCNFSM6AAAAABEPKZXH2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3TOOJUHEYDEMQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

Karla Guzmán · Answer 2 · Mon Apr 01 2024 23:21:01 GMT+0800 (China Standard Time)

Hello. No, the bam file is not empty. However i tried with fastq files and worked perfectly!!!

Shashwat Sahay · Answer 3 · Fri Apr 19 2024 05:42:29 GMT+0800 (China Standard Time)

Same error here!!!!

Any solutions will be deeply appreciated

first time around it ran without hiccups though

Soo Lee · Answer 4 · Fri Apr 19 2024 05:58:58 GMT+0800 (China Standard Time)

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 — Reply to this email directly, view it on GitHub <#51 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHLO3E4VXMP5TYOZNWYRMLY6A45VAVCNFSM6AAAAABEPKZXH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRVGM3TIMRXGQ> . You are receiving this because you commented.Message ID: ***@***.***>

Shashwat Sahay · Answer 5 · Fri Apr 19 2024 12:23:24 GMT+0800 (China Standard Time)

nope that wasn't the case interestingly if i just re-ran it it worked fine which confuses me even further

german nudelman · Answer 6 · Fri Aug 09 2024 06:20:13 GMT+0800 (China Standard Time)

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?