deBAF error about hatchet HOT 5 CLOSED

The new version of HATCHet includes a new step called SNPCalling and it has a slightly different structure. We are working on updating the documentation and in the meanwhile could you please check out the complete demo available at:

complete demo

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The new version of HATCHet includes a new step called SNPCalling and it has a slightly different structure. We are working on updating the documentation and in the meanwhile could you please check out the complete demo available at:

complete demo

Started with the demo. Downloaded the files and now execute runUnphased.sh.

In the SNPcaller-step I get a couple of errors all like this:

Process Caller-5: Traceback (most recent call last): File "/home/zyto/unger/anaconda3/envs/Hatchet/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/zyto/unger/anaconda3/envs/Hatchet/lib/python3.7/site-packages/hatchet/utils/SNPCaller.py", line 121, in run snps = self.callSNPs(bamfile=next_task[0], samplename=next_task[1], chromosome=next_task[2]) File "/home/zyto/unger/anaconda3/envs/Hatchet/lib/python3.7/site-packages/hatchet/utils/SNPCaller.py", line 138, in callSNPs raise ValueError(sp.error('SNP Calling failed on {} of {}, please check errors in {}!').format(chromosome, samplename, errname)) ValueError: SNP Calling failed on chr5 of Normal, please check errors in /home/zyto/unger/WES_Rezidiv_HNSCC_Clonality/Hatchet/hatchet/examples/demo-complete/snps/Normal_chr5_bcftools.log!

Here the Normal_chr5_bcftools.log:

E::bgzf_read] Read block operation failed with error 4 after 44546 of 56208 bytes Failed to open https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/GATK/00-All.vcf.gz: could not load index

Any suggestion?

from hatchet.

The new version of HATCHet includes a new step called SNPCalling and it has a slightly different structure. We are working on updating the documentation and in the meanwhile could you please check out the complete demo available at:
complete demo

Started with the demo. Downloaded the files and now execute runUnphased.sh.

In the SNPcaller-step I get a couple of errors all like this:

Process Caller-5: Traceback (most recent call last): File "/home/zyto/unger/anaconda3/envs/Hatchet/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/zyto/unger/anaconda3/envs/Hatchet/lib/python3.7/site-packages/hatchet/utils/SNPCaller.py", line 121, in run snps = self.callSNPs(bamfile=next_task[0], samplename=next_task[1], chromosome=next_task[2]) File "/home/zyto/unger/anaconda3/envs/Hatchet/lib/python3.7/site-packages/hatchet/utils/SNPCaller.py", line 138, in callSNPs raise ValueError(sp.error('SNP Calling failed on {} of {}, please check errors in {}!').format(chromosome, samplename, errname)) ValueError: SNP Calling failed on chr5 of Normal, please check errors in /home/zyto/unger/WES_Rezidiv_HNSCC_Clonality/Hatchet/hatchet/examples/demo-complete/snps/Normal_chr5_bcftools.log!

Here the Normal_chr5_bcftools.log:

E::bgzf_read] Read block operation failed with error 4 after 44546 of 56208 bytes Failed to open https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/GATK/00-All.vcf.gz: could not load index

Any suggestion?

Manually downloading did the trick...

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@brian-arnold please close the issue after updating the documentation with downloading and local usage instructions

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The config.sh file now allows users to specify the LIST variable, directing HATCHet to use a locally stored VCF of known germline SNP positions instead of HATCHet automatically downloading one from the internet. If LIST is left blank ("") in the config.sh file, then HATCHet attempts to download a list of SNP positions based on the reference genome version and chromosome annotation (which are specified by REF_VERS and CHR_NOTATION in config.sh).

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