Issue --end flag resquested in whole alignment Nanocaller

Question

Issue --end flag resquested in whole alignment Nanocaller

Opened this issue 4 years ago · 6 comments

Dear all.

I'm using your Nanocaller tool in my Pacbio data. However I'm facing some issues related with the -end flag.

Currently Im planning to extract all SNPs and Indel from a bam file derived from CCS_reads aligned to contigs assembly. Despite the --end flag being optional, the tool is asking me to define this -end flag

How can I fix it?

Thanks for the help

Answer 1 · 2020-09-09T20:06:54.000Z

For NanoCaller, you are required to specify a contig name. The -end flag is optional in the sense that if a user does not provide a value for -end flag, then we use the reference genome FASTA file(.fai index file to be precise) to infer the end coordinates for the specified contig. Are you providing an indexed reference genome FASTA file, and are you specifying a contig?

Answer 2 · 2020-09-09T20:20:35.000Z

I'm not specifying a contig name because I want to extract the SNPs and indels in all the contigs, when you mean contig name is a general name for all the contigs? Thanks El mié., 9 sept. 2020 a las 15:07, umahsn (<notifications@github.com>) escribió:

…

For NanoCaller, you are required to specify a contig name. The -end flag is optional in the sense that if a user does not provide a value for -end flag, then we use the reference genome FASTA file(.fai index file to be precise) to infer the end coordinates for the specified contig. Are you providing an indexed reference genome FASTA file, and are you specifying a contig? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHFDTT6XI3CRYU6BHPOKFATSE7N63ANCNFSM4RC6743Q> .

-- *Adriana María Gallego Rúa* *Investigadora **Laboratorio de Biotecnología* *Universidad de Antioquia* *ColombiaMedellín-2020*

Answer 3 · 2020-09-09T20:56:12.000Z

This is the specific error is showing in_dict={'chrom':args.chrom, 'start':start, 'end':end, 'sam_path':args.bam, 'fasta_path':args.ref, \ NameError: name 'end' is not defined When I run next script NanoCaller.py -bam file.sorted.bam -mode both -seq pacbio -model NanoCaller3 -vcf nanocaller -chrom CHROM -ref contigs_assembly.fasta -prefix my_test -cpu 32 And the reference fasta file as well the .fai file are both in the same directory Thanks El mié., 9 sept. 2020 a las 15:20, adriana gallego (< adriana.gallego.02@gmail.com>) escribió:

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I'm not specifying a contig name because I want to extract the SNPs and indels in all the contigs, when you mean contig name is a general name for all the contigs? Thanks El mié., 9 sept. 2020 a las 15:07, umahsn ***@***.***>) escribió: > For NanoCaller, you are required to specify a contig name. The -end flag > is optional in the sense that if a user does not provide a value for -end > flag, then we use the reference genome FASTA file(.fai index file to be > precise) to infer the end coordinates for the specified contig. Are you > providing an indexed reference genome FASTA file, and are you specifying a > contig? > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#5 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AHFDTT6XI3CRYU6BHPOKFATSE7N63ANCNFSM4RC6743Q> > . > -- *Adriana María Gallego Rúa* *Investigadora **Laboratorio de Biotecnología* *Universidad de Antioquia* *ColombiaMedellín-2020*

-- *Adriana María Gallego Rúa* *Investigadora **Laboratorio de Biotecnología* *Universidad de Antioquia* *ColombiaMedellín-2020*

Answer 4 · 2020-09-10T18:14:35.000Z

The problem is that the specified contig or chromosome is not found in the reference .fai file. Can you confirm whether that is the case or not?

Answer 5 · 2020-09-21T19:07:59.000Z

We have addressed several of your concerns in an updated version of NanoCaller. Please refer to issue #6.

Answer 6 · 2020-09-21T22:26:40.000Z

Thanks! El lun., 21 sept. 2020 a las 14:08, umahsn (<notifications@github.com>) escribió:

…

We have addressed several of your concerns in an updated version of NanoCaller. Please refer to issue #6 <#6>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHFDTTZ35RMVMW6VRAK7XFDSG6QB5ANCNFSM4RC6743Q> .

-- *Adriana María Gallego Rúa* *Investigadora **Laboratorio de Biotecnología* *Universidad de Antioquia* *ColombiaMedellín-2020*