jts
commented
1 year ago Hi,
I think there is a small error in your command, there should not be a --modbam-output option (providing --modbam-output-name turns modbam mode on).
Jared
On Mon, Jan 23, 2023 at 5:35 AM GianlucaMattei @.***> wrote:
Hello, I am trying to obtain a modbam file using Nanopolish call-methylation:
nanopolish call-methylation -r ${DEFPATH}/${SAMPLE}.fastq -b ${DEFPATH}/${SAMPLE}.${REF}.${ALIGNER}.${VERSION}.srt.bam -g /data2/utility/references/genomics/hs37d5.decoy.fa -t ${THN} -w 7:101458959-101927249 --modbam-output --modbam-output-name ${DEFPATH}/${SAMPLE}.methylcalls.${REF}.${ALIGNER}.${VERSION}.mod.bam Anyway when I run this command after few seconds I got this error:
[bam process] iterating over region: /data2/gmattei/Nanopore/Methylation/Nanopolish/S1A14.methylcalls.hs37d5.decoy.Minimap2.2.24-r1122.mod.bam [E::sam_itr_next] Null iterator
Additional info: Originally I had 5 different ONT runs (to increase to coverage), thus I concatenated the fastq files in a single one by:
cat ${DEFPATH}/Runs/${SAMPLE}run/fastq_pass/ > ${DEFPATH}/${SAMPLE}.fastq
during Nanopolish indexing I used the folder containing all the fast5 from the different 5 runs:
ls ${DEFPATH}/Fast5/ S1A14_run_1 S1A14_run_2 S1A14_run_3 S1A14_run_4 S1A14_run_5
all of which contain a fast5_pass folder
The command I used for indexing:
nanopolish index -d ${DEFPATH}/Fast5/ ${DEFPATH}/${SAMPLE}.fastq
I am using the last version of Nanopolish (0.14), I aligned the fastq to hs37d5.decoy.fa with minimap2 (version 2.24-r1122).
Is that a bug or I am doing something wrong? Thanks G.
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GianlucaMattei
Hello, I am trying to obtain a modbam file using Nanopolish call-methylation:
Anyway when I run this command after few seconds I got this error:
Additional info: Originally I had 5 different ONT runs (to increase to coverage), thus I concatenated the fastq files in a single one by:
during Nanopolish indexing I used the folder containing all the fast5 from the different 5 runs:
ls ${DEFPATH}/Fast5/ S1A14_run_1 S1A14_run_2 S1A14_run_3 S1A14_run_4 S1A14_run_5all of which contain a fast5_pass folderThe command I used for indexing:
I am using the last version of Nanopolish (0.14), I aligned the fastq to hs37d5.decoy.fa with minimap2 (version 2.24-r1122).
Is that a bug or I am doing something wrong? Thanks G.