WebSamtools does not retrieve the entire alignment file unless it is asked to do so. If an index is needed, samtools looks for the index suffix appended to the filename, and if that isn't found it tries again without the filename suffix (for example in.bam.bai followed by … Consider using samtools collate instead if you need name collated data without a … samtools fastq -0 /dev/null -s single.fq -N in_name.bam > paired.fq BUGS. The … samtools tview – display alignments in a curses-based interactive viewer. … 0x4 bit not set primary mapped. 0x4, 0x100 and 0x800 bits not set paired in … Do not add a @PG line to the header of the output file. EXAMPLES. Import SAM to … Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an … WebAug 14, 2015 · I had the same issue and found that there was no perl at #!/usr/bin/perl. neither perl -v or /usr/bin/perl -v were working. I did a find / -name for perl then added a symbolic link from /usr/bin to the real location. perl -v -bash: perl: command not found /usr/bin/perl -v -bash: /usr/bin/perl: No such file or directory
samtools: command not found · Issue #9 · CRG …
WebFeb 3, 2024 · sh: samtools: command not found · Issue #1 · BenvenLab/eSNPKaryotyping · GitHub BenvenLab / eSNPKaryotyping Public sh: samtools: command not found #1 Open amab424 opened this issue on Feb 3, 2024 · 4 comments amab424 commented on Feb 3, 2024 . Already have an account? Sign in to … WebIt also looks like you downloaded htslib as a zip file from GitHub. If samtools doesn't find a copy of htslib in its own directory (as supplied with the tar file) it will look in `../htslib`. Try … easy tabouli salad recipe
sh: samtools: command not found (Tophat) - SEQanswers
WebMar 15, 2024 · Hmm, I'm not sure sorry. The main branch of coverm now no longer uses remove_minimap2_duplicated_headers but requires minimap2 2.20 - you could try that. However my suspicion is still that it is running out of RAM - does it give a different result when you request say double the RAM in your (PBS?) queue submission? WebMar 6, 2024 · [E::idx_find_and_load] Could not retrieve index file for 'calls_to_draft.bam' Why that would be the case is not clear to me. I should say medaka==0.11.5 is fairly old at this point, If you can upgrade to the latest 1.2.3 (on bioconda) or 1.2.4 (on pypi) we will be able to prvide further assistance. WebFeb 10, 2024 · The text was updated successfully, but these errors were encountered: easy tabs web part sharepoint 2013