All the restrictions can be found in http://samtools.sourceforge.net/SAM1.pdf. ADD COMMENT • link modified 3.4 years ago • written 3.4 years ago by Alex Reynolds ♦ 15k 0 3.4 years ago by Raghav • 100 Allahabad, India Raghav • 100 ERROR: Record 44, Read name seq.998, MAPQ should be 0 for unmapped read. The line numbersgiven in the error message almost certainly count records ( = lines )in the .sam file. http://back2cloud.com/parse-error/parse-error-at-line-sequence-and-quality-are-inconsistent.php
What is the actual problem here? 1 vote Vote Vote Vote Vote Sign in prestine Your name Your email address Check! It does not accept just the * , if the qualities are missing. samtools mpileup Aborted (Core dumped) I'm just trying to use samtools mpileup and it is aborting with out showing any error for some ba... Thanks much to all who offered suggestions, I offer my sincere gratitude. https://www.biostars.org/p/72880/
As for the stderr and stdout, I left out the full version of the command. Next, Iconverted these 500 SAMs to BAMs using the following command:*samtools view -bS file.sam > file.bam*using samtools version 0.1.18 (r982:295).I could convert 443 out of the SAMs into BAMs without any Could be that the fastq-file you put in is corrupted at that position, leading to a broken SAM-file. Create a password I agree to the terms of service Signed in as (Sign out) Close Close 1 vote 2 votes 3 votes Remove votes You have left! (?) (thinking…) Rohit
Implement Bgzip Into C Program Dear all, I'm currently writing a program that need random access to large files. XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:0C7A17 HWUSI-EAS566_0006:1:1:1026:12890#0 4 * 0 0 * * 0 0 TGGCTAAGAGGGAGTGGGTGTTGCGG DDDDA5>A:A==0>[email protected]?DB-D= HWUSI-EAS566_0006:1:1:1027:12527#0 4 * 0 0 * * 0 0 CCTTCTCTCTTCCTCGGCGCTGCCTA ECEAEBE?CEB??C=?BDBB:@@5=A HWUSI-EAS566_0006:1:1:1028:10989#0 ADD REPLY • link written 3.4 years ago by Philipp Bayer ♦ 3.7k Dear Sir Philipp, I got what you want to say here, it might be possible that there may ADD COMMENT • link written 3.4 years ago by Raghav • 100 A BAI index file associated with a BAM file is a like an index of a book, which helps
That last recommendation did the trick - the import (or view) from a sam to bam file is now proceeding. Click here to register now, and join the discussion Community Links Members List Search Forums Show Threads Show Posts Tag Search Advanced Search Go to Page... Well, what does line 1170 look like in your SAM file? http://seqanswers.com/forums/showthread.php?t=17353 I want to compare myself to anothe...
If you compare the code in sam_view.c's main_samview(), you will see that there is no need to call sam_header_read() yourself; instead just use sam->headers. What I have done are: 1... Sam To Bam Conversion Reference Fasta File Hello, I had some data in "eland_export.txt" format and I want to convert it to the SAM format f... You can always check your SAM-files using Picard's ValidateSamFile and see what it has to say about your SAM-file.
adds an index, so that you can retrieve portions of it without filtering the rest." what index you are talking about (is it related with reference index or some thing else) this page ADD REPLY • link written 3.3 years ago by John Marshall • 800 Since you are already moving the code to github perhaps it would be a good time to also Samtools Manual I have tried the following commands too - samtools view -bt Pan_troglodytes.fa.fai -S ref_aln_scaf.sam -o ref_aln_scaf.bam samtools view -bt Pan_troglodytes.fa.fai ref_aln_scaf.sam > ref_aln_scaf.bam The sam file has some words such as But I have a problem when I use samtools to convert the sam files into bam inorder to check the statistics.
No, thanks [email protected] Discussion: samtools view -bS - errors when converting .sam to .bam (too old to reply) Thorhildur Juliusdottir 2013-02-05 12:23:04 UTC PermalinkRaw Message Dear all,I generated 500 .SAM files http://back2cloud.com/parse-error/parse-error-at-line.php I do not know if the problem still exists in the newest version, but I still want to mention it. how does the SAM file EOF marker look like? Line 9991286, sequence length 15 vs 100 from CIGAR Parse error at line 9991286: CIGAR and sequence length are inconsistent [bam_sort_core] merging from 7 files... [samopen] SAM header is present: 25
Parse error at line 90: sequence and quality are inconsistent I'm using bwa aln to find coordinates and bwa sampe to generate alignments. Myron myronpeto View Public Profile Send a private message to myronpeto Find More Posts by myronpeto 02-02-2012, 04:08 PM #6 Richard Finney Senior Member Location: bethesda Join Date: I can't find it anywhere. > > > > [samopen] SAM header is present: 2957 sequences. > > Parse error at line 3512359: sequence and quality are inconsistent > > createbam.sh: Check This Out Xiaowu ________________________________________ From: Heng Li [[email protected]] Sent: Monday, January 04, 2010 9:07 AM To: Kevin Lam Cc: [email protected]
Blackwell 2013-02-05 12:43:10 UTC PermalinkRaw Message "sequence and quality are inconsistent" probably is triggered by arecord where the string of base call quality values has a differentnumber of characters from the HWUSI-EAS566_0006:1:1:1031:18950#0 4 * 0 0 * * 0 0 GTAATGGCTTCAAGGACTATCAATGC DE:-DD5CDCA?=C5)6>@2CC=5A= HWUSI-EAS566_0006:1:1:1037:2137#0 4 * 0 0 * * 0 0 GGCTTGCTAAGCAGAGGCCGGAAGCG F:[email protected]=B:[email protected]@EB:[email protected] HWUSI-EAS566_0006:1:1:1037:19136#0 4 * 0 0 * * 0 0 ADD REPLY • link written 3.3 years ago by Daniel Standage ♦ 3.6k 0 3.3 years ago by Istvan Albert ♦♦ 66k University Park, USA Istvan Albert ♦♦ 66k wrote: Your
Please don't fill out this field. You seem to have CSS turned off. Your symptom is often the result of piping stderr to same same stdout in a previous process. Hello, I have some SAM files which lack the header.
All Rights Reserved. But I just ran Picard tools on the output and I still seems funny. Changing the MAPQ to 0 for unmapped reads and including an NM tag should not be a problem. this contact form This makes it hard to see onthe screen exactly how many characters there are.- tom blackwell -Post by Thorhildur JuliusdottirDear all,I generated 500 .SAM files with BWA
I don't know why you would use circos to visualize reads, but you could search other threads on biostars for SAM or BAM viewers. Could you > should the 3512359-th line in bwa SAM output? > > Thanks, > > Heng > > On Mon, Jan 04, 2010 at 11:56:57AM +0800, Kevin Lam wrote: > All Rights Reserved. I used the following command: [email protected]:/data/SIM3_TEST1/test_rum# java -jar ../../Tools/picard-tools-1.67/ValidateSamFile.jar I=RUM_sorted.bam Summarized the errors are: [Wed May 02 15:11:35 UTC 2012] net.sf.picard.sam.ValidateSamFile INPUT=RUM_sorted.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT
These headers will be destroyed for you by samclose(), so there is no need to call bam_header_destroy() yourself either. Continue anyway. ## sed -n *716791p* S4-n4-o2-e2.sam S4:1282_1246_511 0 56694721|ref|NC_006560.1| 49629 0 45M3S * 0 0 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGGGGGGGGGAAA ]]]]]]]]]]]]]]]]]]]]]]]]]]]LIV.886[H=GPQST]]] XT:A:R CM:i:0 X0:i:2 X1:i:0 XM:i:3 XO:i:1 XG:i:3 MD:Z:45 ##cat createS3bam.err [samopen] SAM header k-mer counting into R using perfect hashing I worked in DNA K-mers counting and I prepare this formulation to solve the counting using perfec... Contact Us - SEQanswers Home - Archive - Top Powered by vBulletin Version 3.8.9Copyright ©2000 - 2016, vBulletin Solutions, Inc.
Myron myronpeto View Public Profile Send a private message to myronpeto Find More Posts by myronpeto 02-03-2012, 03:17 AM #8 dnusol Senior Member Location: Spain Join Date: Jul I can't find it anywhere. > > [samopen] SAM header is present: 2957 sequences. > Parse error at line 3512359: sequence and quality are inconsistent > createbam.sh: line 1: 10236 Aborted Similar posts • Search » Sam To Bam I sequenced a mito genome using paired end method on the mi-seq I mapped all the reads back to re... Continue anyway. ~ Cheers kevin Thread view [Samtools-help] [bam_header_read] EOF marker is absent.
This GDB was configured as "x86_64-apple-darwin"...Reading symbols for shared libraries ... From: Kevin Lam
I have sucessfully trimmed out the ... your valuable comments and suggestions are always welcome. The code and Error message l... From the record in the .sam file it seems the sequence and quality strings are of different length and the problem is upstream of the conversion from .sam to .bam Regardless,