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Parse Error At Line 1 Invalid Cigar Character

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... DLL Files are Lost There are cases that files required to run certain programs are nowhere found causing DLL files to get lost. 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 reference.fa has a separate reference.fa.fai file. Source

This might help. Yes, anyone can just re-install the operating system and don�t bother about dealing with the real problem. Insufficient Virtual Memory The RAM of your PC is also one of the common areas where error occurs. This is an operating system problem that can�t be resolved using certain shortcut keys considering that the change of a software or hardware on your PC caused it.

We've just sent you an email to . If you simply have to download, the most important thing to consider is the reliability of your source. Please refer to our Privacy Policy or Contact Us for more details You seem to have CSS turned off. 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

I can only think that the problem is the header of sam file. Disconnecting a device which may cause the sudden change in the hardware settings could solve the issue. Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. You seem to have CSS turned off.

I can't convert SAM to BAM. The main cause of its error will serve as your basis on which among the two troubleshoot options you must think about. invalid email (thinking…) Reset or sign in with UserVoice password Forgot password? Parse error at line 9962791: sequence and quality are inconsistent [bam_sort_core] merging from 7 files... [samopen] SAM header is present: 25 sequences. [sam_read1] reference 'XU:i:1' is recognized as '*'.

These were originally ob... what is the CIGAR string? apply cufflinks to ENCODE RNA-Seq data Dear all, I am trying to analyze ENCODE RNA-seq data with cufflinks tool. Parse error at line 1: invalid CIGAR character Aborted If I run: >samtools import reference.fasta aln.sam prova.bam the error [sam_header_read2] 1102 sequences loaded.

How to fi... website here Please don't fill out this field. Could you share any script or any one-liner by which I can identify all such bad CIGAR value and remove them? I suggest you ... ← General Problem with sam to bam converison after alignment of scaffolds to reference Hello.

Second: it seems that the result of CRAC is not reproducible and depend on the number of threads used, i found a difference in size of the output file: 526909440 Jun this contact form Pileup error: line length exceeds XXX in sequence YYY Hi,    I mapped my reads, filtered unpaired reads, converted to BAM and now I want to generate ... Post navigation Previous PostLoopmidi ErrorNext PostOffice Space Copier Error Quote Search for: Proudly powered by WordPress [email protected] Discussion: invalid CIGAR character (too old to reply) Francois Sabot 2010-09-16 11:50:38 UTC PermalinkRaw It does not have the '@' headers. > > I'm trying to generate .bam with samtools view, but getting the following > error: > > ############################## > > samtools view -bt

And the sameproblem came up with the satble last version of samtools...Can you help me ?FrancoisPS: I used BWA 0.5.8a for my mapping-------------------------------------------------------------------------------Start uncovering the many advantages of virtual appliancesand start Add your answer Question followers (3) Shishir K Gupta Universität Heidelberg Nick Riddiford Institut Curie Mohamed Ashick Institut de Génétique et de Biologie Moléculaire et Cellulaire Views 1220 Create the index files with samtools faidx sequence.fa This creates the index file *.fai. have a peek here what is the CIGAR string? > > > > What version of samtools do you have? > > > > My initial guess would have been an X/= which was not

Find More Posts by dawe 11-12-2009, 04:00 AM #3 m_elena_bioinfo Member Location: Ospedali Riuniti di Bergamo, ITALY Join Date: Oct 2009 Posts: 99 Hi dawe, thank you very much. Or it is possible that the run simply didn't fully complete - double check that you have sufficient resource allocated (memory and available disk space). Cuffdiff Error: Cuffdiff Requires At Least 2 Sam Files Dear All, I am really confused about the cuffdiff function in cufflinks.

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One solution is buying additional RAM chips to increase RAM space. Create a password I agree to the terms of service Signed in as (Sign out) Close Close Sign in Sign in Sign up Cancel Feedback 10 10 votes General Post But the program doesn't run and the error this time is: [sam_header_read2] 735 sequences loaded. [sam_read1] reference 'hsa-mir-182' is recognized as '*'. Plus there is a difference between content failures (low mapping rates & other issues) and full-out job failures due to technical reasons (these should always be "red", not "green").

Join for free An error occurred while rendering template. All Rights Reserved. Htseq-count input data Dear colleagues, I am a new Galaxy user motivated to exploit its tools to compare two sets of the... Check This Out next-gen samtools perl rnaseq bioinformatics bioperl • 4.3k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 2.6 years ago by Biostar

I want to convert Sam file into Bam. Briefly describe the problem (required): Upload screenshot of ad (required): Select a file, or drag & drop file here. ✔ ✘ Please provide the ad click URL, if possible: Home Browse I'm running the htseq-count... DESeq2 Error on Cloudman Hi I'm working on Cloudman doing RNASeq transcriptome analysis.

Any thoughts? Make certain that all inputs are based on the same reference genome. The input is probably truncated. [sam_header_read2] 66 sequences loaded. [sam_read1] reference '' is recognized as '*'. Sam To Bam I sequenced a mito genome using paired end method on the mi-seq I mapped all the reads back to re...

m_elena_bioinfo View Public Profile Send a private message to m_elena_bioinfo Find More Posts by m_elena_bioinfo 11-12-2009, 03:57 AM #2 dawe Senior Member Location: 4530'25.22"N / 915'53.00"E Join Date: Apr Create a password I agree to the terms of service Signed in as (Sign out) Close Close Post comment Submitting... Any suggestions? Please take a look at my errors: http://goo.gl/Oa2IxR In the link, you will see 2 ima...

Funny huh?? invalid email (thinking…) Reset or sign in with UserVoice password Forgot password? The final command for conversion is samtools view -bt sequence.fa.fai -S bowtie.glob.sam -o bowtie.glob.sam Cheers, Rohit ADD COMMENT • link modified 3.7 years ago • written 3.7 years ago by Rohit This Galaxy wiki has advice if you need to understand how to investigate: Reference Genomes and Mismatch Issues Hopefully this helps!

How Can I Convert Bam To Sam? IGV can't view SAM file I'm trying to view SAM files I have got after alignment using IGV.  When I try to load the SAM fi... Cuffmerge Error: Duplicate Gff Id Encountered Hello, I was doing a RNA analyse and I wished to compare the transcription and expression of two ... Similar Threads Thread Thread Starter Forum Replies Last Post sam2bam error Hit Bioinformatics 1 07-06-2011 12:50 AM Thread Tools 11-12-2009, 03:21 AM #1 m_elena_bioinfo Member Location: Ospedali Riuniti

Cufflinks Gtf Dear Galaxy, I know this issue has been discussed multiple times but I think what I'm trying to d... Parse error at line 32699827: invalid CIGAR character [bam_sort_core] merging from 21 files... Faulty BAM/SAM files after Bowtie2, filtering and sorting Hi, I have some ChIP-seq data which I have aligned with Bowtie2 on Galaxy which gave me BAM file...