This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Qualimap Failed to run bamqc

Hello i tried to run qualimap bamcq on my bam file that i obtain from mapping my reads against the contigs using bowtie2 but it didn't work .

J

ava memory size is set to 1200M
Launching application...

OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1024m; support was removed in 8.0
QualiMap v.2.2.1
Built on 2016-10-03 18:14

Selected tool: bamqc
Available memory (Mb): 32
Max memory (Mb): 1118
Starting bam qc....
Loading sam header...
Wed Apr 15 18:43:06 CEST 2020       WARNING According to header the BAM file is not sorted by coordinate!
Loading locator...
Loading reference...
Number of windows: 400, effective number of windows: 3114
Chunk of reads size: 1000
Number of threads: 48
Processed 311 out of 3114 windows...
Processed 622 out of 3114 windows...
Processed 933 out of 3114 windows...
Processed 1244 out of 3114 windows...
Processed 1555 out of 3114 windows...
Failed to run bamqc
java.lang.RuntimeException: The alignment file is unsorted.
Please sort the BAM file by coordinate.
    at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:372)
    at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:242)
    at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
    at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)

Wed Apr 15 18:43:06 CEST 2020       WARNING Cleanup output dir

i don't know what went wrong . please HELP .

Thank you

assembly alignment software error r
• 3,161 views • link
written by Bioinfo • Bioinfo

1 answer

Error is noted in log above:

java.lang.RuntimeException: The alignment file is unsorted.
Please **sort the BAM file by coordinate**.
• 0 views • link
written by GenoMax GenoMax

how to sort the BAM file by coordinate , i used bowtie for mapping then i used samtools ?? bowtie2 --threads 10 --very-sensitive-local -I 0 -X 200 -x DATABASE -1 R_1.fq.gz -2 R_2.fq.gz -S Results.sam then samtools view -b -h Results.sam > Results.bam

• 0 views • link
written by Bioinfo • Bioinfo 
samtools sort -o sorted.bam original.bam
• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this
  • Phased haplotype using WGS data from Nebula Genomics and GATK
    written by biostars • biostars
    I am a technically-competent non-bioinformatician with a set of three WGS sequences for a grandmother, son, and daughter that were provided by Nebula Genomics (for …
  • Issues running scAPAtrap
    written by Ana • Ana
    Hi all! I am trying to obtain polyA tail length from my scRNAseq bam files using scAPAtrap however I am running into a problem that …
  • qualimap - bed file error - BED format error, there should be at least 6 fields.
    written by hello_bioinf • hello_bioinf
    Hello, I am trying to run qualimap, my code is as below: TOOL=qualimap EXOME_IDs_FILE=/scratch/c.c21087028/Polyposis_Exome_Analysis_Novogene/fastp/All_fastp_input/List_of_33_exome_IDs SORTEDBAM=/scratch/c.c21087028/Polyposis_Exome_Analysis_Novogene/samtools/sort/{}PE_samtoolssorted.bam QUALIMAPBAMQCOUTPUTDIR=/scratch/c.c21087028/Polyposis_Exome_Analysis_Novogene/coveragetest/qualimap/{} QUALIMAPBAMQCOUTPUTFILE=/scratch/c.c21087028/Polyposis_Exome_Analysis_Novogene/coveragetest/qualimap/{}.pdf BEDFILEGFF=/scratch/c.c21087028/Polyposis_Exome_Analysis_Novogene/deepvariant/bed/novogene_agilent_human_region_hg38_recoded.bed MAKEDIRECTORYIDS=/scratch/c.c21087028/Polyposis_Exome_Analysis_Novogene/coveragetest/qualimap/{} cd /scratch/c.c21087028/ # samtools flagstat on …
  • Problem with qualimap BAM file
    written by luzglongoria • luzglongoria
    HI there, I have run STAR with the my reference genome. I got the SAM file that I converted in BAM file. Now, I want …
  • Do I have adapters in my reads?
    written by ntsopoul • ntsopoul
    Hi, I had downloaded some FASTQ files from SRA that I wanted to analyze. I checked in FASTQC (see https://ibb.co/vd0CxH3) and I could not see …
  • Cuffmerge and cuffdiff error
    written by carrilloarzola3 • carrilloarzola3
    I am trying to use cuffmerge in order to merge 4 transcript assemblies that I have obtained through cufflinks. The data has worked through tophat, …
  • Cuffmerge error while merging gtf files
    written by AP • AP
    Hi everyone, I was trying to merge my **transcripts.gtf** files from cufflinks using cuffmerge but i am getting bunch of errors. SCRIPT: cuffmerge -s Fov89-1A_65_contigs.fasta …
  • GATK Haplotype Caller
    written by plink_9857 plink_9857
    Hi - I am encountering errors when using GATK haplotypecaller with UCSC annotated VCF (bcftools), and BAM files with defined read groups. I also tried …
  • Picard: EstimateLibraryComplexity -> OutOfMemoryError
    written by David Langenberger David Langenberger
    I want to run `EstimateLibraryComplexity.jar` with a 9.8GB big bam file, but I always get a `OutOfMemoryError`. I already tried `-Xmx` (up to 60GB) and …
  • Struggling With Cufflinks Into Cuffmerge
    written by Craig Anderson • Craig Anderson
    <p><strong>Heya, I'm trying to stick RNAseq data through tophat and cufflinks, however, cufflinks doesn't like the accepted_hits.bam (we're on v1.2.0 now, but its still the …