gravatar for lhaiyan3

2 hours ago by

United States

Hi,
I tried to use chromHMM BinarizeBam command, but I got the following wrong message,
[+] Loading ChromHMM 1.22 ...
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File siCtrl/17_siCtrl_H3K14ac.bed; Line 1
Line: chrM 0 64 VH00271:6:AAAF3KNHV:1:1201:55269:30079 60 +
at htsjdk.samtools.SAMLineParser.reportFatalErrorParsingLine(SAMLineParser.java:432)
at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:217)
at htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:248)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:236)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:212)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:544)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:518)
at edu.mit.compbio.ChromHMM.Preprocessing.loadGrid(Preprocessing.java:259)
at edu.mit.compbio.ChromHMM.Preprocessing.makeBinaryDataFromBed(Preprocessing.java:1052)
at edu.mit.compbio.ChromHMM.ChromHMM.main(ChromHMM.java:13265)

Here is my command,
java -mx4000M -Djava.awt.headless=true -jar $CHROMHMM_JAR BinarizeBam hg19.sizes siCtrl cellmarkfiletable siCtrl_ChromHMM_output

I used the following command to get the bam file,
bwa mem -M -t 32 -R "$RG" $ref ${sampleName}_trim.fastq >${sampleName}.sam
java -Xmx60g -XX:ParallelGCThreads=5 -jar $PICARDJARPATH/picard.jar SortSam INPUT=${sampleName}.sam OUTPUT=${sampleName}.bam SORT_ORDER=coordinate

My bam file looks like this,
@HD VN:1.6 SO:coordinate
@SQ SN:chrM LN:16571
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@RG ID:11_siCtrl_H3K4me1 LB:11_siCtrl_H3K4me1 SM:11_siCtrl_H3K4me1 PL:ILLUMINA
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem -M -t 32 -R @RGtID:11_siCtrl_H3K4me1tLB:11_siCtrl_H3K4me1tSM:11_siCtrl_H3K4me1tPL:ILLUMINA /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa 11_siCtrl_H3K4me1_trim.fastq
@PG ID:samtools PN:samtools PP:bwa VN:1.11 CL:samtools view -H 11_siCtrl_H3K4me1.bam

Can anyone please give me some suggestions how to get the correct bam format for the chromHMM command? Thanks very much.

best

HY



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