User: shuksi1984

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shuksi198420
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Posts by shuksi1984

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Comment: C: GATK3 error message
... I ran the above command and got same output. I could not find any file in my working directory, except the output as shown above. I am unable to understand. Kindly, explain ...
written 2 days ago by shuksi198420
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Comment: C: GATK3 error message
... your data is corrupted bam file is corrupted? ...
written 3 days ago by shuksi198420
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Comment: C: GATK3 error message
... Can you share the link to download hg38gatkbundle reference genome? I am trying with the given link: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta.gz ...
written 3 days ago by shuksi198420
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Comment: C: GATK3 error message
... > what is the version of gatk ? GATK3.8 Output of grep -v '^>' /path/to/Homo_sapiens_assembly38.fasta | tr -d '[ATGCNatgcn\n]' | grep -o '.' | sort | uniq -c is: 2 \ 2 B 1 F 1 I 15 K 8 M 2 O 26 R 4 S 13 W 33 Y ...
written 3 days ago by shuksi198420
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GATK3 error message
... I ran following command: java -Xmx4g -jar /path/to/gatk3.8.jar -T RealignerTargetCreator -R /path/to/Homo_sapiens_assembly38.fasta -I SP1_markduplicate.bam -o SP1_realignedtargets.list I got following error message: ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in ...
software error next-gen written 3 days ago by shuksi198420 • updated 3 days ago by Devon Ryan81k
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Comment: C: sortsam (picard) error in identifyting samfile
... bwa-Version: 0.7.12-r1039 OS-Ubuntu 16.04.3 LTS (xenial) > In the command you gave above I cannot see why this happens It is because I used, nohup? ...
written 4 days ago by shuksi198420
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Comment: C: sortsam (picard) error in identifyting samfile
... The command grep -m 10 -v "^@" SRR6876052_mem.sam Gives following output: [M::bwa_idx_load_from_disk] read 3171 ALT contigs [M::process] read 66226 sequences (10000126 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 27774, 2, 0) [M::mem_pestat] skip ...
written 4 days ago by shuksi198420
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Comment: C: sortsam (picard) error in identifyting samfile
... > Beside this we need the first few lines that doesn't start by @ how do we achieve that? Is my file corrupt? ...
written 4 days ago by shuksi198420
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Comment: C: sortsam (picard) error in identifyting samfile
... Following are the 1st few lines of sam file >@SQ SN:chr1 LN:248956422 > @SQ SN:chr2 LN:242193529 >@SQ SN:chr3 LN:198295559 > @SQ SN:chr4 LN:190214555 > @SQ SN:chr5 LN:181538259 > @SQ SN:chr6 LN:170805979 >@SQ SN:chr7 LN:159345973 >@SQ SN:chr8 LN:145138636 >@SQ ...
written 4 days ago by shuksi198420
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sortsam (picard) error in identifyting samfile
... What does SAMFormatException mean? How to troubleshoot this error. I got following error: > Exception in thread "main" htsjdk.samtools.SAMFormatException: Error > parsing text SAM file. Not enough fields; File SRR6876052_mem.sam; > Line 1 My command is: nohup java -jar path/to/pi ...
software error next-gen written 4 days ago by shuksi198420

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Rising Star 12 days ago, created 50 posts within first three months of joining.

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