Tweet
Error when bbmapping RNA-seq data
Hello 
I was using BBMap already for successful mapping of RNA-seq data (paired-end, Illumina) to a multi-FASTA transcriptome. Now I tried to map the very same data to the human GRCh38 genome (downloaded from NCBI human genome resources). I used the following command:
Would you have any idea, why this error comes up and how I could solve it?
Thanks a lot in advance and have a great day,
Elena
I was using BBMap already for successful mapping of RNA-seq data (paired-end, Illumina) to a multi-FASTA transcriptome. Now I tried to map the very same data to the human GRCh38 genome (downloaded from NCBI human genome resources). I used the following command:
bbmap.sh ref=$mapping_ref build="$BBmap_ref_ID" in=$BBduked_reads1 in2=$BBduked_reads2 \
outu=unmapped_"$name1"_"$date".sam outm=mapped_"$name1"_"$date".sam \
maxindel=200k mdtag=true sam=1.4 subfilter=3 pairedonly=true
Unfortunately, I got the following error:outu=unmapped_"$name1"_"$date".sam outm=mapped_"$name1"_"$date".sam \
maxindel=200k mdtag=true sam=1.4 subfilter=3 pairedonly=true
[...]
Retaining first best site only for ambiguous mappings.
Writing reference.
Executing dna.FastaToChromArrays2 [/scratch/hpc-prf-ptma2/ptma2001/bbmap/GRCh38_genome_16032022.fna, 6, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false]
Set genScaffoldInfo=true
Writing chunk 1
Writing chunk 2
Exception in thread "main" java.lang.NumberFormatException: For input string: "ӌ�jHN�H��¬���l��,ΚK��/S��ͩm���T
�!�l��X��o�ã’*s$�s^��m�h
[email protected]�
�m��$֧����@�H,���xI%_ Uz�?� S�B�2[*i�_����)i�NEր�ٜ�?Z�i£�� "
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at dna.Data.setGenome2(Data.java:1016)
at dna.Data.setGenome(Data.java:769)
at align2.BBMap.loadIndex(BBMap.java:316)
at align2.BBMap.main(BBMap.java:32)
Retaining first best site only for ambiguous mappings.
Writing reference.
Executing dna.FastaToChromArrays2 [/scratch/hpc-prf-ptma2/ptma2001/bbmap/GRCh38_genome_16032022.fna, 6, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false]
Set genScaffoldInfo=true
Writing chunk 1
Writing chunk 2
Exception in thread "main" java.lang.NumberFormatException: For input string: "ӌ�jHN�H��¬���l��,ΚK��/S��ͩm���T
�!�l��X��o�ã’*s$�s^��m�h
[email protected]�
�m��$֧����@�H,���xI%_ Uz�?� S�B�2[*i�_����)i�NEր�ٜ�?Z�i£�� "
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at dna.Data.setGenome2(Data.java:1016)
at dna.Data.setGenome(Data.java:769)
at align2.BBMap.loadIndex(BBMap.java:316)
at align2.BBMap.main(BBMap.java:32)
Would you have any idea, why this error comes up and how I could solve it?
Thanks a lot in advance and have a great day,
Elena