Originally posted by GenoMax
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Dear Brian,
I am using bbmap for mapping and callvariants.sh for variant calling on PE Illumina reads.
I am comparing two mice strains. I am therefore downsampling my .sam files to have the same number of mapped reads going into the alignment.
When I input the original file containing ~680k mapped PE reads I get 2283 variants. When I run the down sampled file containing ~200k mapped PE reads I get 3375 variants.
I would expect to get a lower number of variants when I put in less reads. Could you explain this to me? I am clearly missing something that might be important for my analysis
(I am using the exact same criteria for variant calling and filtering for the two samples)
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I am trying to run BBmap on the cluster, but got the error below. Can anyone help me to solve the error?
Thanks,
[hgx080@quser10 DNA_all]$ /home/hgx080/bbmap/bbmap.sh ref=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/assemble/final/idba/DNA-all/DNA-all-contig.fa in=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/clean_reads/Wells02/filter_reads/RNA-Ac-1_S7_filter.fa out=RNA-Ac-1_S7_filter.test.sam minid=0.95 ambig=random reads=100000 -Xmx100g -eoom
java -Djava.library.path=/home/hgx080/bbmap/jni/ -ea -Xmx100g -cp /home/hgx080/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/assemble/final/idba/DNA-all/DNA-all-contig.fa in=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/clean_reads/Wells02/filter_reads/RNA-Ac-1_S7_filter.fa out=RNA-Ac-1_S7_filter.test.sam minid=0.95 ambig=random reads=100000 -Xmx100g -eoom
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/assemble/final/idba/DNA-all/DNA-all-contig.fa, in=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/clean_reads/Wells02/filter_reads/RNA-Ac-1_S7_filter.fa, out=RNA-Ac-1_S7_filter.test.sam, minid=0.95, ambig=random, reads=100000, -Xmx100g, -eoom]
Version 38.11
Choosing a site randomly for ambiguous mappings.
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.908
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Max reads: 100000
Set genome to 1
Exception in thread "Thread-0" java.lang.RuntimeException: java.lang.RuntimeException: java.io.EOFException: Unexpected end of ZLIB input stream
at align2.ChromLoadThread.run(ChromLoadThread.java:79)
Caused by: java.lang.RuntimeException: java.io.EOFException: Unexpected end of ZLIB input stream
at fileIO.ReadWrite.readObject(ReadWrite.java:806)
at fileIO.ReadWrite.read(ReadWrite.java:1246)
at dna.ChromosomeArray.read(ChromosomeArray.java:65)
at align2.ChromLoadThread.run(ChromLoadThread.java:76)
Caused by: java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117)
at java.io.ObjectInputStream$PeekInputStream.read(ObjectInputStream.java:2620)
at java.io.ObjectInputStream$BlockDataInputStream.read(ObjectInputStream.java:3031)
at java.io.ObjectInputStream$BlockDataInputStream.readFully(ObjectInputStream.java:3061)
at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1914)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1529)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2245)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2169)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2027)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1535)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:422)
at fileIO.ReadWrite.readObject(ReadWrite.java:802)
... 3 more
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Hello! Thanks for all of the wonderful bbmap scripts. Today I was was trying to use bbfakereads.sh but the script can not locate or open the jgi/FakeReads file. Any thoughts? I noticed a Fakereads files in the current/jgi directory. Do you think the path in the script is incorrect?
Thanks for your time and help!
bbfakereads.sh in=scaffolds.fasta out=fakePE_R1.fasta out2=fakePE.R2.fasta length=150
java -ea -Xmx600m -cp /media/bioinformaticprograms/BBMap/sh/current/ jgi.FakeReads in=scaffolds.fasta out=fakePE_R1.fasta out2=fakePE.R2.fasta length=150
Error: Could not find or load main class jgi.FakeReads
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You're right. It wasn't downloaded correctly. At first I used git to download the bbmap package. But when I just downloaded with wget from https://sourceforge.net/projects/bbm...p_38.12.tar.gz everything was organized correctly.
Thanks for the help.
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Add hg19 masked reference to distribution
Hello,
I'm using BBTools via bioconda and the corresponding quay.io docker container. The image has the necessary resources, e.g. the adapters fasta file:
Code:(base) Wed 25 Jul - 17:10 ~/code/tick-genome/reflow origin ☊ master 9☀ 1● docker run -it -v $PWD:/data quay.io/biocontainers/bbmap:38.06--2 bash bash-4.2# find . -name adapters.fa ./usr/local/opt/bbmap-38.06/resources/adapters.fa bash-4.2# cd ./usr/local/opt/bbmap-38.06/resources bash-4.2# ll bash: ll: command not found bash-4.2# ls adapters.fa blacklist_silva_species_500.sketch lambda.fa.gz nextera_LMP_linker.fa.gz primes.txt.gz sequencing_artifacts.fa.gz adapters_no_transposase.fa.gz contents.txt lfpe.linker.fa.gz pJET1.2.fa remote_files.txt short.fa blacklist_img_species_300.sketch crelox.fa.gz mtst.fa phix174_ill.ref.fa.gz remote_files_old.txt truseq.fa.gz blacklist_nt_species_1000.sketch favicon.ico nextera.fa.gz phix_adapters.fa.gz sample1.fq.gz truseq_rna.fa.gz blacklist_refseq_species_250.sketch kapatags.L40.fa nextera_LMP_adapter.fa.gz polyA.fa.gz sample2.fq.gz
Code:local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z -cp $CP align2.BBMap minratio=0.9 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/global/projectb/sandbox/gaag/bbtools/hg19 pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount usejni ztd=2 kfilter=25 maxsites=1 k=14 $@
Thank you!
Warmest,
Olga
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Hello Brian,
After running mapPacBio.sh, how can I combine the sequence of the same ID?
for example I want to combine the sequences as following:
m151006_234406_42219_c100867912550000001823195203031665_s1_p0/110457/57769_70466 id=3_0_part_2_6
m151006_234406_42219_c100867912550000001823195203031665_s1_p0/110457/57769_70466 id=3_0_part_3
Thanks,
Fuyou
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pull out sequences with matching primers
Hi Brian,
I was wondering if bbmap has a tool that will pull out reads matching a particular primer sequences? I have fastq files with amplicons from 12 different primers in the same file so i want to make subsets of the reads having specific primers of interest from this.
i have used your tool for other tasks so i figured I would ask if it also has this capability?
Thank you,
Jen
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Hi,
Hoping somebody can help me with this.
I used BBMap and now I would like to extract the reads from by .bam file that are split (/chimeric?) ie. reads that indicate a deletion.
I tried to use samblaster, but it doesn't recognize any reads as split...
(samtools view -h in.bam | samblaster -a -s split.sam -o /dev/null)
Are the split reads marked differently in BBMap compared to other aligners causing samblaster to fail?
IGV shows a good amount of reads with deletions and I can also call deletions using BBTools callvariants.sh - so I know they are in there. I just have a feeling callvariants is calling fewer deletions and with lower coverage than what IGV suggests, so I want to check up on it.
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mkf argument in bbduk.sh (bbmap tool)
Hello,
I am trying to use the flag mkf (minkmerfraction) and I am getting an error that that argument does not exist.
sh /data/barbj/bbmap/bbduk.sh in=./../Stool_001-01.fastq outm=v2fstoolfq.fa literal=CTCAAACTTGGGTAATTAAACC k=17 mkf=0.8
java -Djava.library.path=/data/barbj/bbmap/jni/ -ea -Xmx39767m -Xms39767m -cp /data/barbj/bbmap/current/ jgi.BBDukF in=./../Stool_001-01.fastq outm=v2fstoolfq.fa literal=CTCAAACTTGGGTAATTAAACC k=17 mkf=0.8
Executing jgi.BBDukF [in=./../Stool_001-01.fastq, outm=v2fstoolfq.fa, literal=CTCAAACTTGGGTAATTAAACC, k=17, mkf=0.8]
Exception in thread "main" java.lang.RuntimeException: Unknown parameter mkf=0.8
at jgi.BBDukF.<init>(BBDukF.java:402)
any ideas why this is not working?
Jen
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