Bins with "Infinity" abundance and BBMap error
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Hi Marc,
I'm running Metawatt 3.5.3 and even though the pipeline seems to work fine, it ends with two issues:
I've checked the logbook and the only errors I could find are related to align2.BBMap:
Metawatt [INFO|4:43:52] Running "Map reads to contigs"...
Metawatt [INFO|4:43:52] Map faster [true]
Metawatt [INFO|4:43:52] Minimum Percent ID [98.0]
Metawatt [INFO|4:43:52] Contig connection threshold [400 bp]
Metawatt [INFO|4:43:52] Set processors used [6]
Metawatt [INFO|4:43:52] Use unpaired mappings [false]
Metawatt [INFO|4:43:52] Mapping reads to contigs...
Metawatt [INFO|4:43:52] Project has 1 read set(s)
Metawatt [INFO|4:43:52] Keeping existing uppercase contig file "/tmp/metawatt/ARAST_Automatic.contigs.fa.uc.fasta" - file is up to date.
Metawatt [INFO|4:43:52] Building BBMap index => /tmp/metawatt/ARAST_Automatic.contigs.fa.uc.fasta (build id 1)
Metawatt [INFO|4:43:52] bbmap.sh path=/tmp/metawatt ref=/tmp/metawatt/ARAST_Automatic.contigs.fa.uc.fasta build=1 k=13 midpad=300 startpad=8000 stoppad=8000 minscaf=1
Metawatt [INFO|4:43:52] java -Djava.library.path=/usr/local/bin/jni/ -ea -Xmx2061m -cp /usr/local/bin/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 path=/tmp/metawatt ref=/tmp/metawatt/ARAST_Automatic.contigs.fa.uc.fasta build=1 k=13 midpad=300 startpad=8000 stoppad=8000 minscaf=1
Metawatt [INFO|4:43:52] Error: Could not find or load main class align2.BBMap
Metawatt [INFO|4:43:52] (1/1) Mapping reads for readset "G1_Met1_L1_L2_Paired_R1_Trimmomat_Combined_Reads.fastq" from file G1_Met1_L1_L2_Paired_R1_Trimmomat_Combined_Reads.fastq
Metawatt [INFO|4:43:52] bbmap.sh path=/tmp/metawatt build=1 in=/home/vimac/Metagenomes_Analysis_Projects/C1_Run#1/G1_Met1_3/Trimmomatic_Trimmed-Reads/MetaWatt/input/G1_Met1_L1_L2_Paired_R1_Trimmomat_Combined_Reads.fastq in2=/home/vimac/Metagenomes_Analysis_Projects/C1_Run#1/G1_Met1_3/Trimmomatic_Trimmed-Reads/MetaWatt/input/G1_Met1_L1_L2_Paired_R2_Trimmomat_Combined_Reads.fastq fast=t threads=6 out=stdout ambiguous=best ignorebadquality maxindel=100
Metawatt [INFO|4:43:52] Total reads: 0
Metawatt [INFO|4:43:52] Total bases: 0
Metawatt [INFO|4:43:52] Linked contigs with paired-end reads: Detected 0 connections
Metawatt [INFO|4:43:52] Linked contigs with unpaired reads: Detected 0 connections
Metawatt [INFO|4:43:52] Saving links to to "/home/vimac/Metagenomes_Analysis_Projects/C1_Run#1/G1_Met1_3/Trimmomatic_Trimmed-Reads/MetaWatt/output/ARAST_Automatic.contigs.fa.connections.txt"...
Metawatt [INFO|4:43:52] Saved 0 links, rejected 0 link that were below threshold (400 nt of mapped overlap)
Metawatt [INFO|4:43:52] Map reads to contigs: Loading data...
Metawatt [INFO|4:43:52] Detected absence of assembly coverage information - will use summed coverage from read mapping instead.
Metawatt [INFO|4:43:52] Parsed coverages and edit distances from "/home/vimac/Metagenomes_Analysis_Projects/C1_Run#1/G1_Met1_3/Trimmomatic_Trimmed-Reads/MetaWatt/output/ARAST_Automatic.contigs.fa.read.mapping.results.txt"
Metawatt [INFO|4:43:52] Parsed 0.0 kb of mapped overlap from "/home/vimac/Metagenomes_Analysis_Projects/C1_Run#1/G1_Met1_3/Trimmomatic_Trimmed-Reads/MetaWatt/output/ARAST_Automatic.contigs.fa.connections.txt"
Metawatt [INFO|4:43:52] Warning: no HMM profile DB provided, selected "conserved-genes.hmm"
Metawatt [INFO|4:43:52] Computing quality with profile DB "conserved-genes.hmm"...
Metawatt [INFO|4:43:53] Completed bin computations.
I guess both problems are related. Any suggestions on how to solve them.
Thanks.
Vimac
Hi,
I'm also having the same issue.
I'm running the latest version of metawatt and the generated bins contain all "inifinity" abundance.
As Vimac, I checked the logfile and I find this error realted to Bbmap:
Metawatt [INFO|12:38:17] Running "Map reads to contigs"...
Metawatt [INFO|12:38:17] Map faster [true]
Metawatt [INFO|12:38:17] Minimum Percent ID [98.0]
Metawatt [INFO|12:38:17] Contig connection threshold [400 bp]
Metawatt [INFO|12:38:17] Set processors used [4]
Metawatt [INFO|12:38:17] Use unpaired mappings [false]
Metawatt [INFO|12:38:17] Mapping reads to contigs...
Metawatt [INFO|12:38:17] Project has 1 read set(s)
Metawatt [INFO|12:38:17] Keeping existing uppercase contig file "/tmp/metawatt/Metagen-1.contigs.fa.uc.fasta" - file is up to date.
Metawatt [INFO|12:38:17] Building BBMap index => /tmp/metawatt/Metagen-1.contigs.fa.uc.fasta (build id 1)
Metawatt [INFO|12:38:17] bbmap.sh path=/tmp/metawatt ref=/tmp/metawatt/Metagen-1.contigs.fa.uc.fasta build=1 k=13 midpad=300 startpad=8000 stoppad=8000 minscaf=1
Metawatt [INFO|12:38:18] java -Djava.library.path=/usr/local/bin/jni/ -ea -Xmx2685m -cp /usr/local/bin/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 path=/tmp/metawatt ref=/tmp/metawatt/Metagen-1.contigs.fa.uc.fasta build=1 k=13 midpad=300 startpad=8000 stoppad=8000 minscaf=1
Metawatt [INFO|12:38:18] Error: Could not find or load main class align2.BBMap
Metawatt [INFO|12:38:18] (1/1) Mapping reads for readset "Metagen-1_L1_L2_Paired_R1_Reads.fastq.gz" from file Metagen-1_L1_L2_Paired_R1_Reads.fastq.gz
Metawatt [INFO|12:38:18] bbmap.sh path=/tmp/metawatt build=1 in=/home/Metagenomes_Projects/Metagenome-1/MetaWatt_Automatic_bins_diamond_latest/input/Metagen-1_L1_L2_Paired_R1_Reads.fastq.gz in2=/home/Metagenomes_Projects/Metagenome-1/MetaWatt_Automatic_bins_diamond_latest/input/Metagen-1_L1_L2_Paired_R2_Reads.fastq.gz fast=t threads=4 out=stdout ambiguous=best ignorebadquality maxindel=100
Metawatt [INFO|12:38:18] Total reads: 0
Metawatt [INFO|12:38:18] Total bases: 0
Metawatt [INFO|12:38:18] Linked contigs with paired-end reads: Detected 0 connections
Metawatt [INFO|12:38:18] Linked contigs with unpaired reads: Detected 0 connections
Any suggestions?
Thank you.
Hi,
I managed to fix the problem. It seems like java was unable to find the /jni and /current directories in usr/local/bin. So I just copied the two directories from my BBMap folder to usr/local/bin and it worked.
Vimac