annotate test-data/3/out.log @ 0:35aa0df55a62 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty

MaxBin 2.2.4
Input contig: /tmp/tmpES_iZn/files/000/dataset_1.dat
out header: out
Reassembly: 1
Located reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat]
Running Bowtie2 on reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat]...this may take a while...
Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpES_iZn/files/000/dataset_1.dat]...
Try harder to dig out marker genes from contigs.
Done data collection. Running MaxBin...
Command: /home/berntm/miniconda3/envs/__maxbin2@2.2.4/opt/MaxBin-2.2.4/src/MaxBin -fasta out.contig.tmp  -abund out.contig.tmp.reads.abund1 -seed out.seed -out out -min_contig_length 1000 
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
	contig-201_2 [11.293216]
	contig-201_100 [10.048304]
Get 2 seeds.

Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13
Iteration 14

EM finishes successfully.

Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time:  0 days 00:00:00

Performing reassembly. Reads file found.
Separating reads according to the bins...
Reassembling bin 001
Command: idba_ud -r out.reads.001 -o out.tmp --pre_correction --num_threads 1 1>out.idba.out 2>out.idba.err
Placing reassembled contigs into out.reassem
cp out.tmp/scaffold.fa out.reassem/out.001.fasta
Reassembling bin 002
Command: idba_ud -r out.reads.002 -o out.tmp --pre_correction --num_threads 1 1>out.idba.out 2>out.idba.err
Placing reassembled contigs into out.reassem
cp out.tmp/scaffold.fa out.reassem/out.002.fasta
Deleting intermediate files.


========== Job finished ==========
Yielded 2 bins for contig (scaffold) file /tmp/tmpES_iZn/files/000/dataset_1.dat

Here are the output files for this run.
Please refer to the README file for further details.

Summary file: out.summary
Marker counts: out.marker
Marker genes for each bin: out.marker_of_each_gene.tar.gz
Bin files: out.001.fasta - out.002.fasta
Unbinned sequences: out.noclass

Store abundance information of reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat] in [out.abund1].


========== Elapsed Time ==========
0 hours 2 minutes and 34 seconds.