comparison test-data/4/out.log @ 5:7160fa1ecb30 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 5efe64a2c3cb7495d708f539d341fa53fba07fe4

5:7160fa1ecb30

MaxBin 2.2.7
Input contig: /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat
out header: out
Min contig length: 1000
Max iteration: 50
Probability threshold: 0.5
Thread: 1
Located reads file [test4_reads.fastqsanger_0]
Located reads file [test4_reads.fastqsanger_1]
Running Bowtie2 on reads file [test4_reads.fastqsanger_0]...this may take a while...
Running Bowtie2 on reads file [test4_reads.fastqsanger_1]...this may take a while...
Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat]...
Try harder to dig out marker genes from contigs.
Done data collection. Running MaxBin...
Command: /home/gitpod/miniconda3/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp  -abund out.contig.tmp.reads.abund1 -abund2 out.contig.tmp.reads.abund2 -seed out.seed -out out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
	k141_99 [0.017288] [0.017288]
	k141_239 [0.015466] [0.015466]
Get 2 seeds.

Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8

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 00:00:01

Deleting intermediate files.


========== Job finished ==========
Yielded 2 bins for contig (scaffold) file /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat

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

Summary file: out.summary
Genome abundance info file: out.abundance
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
Marker plot: out.marker.pdf

Store abundance information of reads file [test4_reads.fastqsanger_0] in [out.abund1].
Store abundance information of reads file [test4_reads.fastqsanger_1] in [out.abund2].


========== Elapsed Time ==========
0 hours 0 minutes and 3 seconds.