annotate test-data/maxbin2/log_file.txt @ 11:9f1c8dc0253e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator commit 5afafa93bbb331db2e3f2e700714ff60bf467b27

MaxBin 2.2.7
Input contig: /shared/ifbstor1/galaxy/datasets2/9/e/8/dataset_9e8cd0b6-cb85-4c33-98e5-9372b097fa40.dat
out header: out
Min contig length: 1000
Max iteration: 50
Probability threshold: 0.5
Thread: 10
Located reads file [HSMA33QY.fastq]
Running Bowtie2 on reads file [HSMA33QY.fastq]...this may take a while...
Searching against 107 marker genes to find starting seed contigs for [/shared/ifbstor1/galaxy/datasets2/9/e/8/dataset_9e8cd0b6-cb85-4c33-98e5-9372b097fa40.dat]...
Done data collection. Running MaxBin...
Command: /shared/ifbstor1/galaxy/mutable-data/dependencies/_conda/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp  -abund out.contig.tmp.reads.abund1 -seed out.seed -out out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 -thread 10
Done data collection. Running MaxBin...
Command: /shared/ifbstor1/galaxy/mutable-data/dependencies/_conda/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.0002.fasta  -abund out.contig.tmp.reads.abund1 -seed out.0002.out.seed -out out.0002.out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 -thread 10
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
	k141_16093 [13.919579]
	k141_35827 [21.405429]
	k141_32187 [11.332857]
	k141_16792 [20.304843]
	k141_10178 [11.294563]
	k141_2436 [19.777457]
	k141_18047 [33.333916]
	k141_15329 [24.868185]
	k141_34672 [9.952122]
	k141_19156 [27.248337]
Get 10 seeds.

Start EM process.
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Iteration 50

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: 156 (1.66%)
Elapsed time:  0 days 00:00:33

Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
	k141_16494 [26.817735]
	k141_29344 [22.460258]
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

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

Deleting intermediate files.


========== Job finished ==========
Yielded 11 bins for contig (scaffold) file /shared/ifbstor1/galaxy/datasets2/9/e/8/dataset_9e8cd0b6-cb85-4c33-98e5-9372b097fa40.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.011.fasta
Unbinned sequences: out.noclass
Marker plot: out.marker.pdf

Store abundance information of reads file [HSMA33QY.fastq] in [out.abund1].


========== Elapsed Time ==========
0 hours 7 minutes and 28 seconds.