view test-data/maxbin2/log_file.txt @ 8:3d0223265277 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 467268e67eacec382584d02a97d22fe34ded2f71

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.
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
Iteration 15
Iteration 16
Iteration 17
Iteration 18
Iteration 19
Iteration 20
Iteration 21
Iteration 22
Iteration 23
Iteration 24
Iteration 25
Iteration 26
Iteration 27
Iteration 28
Iteration 29
Iteration 30
Iteration 31
Iteration 32
Iteration 33
Iteration 34
Iteration 35
Iteration 36
Iteration 37
Iteration 38
Iteration 39
Iteration 40
Iteration 41
Iteration 42
Iteration 43
Iteration 44
Iteration 45
Iteration 46
Iteration 47
Iteration 48
Iteration 49
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.