Mercurial > repos > iuc > tooldistillator_summarize

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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 467268e67eacec382584d02a97d22fe34ded2f71
author iuc
date Fri, 18 Jul 2025 10:11:48 +0000
parents 7fe1fe92de41
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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1 MaxBin 2.2.7
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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2 Input contig: /shared/ifbstor1/galaxy/datasets2/9/e/8/dataset_9e8cd0b6-cb85-4c33-98e5-9372b097fa40.dat
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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3 out header: out
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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4 Min contig length: 1000
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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5 Max iteration: 50
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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6 Probability threshold: 0.5
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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7 Thread: 10
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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8 Located reads file [HSMA33QY.fastq]
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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9 Running Bowtie2 on reads file [HSMA33QY.fastq]...this may take a while...
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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10 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]...
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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11 Done data collection. Running MaxBin...
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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12 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
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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13 Done data collection. Running MaxBin...
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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14 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
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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15 Minimum contig length set to 1000.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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16 Reading seed list...
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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17 Looking for seeds in sequences.
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18 k141_16093 [13.919579]
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19 k141_35827 [21.405429]
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20 k141_32187 [11.332857]
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21 k141_16792 [20.304843]
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22 k141_10178 [11.294563]
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23 k141_2436 [19.777457]
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24 k141_18047 [33.333916]
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25 k141_15329 [24.868185]
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26 k141_34672 [9.952122]
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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27 k141_19156 [27.248337]
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28 Get 10 seeds.
7fe1fe92de41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit b14e0602e63d833befda354faa901e4b3e8d06fe
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29
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30 Start EM process.
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31 Iteration 1
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32 Iteration 2
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33 Iteration 3
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34 Iteration 4
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35 Iteration 5
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36 Iteration 6
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37 Iteration 7
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38 Iteration 8
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39 Iteration 9
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40 Iteration 10
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41 Iteration 11
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42 Iteration 12
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43 Iteration 13
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44 Iteration 14
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45 Iteration 15
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46 Iteration 16
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47 Iteration 17
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48 Iteration 18
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49 Iteration 19
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50 Iteration 20
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51 Iteration 21
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52 Iteration 22
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53 Iteration 23
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54 Iteration 24
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55 Iteration 25
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56 Iteration 26
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57 Iteration 27
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58 Iteration 28
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59 Iteration 29
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61 Iteration 31
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62 Iteration 32
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63 Iteration 33
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64 Iteration 34
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65 Iteration 35
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66 Iteration 36
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67 Iteration 37
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68 Iteration 38
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69 Iteration 39
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70 Iteration 40
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71 Iteration 41
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72 Iteration 42
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73 Iteration 43
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74 Iteration 44
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75 Iteration 45
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76 Iteration 46
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77 Iteration 47
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78 Iteration 48
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79 Iteration 49
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80 Iteration 50
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81
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82 EM finishes successfully.
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83
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84 Classifying sequences based on the EM result.
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85 Minimum probability for binning: 0.50
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86 Ignoring 0 bins without any sequences.
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87 Number of unclassified sequences: 156 (1.66%)
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88 Elapsed time: 0 days 00:00:33
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89
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90 Minimum contig length set to 1000.
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91 Reading seed list...
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92 Looking for seeds in sequences.
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93 k141_16494 [26.817735]
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94 k141_29344 [22.460258]
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95 Get 2 seeds.
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96
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97 Start EM process.
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98 Iteration 1
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99 Iteration 2
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100 Iteration 3
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101 Iteration 4
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102 Iteration 5
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103 Iteration 6
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104 Iteration 7
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105 Iteration 8
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106 Iteration 9
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107 Iteration 10
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108
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109 EM finishes successfully.
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110
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111 Classifying sequences based on the EM result.
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112 Minimum probability for binning: 0.50
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113 Ignoring 0 bins without any sequences.
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114 Number of unclassified sequences: 0 (0.00%)
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115 Elapsed time: 0 days 00:00:00
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116
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117 Deleting intermediate files.
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118
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119
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120 ========== Job finished ==========
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121 Yielded 11 bins for contig (scaffold) file /shared/ifbstor1/galaxy/datasets2/9/e/8/dataset_9e8cd0b6-cb85-4c33-98e5-9372b097fa40.dat
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122
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123 Here are the output files for this run.
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124 Please refer to the README file for further details.
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125
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126 Summary file: out.summary
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127 Marker counts: out.marker
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128 Marker genes for each bin: out.marker_of_each_gene.tar.gz
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129 Bin files: out.001.fasta - out.011.fasta
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130 Unbinned sequences: out.noclass
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131 Marker plot: out.marker.pdf
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132
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133 Store abundance information of reads file [HSMA33QY.fastq] in [out.abund1].
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134
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135
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136 ========== Elapsed Time ==========
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137 0 hours 7 minutes and 28 seconds.
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138