Job ID = 11245194 sra ファイルのダウンロード中... Completed: 411721K bytes transferred in 7 seconds (449861K bits/sec), in 1 file. Completed: 339439K bytes transferred in 6 seconds (404852K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 3261229 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669649/SRR7818263.sra Written 3261229 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669649/SRR7818263.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669649/SRR7818262.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669649/SRR7818262.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:07 7261229 reads; of these: 7261229 (100.00%) were paired; of these: 1613628 (22.22%) aligned concordantly 0 times 4871954 (67.10%) aligned concordantly exactly 1 time 775647 (10.68%) aligned concordantly >1 times ---- 1613628 pairs aligned concordantly 0 times; of these: 65108 (4.03%) aligned discordantly 1 time ---- 1548520 pairs aligned 0 times concordantly or discordantly; of these: 3097040 mates make up the pairs; of these: 2864380 (92.49%) aligned 0 times 156308 (5.05%) aligned exactly 1 time 76352 (2.47%) aligned >1 times 80.28% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 135416 / 5700158 = 0.0238 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Tue, 09 Oct 2018 23:57:18: # Command line: callpeak -t SRX4669649.bam -f BAM -g 12100000 -n SRX4669649.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669649.20 # format = BAM # ChIP-seq file = ['SRX4669649.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 09 Oct 2018 23:57:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:57:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:57:18: # Command line: callpeak -t SRX4669649.bam -f BAM -g 12100000 -n SRX4669649.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669649.10 # format = BAM # ChIP-seq file = ['SRX4669649.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 09 Oct 2018 23:57:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:57:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:57:18: # Command line: callpeak -t SRX4669649.bam -f BAM -g 12100000 -n SRX4669649.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669649.05 # format = BAM # ChIP-seq file = ['SRX4669649.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 09 Oct 2018 23:57:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:57:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:57:25: 1000000 INFO @ Tue, 09 Oct 2018 23:57:25: 1000000 INFO @ Tue, 09 Oct 2018 23:57:25: 1000000 INFO @ Tue, 09 Oct 2018 23:57:32: 2000000 INFO @ Tue, 09 Oct 2018 23:57:32: 2000000 INFO @ Tue, 09 Oct 2018 23:57:32: 2000000 INFO @ Tue, 09 Oct 2018 23:57:39: 3000000 INFO @ Tue, 09 Oct 2018 23:57:39: 3000000 INFO @ Tue, 09 Oct 2018 23:57:39: 3000000 INFO @ Tue, 09 Oct 2018 23:57:46: 4000000 INFO @ Tue, 09 Oct 2018 23:57:46: 4000000 INFO @ Tue, 09 Oct 2018 23:57:47: 4000000 INFO @ Tue, 09 Oct 2018 23:57:53: 5000000 INFO @ Tue, 09 Oct 2018 23:57:53: 5000000 INFO @ Tue, 09 Oct 2018 23:57:54: 5000000 INFO @ Tue, 09 Oct 2018 23:57:59: 6000000 INFO @ Tue, 09 Oct 2018 23:58:00: 6000000 INFO @ Tue, 09 Oct 2018 23:58:01: 6000000 INFO @ Tue, 09 Oct 2018 23:58:06: 7000000 INFO @ Tue, 09 Oct 2018 23:58:07: 7000000 INFO @ Tue, 09 Oct 2018 23:58:08: 7000000 INFO @ Tue, 09 Oct 2018 23:58:12: 8000000 INFO @ Tue, 09 Oct 2018 23:58:14: 8000000 INFO @ Tue, 09 Oct 2018 23:58:15: 8000000 INFO @ Tue, 09 Oct 2018 23:58:19: 9000000 INFO @ Tue, 09 Oct 2018 23:58:21: 9000000 INFO @ Tue, 09 Oct 2018 23:58:22: 9000000 INFO @ Tue, 09 Oct 2018 23:58:25: 10000000 INFO @ Tue, 09 Oct 2018 23:58:27: 10000000 INFO @ Tue, 09 Oct 2018 23:58:29: 10000000 INFO @ Tue, 09 Oct 2018 23:58:32: 11000000 INFO @ Tue, 09 Oct 2018 23:58:34: 11000000 INFO @ Tue, 09 Oct 2018 23:58:34: #1 tag size is determined as 75 bps INFO @ Tue, 09 Oct 2018 23:58:34: #1 tag size = 75 INFO @ Tue, 09 Oct 2018 23:58:34: #1 total tags in treatment: 5513069 INFO @ Tue, 09 Oct 2018 23:58:34: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:58:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:58:34: #1 tags after filtering in treatment: 4484328 INFO @ Tue, 09 Oct 2018 23:58:34: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:58:34: #1 finished! INFO @ Tue, 09 Oct 2018 23:58:34: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:58:35: #2 number of paired peaks: 27 WARNING @ Tue, 09 Oct 2018 23:58:35: Too few paired peaks (27) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 09 Oct 2018 23:58:35: Process for pairing-model is terminated! cat: SRX4669649.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669649.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4669649.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4669649.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:58:36: 11000000 INFO @ Tue, 09 Oct 2018 23:58:37: #1 tag size is determined as 75 bps INFO @ Tue, 09 Oct 2018 23:58:37: #1 tag size = 75 INFO @ Tue, 09 Oct 2018 23:58:37: #1 total tags in treatment: 5513069 INFO @ Tue, 09 Oct 2018 23:58:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:58:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:58:37: #1 tags after filtering in treatment: 4484328 INFO @ Tue, 09 Oct 2018 23:58:37: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:58:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:58:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:58:37: #2 number of paired peaks: 27 WARNING @ Tue, 09 Oct 2018 23:58:37: Too few paired peaks (27) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 09 Oct 2018 23:58:37: Process for pairing-model is terminated! cat: SRX4669649.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669649.20_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4669649.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4669649.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:58:38: #1 tag size is determined as 75 bps INFO @ Tue, 09 Oct 2018 23:58:38: #1 tag size = 75 INFO @ Tue, 09 Oct 2018 23:58:38: #1 total tags in treatment: 5513069 INFO @ Tue, 09 Oct 2018 23:58:38: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:58:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:58:38: #1 tags after filtering in treatment: 4484328 INFO @ Tue, 09 Oct 2018 23:58:38: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:58:38: #1 finished! INFO @ Tue, 09 Oct 2018 23:58:38: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:58:39: #2 number of paired peaks: 27 WARNING @ Tue, 09 Oct 2018 23:58:39: Too few paired peaks (27) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 09 Oct 2018 23:58:39: Process for pairing-model is terminated! cat: SRX4669649.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669649.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4669649.05_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4669649.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。