Job ID = 11244995 sra ファイルのダウンロード中... Completed: 450078K bytes transferred in 7 seconds (493764K 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 13387522 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554709/SRR7696382.sra Written 13387522 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554709/SRR7696382.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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:08:09 13387522 reads; of these: 13387522 (100.00%) were paired; of these: 7087311 (52.94%) aligned concordantly 0 times 3940779 (29.44%) aligned concordantly exactly 1 time 2359432 (17.62%) aligned concordantly >1 times ---- 7087311 pairs aligned concordantly 0 times; of these: 3174 (0.04%) aligned discordantly 1 time ---- 7084137 pairs aligned 0 times concordantly or discordantly; of these: 14168274 mates make up the pairs; of these: 8601219 (60.71%) aligned 0 times 3603154 (25.43%) aligned exactly 1 time 1963901 (13.86%) aligned >1 times 67.88% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 1497546 / 6301777 = 0.2376 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 23:16:38: # Command line: callpeak -t SRX4554709.bam -f BAM -g 12100000 -n SRX4554709.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554709.05 # format = BAM # ChIP-seq file = ['SRX4554709.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 23:16:38: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:16:38: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:16:38: # Command line: callpeak -t SRX4554709.bam -f BAM -g 12100000 -n SRX4554709.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554709.20 # format = BAM # ChIP-seq file = ['SRX4554709.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 23:16:38: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:16:38: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:16:38: # Command line: callpeak -t SRX4554709.bam -f BAM -g 12100000 -n SRX4554709.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554709.10 # format = BAM # ChIP-seq file = ['SRX4554709.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 23:16:38: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:16:38: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:16:43: 1000000 INFO @ Tue, 09 Oct 2018 23:16:43: 1000000 INFO @ Tue, 09 Oct 2018 23:16:43: 1000000 INFO @ Tue, 09 Oct 2018 23:16:49: 2000000 INFO @ Tue, 09 Oct 2018 23:16:49: 2000000 INFO @ Tue, 09 Oct 2018 23:16:49: 2000000 INFO @ Tue, 09 Oct 2018 23:16:54: 3000000 INFO @ Tue, 09 Oct 2018 23:16:54: 3000000 INFO @ Tue, 09 Oct 2018 23:16:55: 3000000 INFO @ Tue, 09 Oct 2018 23:17:00: 4000000 INFO @ Tue, 09 Oct 2018 23:17:00: 4000000 INFO @ Tue, 09 Oct 2018 23:17:01: 4000000 INFO @ Tue, 09 Oct 2018 23:17:05: 5000000 INFO @ Tue, 09 Oct 2018 23:17:05: 5000000 INFO @ Tue, 09 Oct 2018 23:17:06: 5000000 INFO @ Tue, 09 Oct 2018 23:17:11: 6000000 INFO @ Tue, 09 Oct 2018 23:17:11: 6000000 INFO @ Tue, 09 Oct 2018 23:17:12: 6000000 INFO @ Tue, 09 Oct 2018 23:17:16: 7000000 INFO @ Tue, 09 Oct 2018 23:17:16: 7000000 INFO @ Tue, 09 Oct 2018 23:17:18: 7000000 INFO @ Tue, 09 Oct 2018 23:17:22: 8000000 INFO @ Tue, 09 Oct 2018 23:17:22: 8000000 INFO @ Tue, 09 Oct 2018 23:17:24: 8000000 INFO @ Tue, 09 Oct 2018 23:17:27: 9000000 INFO @ Tue, 09 Oct 2018 23:17:27: 9000000 INFO @ Tue, 09 Oct 2018 23:17:29: 9000000 INFO @ Tue, 09 Oct 2018 23:17:32: 10000000 INFO @ Tue, 09 Oct 2018 23:17:32: 10000000 INFO @ Tue, 09 Oct 2018 23:17:34: 10000000 INFO @ Tue, 09 Oct 2018 23:17:37: 11000000 INFO @ Tue, 09 Oct 2018 23:17:37: 11000000 INFO @ Tue, 09 Oct 2018 23:17:40: 11000000 INFO @ Tue, 09 Oct 2018 23:17:42: 12000000 INFO @ Tue, 09 Oct 2018 23:17:42: 12000000 INFO @ Tue, 09 Oct 2018 23:17:46: 12000000 INFO @ Tue, 09 Oct 2018 23:17:48: 13000000 INFO @ Tue, 09 Oct 2018 23:17:48: 13000000 INFO @ Tue, 09 Oct 2018 23:17:52: 13000000 INFO @ Tue, 09 Oct 2018 23:17:53: 14000000 INFO @ Tue, 09 Oct 2018 23:17:53: 14000000 INFO @ Tue, 09 Oct 2018 23:17:57: 14000000 INFO @ Tue, 09 Oct 2018 23:17:59: 15000000 INFO @ Tue, 09 Oct 2018 23:17:59: 15000000 INFO @ Tue, 09 Oct 2018 23:18:00: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:00: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:00: #1 total tags in treatment: 4802685 INFO @ Tue, 09 Oct 2018 23:18:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:00: #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 23:18:00: #1 tags after filtering in treatment: 2815889 INFO @ Tue, 09 Oct 2018 23:18:00: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:18:00: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:00: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:00: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:00: #1 total tags in treatment: 4802685 INFO @ Tue, 09 Oct 2018 23:18:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:00: #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 23:18:00: #1 tags after filtering in treatment: 2815889 INFO @ Tue, 09 Oct 2018 23:18:00: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:18:00: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:00: #2 number of paired peaks: 29 WARNING @ Tue, 09 Oct 2018 23:18:00: Too few paired peaks (29) 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 23:18:00: Process for pairing-model is terminated! cat: SRX4554709.10_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 `SRX4554709.10_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 `SRX4554709.10_*.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 `SRX4554709.10_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 23:18:00: #2 number of paired peaks: 29 WARNING @ Tue, 09 Oct 2018 23:18:00: Too few paired peaks (29) 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 23:18:00: Process for pairing-model is terminated! cat: SRX4554709.20_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 `SRX4554709.20_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 `SRX4554709.20_*.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 `SRX4554709.20_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 23:18:03: 15000000 INFO @ Tue, 09 Oct 2018 23:18:04: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:04: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:04: #1 total tags in treatment: 4802685 INFO @ Tue, 09 Oct 2018 23:18:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:04: #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 23:18:04: #1 tags after filtering in treatment: 2815889 INFO @ Tue, 09 Oct 2018 23:18:04: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:18:04: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:04: #2 number of paired peaks: 29 WARNING @ Tue, 09 Oct 2018 23:18:04: Too few paired peaks (29) 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 23:18:04: Process for pairing-model is terminated! cat: SRX4554709.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554709.05_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 `SRX4554709.05_*.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 `SRX4554709.05_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。