Job ID = 11162626 sra ファイルのダウンロード中... Completed: 714778K bytes transferred in 11 seconds (488412K 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: SINGLE fastq に変換中... Read 23041872 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3585229/SRR6495928.sra Written 23041872 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3585229/SRR6495928.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: 00:04:57 23041872 reads; of these: 23041872 (100.00%) were unpaired; of these: 3895876 (16.91%) aligned 0 times 16436808 (71.33%) aligned exactly 1 time 2709188 (11.76%) aligned >1 times 83.09% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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_rmdupse_core] 10863315 / 19145996 = 0.5674 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 @ Wed, 05 Sep 2018 10:44:00: # Command line: callpeak -t SRX3585229.bam -f BAM -g 12100000 -n SRX3585229.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3585229.05 # format = BAM # ChIP-seq file = ['SRX3585229.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 @ Wed, 05 Sep 2018 10:44:00: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:44:00: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:44:00: # Command line: callpeak -t SRX3585229.bam -f BAM -g 12100000 -n SRX3585229.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3585229.10 # format = BAM # ChIP-seq file = ['SRX3585229.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 @ Wed, 05 Sep 2018 10:44:00: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:44:00: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:44:00: # Command line: callpeak -t SRX3585229.bam -f BAM -g 12100000 -n SRX3585229.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3585229.20 # format = BAM # ChIP-seq file = ['SRX3585229.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 @ Wed, 05 Sep 2018 10:44:00: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:44:00: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:44:08: 1000000 INFO @ Wed, 05 Sep 2018 10:44:08: 1000000 INFO @ Wed, 05 Sep 2018 10:44:08: 1000000 INFO @ Wed, 05 Sep 2018 10:44:16: 2000000 INFO @ Wed, 05 Sep 2018 10:44:16: 2000000 INFO @ Wed, 05 Sep 2018 10:44:16: 2000000 INFO @ Wed, 05 Sep 2018 10:44:24: 3000000 INFO @ Wed, 05 Sep 2018 10:44:24: 3000000 INFO @ Wed, 05 Sep 2018 10:44:24: 3000000 INFO @ Wed, 05 Sep 2018 10:44:32: 4000000 INFO @ Wed, 05 Sep 2018 10:44:32: 4000000 INFO @ Wed, 05 Sep 2018 10:44:33: 4000000 INFO @ Wed, 05 Sep 2018 10:44:40: 5000000 INFO @ Wed, 05 Sep 2018 10:44:40: 5000000 INFO @ Wed, 05 Sep 2018 10:44:41: 5000000 INFO @ Wed, 05 Sep 2018 10:44:48: 6000000 INFO @ Wed, 05 Sep 2018 10:44:48: 6000000 INFO @ Wed, 05 Sep 2018 10:44:49: 6000000 INFO @ Wed, 05 Sep 2018 10:44:55: 7000000 INFO @ Wed, 05 Sep 2018 10:44:56: 7000000 INFO @ Wed, 05 Sep 2018 10:44:58: 7000000 INFO @ Wed, 05 Sep 2018 10:45:02: 8000000 INFO @ Wed, 05 Sep 2018 10:45:04: 8000000 INFO @ Wed, 05 Sep 2018 10:45:04: #1 tag size is determined as 50 bps INFO @ Wed, 05 Sep 2018 10:45:04: #1 tag size = 50 INFO @ Wed, 05 Sep 2018 10:45:04: #1 total tags in treatment: 8282681 INFO @ Wed, 05 Sep 2018 10:45:04: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:45:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:45:04: #1 tags after filtering in treatment: 8282681 INFO @ Wed, 05 Sep 2018 10:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:45:04: #1 finished! INFO @ Wed, 05 Sep 2018 10:45:04: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:45:04: #2 number of paired peaks: 0 WARNING @ Wed, 05 Sep 2018 10:45:04: Too few paired peaks (0) 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 @ Wed, 05 Sep 2018 10:45:04: Process for pairing-model is terminated! cat: SRX3585229.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3585229.20_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 `SRX3585229.20_*.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 `SRX3585229.20_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 @ Wed, 05 Sep 2018 10:45:06: #1 tag size is determined as 50 bps INFO @ Wed, 05 Sep 2018 10:45:06: #1 tag size = 50 INFO @ Wed, 05 Sep 2018 10:45:06: #1 total tags in treatment: 8282681 INFO @ Wed, 05 Sep 2018 10:45:06: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:45:06: #1 tags after filtering in treatment: 8282681 INFO @ Wed, 05 Sep 2018 10:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:45:06: #1 finished! INFO @ Wed, 05 Sep 2018 10:45:06: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:45:06: #2 number of paired peaks: 0 WARNING @ Wed, 05 Sep 2018 10:45:06: Too few paired peaks (0) 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 @ Wed, 05 Sep 2018 10:45:06: Process for pairing-model is terminated! cat: SRX3585229.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3585229.05_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 `SRX3585229.05_*.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 `SRX3585229.05_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 INFO @ Wed, 05 Sep 2018 10:45:07: 8000000 INFO @ Wed, 05 Sep 2018 10:45:09: #1 tag size is determined as 50 bps INFO @ Wed, 05 Sep 2018 10:45:09: #1 tag size = 50 INFO @ Wed, 05 Sep 2018 10:45:09: #1 total tags in treatment: 8282681 INFO @ Wed, 05 Sep 2018 10:45:09: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:45:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:45:09: #1 tags after filtering in treatment: 8282681 INFO @ Wed, 05 Sep 2018 10:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:45:09: #1 finished! INFO @ Wed, 05 Sep 2018 10:45:09: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:45:10: #2 number of paired peaks: 0 WARNING @ Wed, 05 Sep 2018 10:45:10: Too few paired peaks (0) 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 @ Wed, 05 Sep 2018 10:45:10: Process for pairing-model is terminated! cat: SRX3585229.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3585229.10_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 `SRX3585229.10_*.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 `SRX3585229.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。