Job ID = 11296958 sra ファイルのダウンロード中... Completed: 238084K bytes transferred in 6 seconds (296152K 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 11389101 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856380/SRR6908198.sra Written 11389101 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856380/SRR6908198.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: 00:02:09 11389101 reads; of these: 11389101 (100.00%) were unpaired; of these: 845866 (7.43%) aligned 0 times 7288347 (63.99%) aligned exactly 1 time 3254888 (28.58%) aligned >1 times 92.57% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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_rmdupse_core] 6284438 / 10543235 = 0.5961 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 @ Mon, 05 Nov 2018 18:05:11: # Command line: callpeak -t SRX3856380.bam -f BAM -g 12100000 -n SRX3856380.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856380.10 # format = BAM # ChIP-seq file = ['SRX3856380.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 @ Mon, 05 Nov 2018 18:05:11: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:11: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:11: # Command line: callpeak -t SRX3856380.bam -f BAM -g 12100000 -n SRX3856380.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856380.20 # format = BAM # ChIP-seq file = ['SRX3856380.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 @ Mon, 05 Nov 2018 18:05:11: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:11: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:11: # Command line: callpeak -t SRX3856380.bam -f BAM -g 12100000 -n SRX3856380.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856380.05 # format = BAM # ChIP-seq file = ['SRX3856380.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 @ Mon, 05 Nov 2018 18:05:11: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:11: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:19: 1000000 INFO @ Mon, 05 Nov 2018 18:05:19: 1000000 INFO @ Mon, 05 Nov 2018 18:05:19: 1000000 INFO @ Mon, 05 Nov 2018 18:05:26: 2000000 INFO @ Mon, 05 Nov 2018 18:05:28: 2000000 INFO @ Mon, 05 Nov 2018 18:05:28: 2000000 INFO @ Mon, 05 Nov 2018 18:05:34: 3000000 INFO @ Mon, 05 Nov 2018 18:05:36: 3000000 INFO @ Mon, 05 Nov 2018 18:05:36: 3000000 INFO @ Mon, 05 Nov 2018 18:05:42: 4000000 INFO @ Mon, 05 Nov 2018 18:05:44: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:05:44: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:05:44: #1 total tags in treatment: 4258797 INFO @ Mon, 05 Nov 2018 18:05:44: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:05:44: #1 tags after filtering in treatment: 4258797 INFO @ Mon, 05 Nov 2018 18:05:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:44: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:44: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:44: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:05:44: Too few paired peaks (28) 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 @ Mon, 05 Nov 2018 18:05:44: Process for pairing-model is terminated! cat: SRX3856380.10_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 `SRX3856380.10_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 `SRX3856380.10_*.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 `SRX3856380.10_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 @ Mon, 05 Nov 2018 18:05:44: 4000000 INFO @ Mon, 05 Nov 2018 18:05:44: 4000000 INFO @ Mon, 05 Nov 2018 18:05:46: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:05:46: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:05:46: #1 total tags in treatment: 4258797 INFO @ Mon, 05 Nov 2018 18:05:46: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:05:46: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:05:46: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:05:46: #1 total tags in treatment: 4258797 INFO @ Mon, 05 Nov 2018 18:05:46: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:05:46: #1 tags after filtering in treatment: 4258797 INFO @ Mon, 05 Nov 2018 18:05:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:46: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:46: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:46: #1 tags after filtering in treatment: 4258797 INFO @ Mon, 05 Nov 2018 18:05:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:46: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:46: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:47: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:05:47: Too few paired peaks (28) 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 @ Mon, 05 Nov 2018 18:05:47: Process for pairing-model is terminated! cat: SRX3856380.20_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 `SRX3856380.20_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 `SRX3856380.20_*.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 `SRX3856380.20_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 @ Mon, 05 Nov 2018 18:05:47: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:05:47: Too few paired peaks (28) 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 @ Mon, 05 Nov 2018 18:05:47: Process for pairing-model is terminated! cat: SRX3856380.05_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 `SRX3856380.05_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 `SRX3856380.05_*.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 `SRX3856380.05_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。