Job ID = 11634680 sra ファイルのダウンロード中... Completed: 558761K bytes transferred in 8 seconds (564800K 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 26892354 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4092960/SRR7175388.sra Written 26892354 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4092960/SRR7175388.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:29 26892354 reads; of these: 26892354 (100.00%) were unpaired; of these: 1508745 (5.61%) aligned 0 times 19379390 (72.06%) aligned exactly 1 time 6004219 (22.33%) aligned >1 times 94.39% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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 12 files... [bam_rmdupse_core] 13235395 / 25383609 = 0.5214 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 @ Fri, 15 Feb 2019 10:33:08: # Command line: callpeak -t SRX4092960.bam -f BAM -g 12100000 -n SRX4092960.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4092960.05 # format = BAM # ChIP-seq file = ['SRX4092960.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 @ Fri, 15 Feb 2019 10:33:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:33:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:33:08: # Command line: callpeak -t SRX4092960.bam -f BAM -g 12100000 -n SRX4092960.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4092960.20 # format = BAM # ChIP-seq file = ['SRX4092960.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 @ Fri, 15 Feb 2019 10:33:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:33:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:33:08: # Command line: callpeak -t SRX4092960.bam -f BAM -g 12100000 -n SRX4092960.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4092960.10 # format = BAM # ChIP-seq file = ['SRX4092960.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 @ Fri, 15 Feb 2019 10:33:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:33:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:33:15: 1000000 INFO @ Fri, 15 Feb 2019 10:33:15: 1000000 INFO @ Fri, 15 Feb 2019 10:33:15: 1000000 INFO @ Fri, 15 Feb 2019 10:33:21: 2000000 INFO @ Fri, 15 Feb 2019 10:33:22: 2000000 INFO @ Fri, 15 Feb 2019 10:33:22: 2000000 INFO @ Fri, 15 Feb 2019 10:33:28: 3000000 INFO @ Fri, 15 Feb 2019 10:33:29: 3000000 INFO @ Fri, 15 Feb 2019 10:33:29: 3000000 INFO @ Fri, 15 Feb 2019 10:33:35: 4000000 INFO @ Fri, 15 Feb 2019 10:33:36: 4000000 INFO @ Fri, 15 Feb 2019 10:33:36: 4000000 INFO @ Fri, 15 Feb 2019 10:33:42: 5000000 INFO @ Fri, 15 Feb 2019 10:33:43: 5000000 INFO @ Fri, 15 Feb 2019 10:33:44: 5000000 INFO @ Fri, 15 Feb 2019 10:33:49: 6000000 INFO @ Fri, 15 Feb 2019 10:33:51: 6000000 INFO @ Fri, 15 Feb 2019 10:33:51: 6000000 INFO @ Fri, 15 Feb 2019 10:33:57: 7000000 INFO @ Fri, 15 Feb 2019 10:33:58: 7000000 INFO @ Fri, 15 Feb 2019 10:33:59: 7000000 INFO @ Fri, 15 Feb 2019 10:34:05: 8000000 INFO @ Fri, 15 Feb 2019 10:34:05: 8000000 INFO @ Fri, 15 Feb 2019 10:34:07: 8000000 INFO @ Fri, 15 Feb 2019 10:34:12: 9000000 INFO @ Fri, 15 Feb 2019 10:34:14: 9000000 INFO @ Fri, 15 Feb 2019 10:34:15: 9000000 INFO @ Fri, 15 Feb 2019 10:34:19: 10000000 INFO @ Fri, 15 Feb 2019 10:34:21: 10000000 INFO @ Fri, 15 Feb 2019 10:34:22: 10000000 INFO @ Fri, 15 Feb 2019 10:34:26: 11000000 INFO @ Fri, 15 Feb 2019 10:34:28: 11000000 INFO @ Fri, 15 Feb 2019 10:34:29: 11000000 INFO @ Fri, 15 Feb 2019 10:34:33: 12000000 INFO @ Fri, 15 Feb 2019 10:34:34: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:34:34: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:34:34: #1 total tags in treatment: 12148214 INFO @ Fri, 15 Feb 2019 10:34:34: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:34:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:34:34: #1 tags after filtering in treatment: 12148214 INFO @ Fri, 15 Feb 2019 10:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:34:34: #1 finished! INFO @ Fri, 15 Feb 2019 10:34:34: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:34:35: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:34:35: 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 @ Fri, 15 Feb 2019 10:34:35: Process for pairing-model is terminated! cat: SRX4092960.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4092960.05_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 `SRX4092960.05_*.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 `SRX4092960.05_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 @ Fri, 15 Feb 2019 10:34:35: 12000000 INFO @ Fri, 15 Feb 2019 10:34:36: 12000000 INFO @ Fri, 15 Feb 2019 10:34:36: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:34:36: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:34:36: #1 total tags in treatment: 12148214 INFO @ Fri, 15 Feb 2019 10:34:36: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:34:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:34:37: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:34:37: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:34:37: #1 total tags in treatment: 12148214 INFO @ Fri, 15 Feb 2019 10:34:37: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:34:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:34:37: #1 tags after filtering in treatment: 12148214 INFO @ Fri, 15 Feb 2019 10:34:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:34:37: #1 finished! INFO @ Fri, 15 Feb 2019 10:34:37: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:34:37: #1 tags after filtering in treatment: 12148214 INFO @ Fri, 15 Feb 2019 10:34:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:34:37: #1 finished! INFO @ Fri, 15 Feb 2019 10:34:37: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:34:37: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:34:37: 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 @ Fri, 15 Feb 2019 10:34:37: Process for pairing-model is terminated! cat: SRX4092960.20_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 `SRX4092960.20_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 `SRX4092960.20_*.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 `SRX4092960.20_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 @ Fri, 15 Feb 2019 10:34:38: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:34:38: 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 @ Fri, 15 Feb 2019 10:34:38: Process for pairing-model is terminated! cat: SRX4092960.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4092960.10_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 `SRX4092960.10_*.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 `SRX4092960.10_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。