Job ID = 9157397 sra ファイルのダウンロード中... Completed: 613970K bytes transferred in 10 seconds (472121K bits/sec), in 1 file, 2 directories. 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... Written 22293459 spots for /home/okishinya/chipatlas/results/ce10/SRX1936237/SRR3879844.sra Written 22293459 spots total 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: 00:05:35 22293459 reads; of these: 22293459 (100.00%) were unpaired; of these: 1266427 (5.68%) aligned 0 times 17528726 (78.63%) aligned exactly 1 time 3498306 (15.69%) aligned >1 times 94.32% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2682250 / 21027032 = 0.1276 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, 27 Jun 2017 11:51:43: # Command line: callpeak -t SRX1936237.bam -f BAM -g ce -n SRX1936237.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936237.10 # format = BAM # ChIP-seq file = ['SRX1936237.bam'] # control file = None # effective genome size = 9.00e+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, 27 Jun 2017 11:51:43: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:51:43: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:51:43: # Command line: callpeak -t SRX1936237.bam -f BAM -g ce -n SRX1936237.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936237.05 # format = BAM # ChIP-seq file = ['SRX1936237.bam'] # control file = None # effective genome size = 9.00e+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, 27 Jun 2017 11:51:43: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:51:43: # Command line: callpeak -t SRX1936237.bam -f BAM -g ce -n SRX1936237.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936237.20 # format = BAM # ChIP-seq file = ['SRX1936237.bam'] # control file = None # effective genome size = 9.00e+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, 27 Jun 2017 11:51:43: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:51:43: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:51:43: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:51:50: 1000000 INFO @ Tue, 27 Jun 2017 11:51:50: 1000000 INFO @ Tue, 27 Jun 2017 11:51:50: 1000000 INFO @ Tue, 27 Jun 2017 11:51:56: 2000000 INFO @ Tue, 27 Jun 2017 11:51:56: 2000000 INFO @ Tue, 27 Jun 2017 11:51:57: 2000000 INFO @ Tue, 27 Jun 2017 11:52:03: 3000000 INFO @ Tue, 27 Jun 2017 11:52:03: 3000000 INFO @ Tue, 27 Jun 2017 11:52:04: 3000000 INFO @ Tue, 27 Jun 2017 11:52:10: 4000000 INFO @ Tue, 27 Jun 2017 11:52:10: 4000000 INFO @ Tue, 27 Jun 2017 11:52:11: 4000000 INFO @ Tue, 27 Jun 2017 11:52:17: 5000000 INFO @ Tue, 27 Jun 2017 11:52:17: 5000000 INFO @ Tue, 27 Jun 2017 11:52:18: 5000000 INFO @ Tue, 27 Jun 2017 11:52:24: 6000000 INFO @ Tue, 27 Jun 2017 11:52:24: 6000000 INFO @ Tue, 27 Jun 2017 11:52:25: 6000000 INFO @ Tue, 27 Jun 2017 11:52:31: 7000000 INFO @ Tue, 27 Jun 2017 11:52:31: 7000000 INFO @ Tue, 27 Jun 2017 11:52:32: 7000000 INFO @ Tue, 27 Jun 2017 11:52:37: 8000000 INFO @ Tue, 27 Jun 2017 11:52:37: 8000000 INFO @ Tue, 27 Jun 2017 11:52:39: 8000000 INFO @ Tue, 27 Jun 2017 11:52:44: 9000000 INFO @ Tue, 27 Jun 2017 11:52:44: 9000000 INFO @ Tue, 27 Jun 2017 11:52:46: 9000000 INFO @ Tue, 27 Jun 2017 11:52:52: 10000000 INFO @ Tue, 27 Jun 2017 11:52:52: 10000000 INFO @ Tue, 27 Jun 2017 11:52:53: 10000000 INFO @ Tue, 27 Jun 2017 11:52:59: 11000000 INFO @ Tue, 27 Jun 2017 11:52:59: 11000000 INFO @ Tue, 27 Jun 2017 11:53:00: 11000000 INFO @ Tue, 27 Jun 2017 11:53:06: 12000000 INFO @ Tue, 27 Jun 2017 11:53:06: 12000000 INFO @ Tue, 27 Jun 2017 11:53:07: 12000000 INFO @ Tue, 27 Jun 2017 11:53:12: 13000000 INFO @ Tue, 27 Jun 2017 11:53:12: 13000000 INFO @ Tue, 27 Jun 2017 11:53:14: 13000000 INFO @ Tue, 27 Jun 2017 11:53:19: 14000000 INFO @ Tue, 27 Jun 2017 11:53:19: 14000000 INFO @ Tue, 27 Jun 2017 11:53:21: 14000000 INFO @ Tue, 27 Jun 2017 11:53:26: 15000000 INFO @ Tue, 27 Jun 2017 11:53:26: 15000000 INFO @ Tue, 27 Jun 2017 11:53:28: 15000000 INFO @ Tue, 27 Jun 2017 11:53:33: 16000000 INFO @ Tue, 27 Jun 2017 11:53:33: 16000000 INFO @ Tue, 27 Jun 2017 11:53:35: 16000000 INFO @ Tue, 27 Jun 2017 11:53:40: 17000000 INFO @ Tue, 27 Jun 2017 11:53:40: 17000000 INFO @ Tue, 27 Jun 2017 11:53:42: 17000000 INFO @ Tue, 27 Jun 2017 11:53:46: 18000000 INFO @ Tue, 27 Jun 2017 11:53:46: 18000000 INFO @ Tue, 27 Jun 2017 11:53:49: 18000000 INFO @ Tue, 27 Jun 2017 11:53:49: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:53:49: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:53:49: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:53:49: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:53:49: #1 total tags in treatment: 18344782 INFO @ Tue, 27 Jun 2017 11:53:49: #1 total tags in treatment: 18344782 INFO @ Tue, 27 Jun 2017 11:53:49: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:53:49: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:53:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:53:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:53:49: #1 tags after filtering in treatment: 18344782 INFO @ Tue, 27 Jun 2017 11:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:53:49: #1 finished! INFO @ Tue, 27 Jun 2017 11:53:49: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:53:49: #1 tags after filtering in treatment: 18344782 INFO @ Tue, 27 Jun 2017 11:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:53:49: #1 finished! INFO @ Tue, 27 Jun 2017 11:53:49: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:53:51: #2 number of paired peaks: 212 WARNING @ Tue, 27 Jun 2017 11:53:51: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 27 Jun 2017 11:53:51: start model_add_line... INFO @ Tue, 27 Jun 2017 11:53:51: #2 number of paired peaks: 212 WARNING @ Tue, 27 Jun 2017 11:53:51: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 27 Jun 2017 11:53:51: start model_add_line... INFO @ Tue, 27 Jun 2017 11:53:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:53:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:53:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:53:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:53:51: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:53:51: #2 alternative fragment length(s) may be 1,45,549,595 bps INFO @ Tue, 27 Jun 2017 11:53:51: #2.2 Generate R script for model : SRX1936237.05_model.r INFO @ Tue, 27 Jun 2017 11:53:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:53:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:53:51: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:53:51: #2 alternative fragment length(s) may be 1,45,549,595 bps INFO @ Tue, 27 Jun 2017 11:53:51: #2.2 Generate R script for model : SRX1936237.20_model.r WARNING @ Tue, 27 Jun 2017 11:53:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:53:51: #2 You may need to consider one of the other alternative d(s): 1,45,549,595 WARNING @ Tue, 27 Jun 2017 11:53:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:53:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:53:51: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 11:53:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:53:51: #2 You may need to consider one of the other alternative d(s): 1,45,549,595 WARNING @ Tue, 27 Jun 2017 11:53:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:53:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:53:51: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:53:51: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:53:51: #1 total tags in treatment: 18344782 INFO @ Tue, 27 Jun 2017 11:53:51: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:53:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:53:51: #1 tags after filtering in treatment: 18344782 INFO @ Tue, 27 Jun 2017 11:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:53:51: #1 finished! INFO @ Tue, 27 Jun 2017 11:53:51: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:53:53: #2 number of paired peaks: 212 WARNING @ Tue, 27 Jun 2017 11:53:53: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 27 Jun 2017 11:53:53: start model_add_line... INFO @ Tue, 27 Jun 2017 11:53:53: start X-correlation... INFO @ Tue, 27 Jun 2017 11:53:53: end of X-cor INFO @ Tue, 27 Jun 2017 11:53:53: #2 finished! INFO @ Tue, 27 Jun 2017 11:53:53: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:53:53: #2 alternative fragment length(s) may be 1,45,549,595 bps INFO @ Tue, 27 Jun 2017 11:53:53: #2.2 Generate R script for model : SRX1936237.10_model.r WARNING @ Tue, 27 Jun 2017 11:53:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:53:53: #2 You may need to consider one of the other alternative d(s): 1,45,549,595 WARNING @ Tue, 27 Jun 2017 11:53:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:53:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:53:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:23: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:23: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:39: #4 Write output xls file... SRX1936237.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:39: #4 Write peak in narrowPeak format file... SRX1936237.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:39: #4 Write summits bed file... SRX1936237.05_summits.bed INFO @ Tue, 27 Jun 2017 11:54:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:54:40: #4 Write output xls file... SRX1936237.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:40: #4 Write peak in narrowPeak format file... SRX1936237.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:40: #4 Write summits bed file... SRX1936237.10_summits.bed INFO @ Tue, 27 Jun 2017 11:54:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:54:41: #4 Write output xls file... SRX1936237.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:41: #4 Write peak in narrowPeak format file... SRX1936237.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:41: #4 Write summits bed file... SRX1936237.20_summits.bed INFO @ Tue, 27 Jun 2017 11:54:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。