Job ID = 9157376 sra ファイルのダウンロード中... Completed: 2942568K bytes transferred in 24 seconds (983355K 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 86067449 spots for /home/okishinya/chipatlas/results/ce10/SRX1674086/SRR3320132.sra Written 86067449 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:16 86067449 reads; of these: 86067449 (100.00%) were unpaired; of these: 9167903 (10.65%) aligned 0 times 65246976 (75.81%) aligned exactly 1 time 11652570 (13.54%) aligned >1 times 89.35% overall alignment rate Time searching: 00:21:17 Overall time: 00:21:17 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 32 files... [bam_rmdupse_core] 49017907 / 76899546 = 0.6374 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 12:11:26: # Command line: callpeak -t SRX1674086.bam -f BAM -g ce -n SRX1674086.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674086.05 # format = BAM # ChIP-seq file = ['SRX1674086.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 12:11:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:11:26: # Command line: callpeak -t SRX1674086.bam -f BAM -g ce -n SRX1674086.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674086.10 # format = BAM # ChIP-seq file = ['SRX1674086.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 12:11:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:11:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:11:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:11:26: # Command line: callpeak -t SRX1674086.bam -f BAM -g ce -n SRX1674086.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674086.20 # format = BAM # ChIP-seq file = ['SRX1674086.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 12:11:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:11:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:11:34: 1000000 INFO @ Tue, 27 Jun 2017 12:11:34: 1000000 INFO @ Tue, 27 Jun 2017 12:11:35: 1000000 INFO @ Tue, 27 Jun 2017 12:11:43: 2000000 INFO @ Tue, 27 Jun 2017 12:11:43: 2000000 INFO @ Tue, 27 Jun 2017 12:11:43: 2000000 INFO @ Tue, 27 Jun 2017 12:11:50: 3000000 INFO @ Tue, 27 Jun 2017 12:11:51: 3000000 INFO @ Tue, 27 Jun 2017 12:11:51: 3000000 INFO @ Tue, 27 Jun 2017 12:11:58: 4000000 INFO @ Tue, 27 Jun 2017 12:11:58: 4000000 INFO @ Tue, 27 Jun 2017 12:11:58: 4000000 INFO @ Tue, 27 Jun 2017 12:12:06: 5000000 INFO @ Tue, 27 Jun 2017 12:12:06: 5000000 INFO @ Tue, 27 Jun 2017 12:12:06: 5000000 INFO @ Tue, 27 Jun 2017 12:12:14: 6000000 INFO @ Tue, 27 Jun 2017 12:12:14: 6000000 INFO @ Tue, 27 Jun 2017 12:12:14: 6000000 INFO @ Tue, 27 Jun 2017 12:12:22: 7000000 INFO @ Tue, 27 Jun 2017 12:12:22: 7000000 INFO @ Tue, 27 Jun 2017 12:12:22: 7000000 INFO @ Tue, 27 Jun 2017 12:12:29: 8000000 INFO @ Tue, 27 Jun 2017 12:12:30: 8000000 INFO @ Tue, 27 Jun 2017 12:12:30: 8000000 INFO @ Tue, 27 Jun 2017 12:12:37: 9000000 INFO @ Tue, 27 Jun 2017 12:12:38: 9000000 INFO @ Tue, 27 Jun 2017 12:12:38: 9000000 INFO @ Tue, 27 Jun 2017 12:12:44: 10000000 INFO @ Tue, 27 Jun 2017 12:12:45: 10000000 INFO @ Tue, 27 Jun 2017 12:12:45: 10000000 INFO @ Tue, 27 Jun 2017 12:12:52: 11000000 INFO @ Tue, 27 Jun 2017 12:12:53: 11000000 INFO @ Tue, 27 Jun 2017 12:12:53: 11000000 INFO @ Tue, 27 Jun 2017 12:12:59: 12000000 INFO @ Tue, 27 Jun 2017 12:13:00: 12000000 INFO @ Tue, 27 Jun 2017 12:13:01: 12000000 INFO @ Tue, 27 Jun 2017 12:13:07: 13000000 INFO @ Tue, 27 Jun 2017 12:13:09: 13000000 INFO @ Tue, 27 Jun 2017 12:13:09: 13000000 INFO @ Tue, 27 Jun 2017 12:13:15: 14000000 INFO @ Tue, 27 Jun 2017 12:13:16: 14000000 INFO @ Tue, 27 Jun 2017 12:13:16: 14000000 INFO @ Tue, 27 Jun 2017 12:13:23: 15000000 INFO @ Tue, 27 Jun 2017 12:13:24: 15000000 INFO @ Tue, 27 Jun 2017 12:13:24: 15000000 INFO @ Tue, 27 Jun 2017 12:13:30: 16000000 INFO @ Tue, 27 Jun 2017 12:13:32: 16000000 INFO @ Tue, 27 Jun 2017 12:13:32: 16000000 INFO @ Tue, 27 Jun 2017 12:13:37: 17000000 INFO @ Tue, 27 Jun 2017 12:13:39: 17000000 INFO @ Tue, 27 Jun 2017 12:13:40: 17000000 INFO @ Tue, 27 Jun 2017 12:13:45: 18000000 INFO @ Tue, 27 Jun 2017 12:13:47: 18000000 INFO @ Tue, 27 Jun 2017 12:13:48: 18000000 INFO @ Tue, 27 Jun 2017 12:13:53: 19000000 INFO @ Tue, 27 Jun 2017 12:13:55: 19000000 INFO @ Tue, 27 Jun 2017 12:13:55: 19000000 INFO @ Tue, 27 Jun 2017 12:14:00: 20000000 INFO @ Tue, 27 Jun 2017 12:14:03: 20000000 INFO @ Tue, 27 Jun 2017 12:14:04: 20000000 INFO @ Tue, 27 Jun 2017 12:14:07: 21000000 INFO @ Tue, 27 Jun 2017 12:14:12: 21000000 INFO @ Tue, 27 Jun 2017 12:14:12: 21000000 INFO @ Tue, 27 Jun 2017 12:14:14: 22000000 INFO @ Tue, 27 Jun 2017 12:14:19: 22000000 INFO @ Tue, 27 Jun 2017 12:14:19: 22000000 INFO @ Tue, 27 Jun 2017 12:14:21: 23000000 INFO @ Tue, 27 Jun 2017 12:14:26: 23000000 INFO @ Tue, 27 Jun 2017 12:14:27: 23000000 INFO @ Tue, 27 Jun 2017 12:14:28: 24000000 INFO @ Tue, 27 Jun 2017 12:14:34: 24000000 INFO @ Tue, 27 Jun 2017 12:14:34: 24000000 INFO @ Tue, 27 Jun 2017 12:14:36: 25000000 INFO @ Tue, 27 Jun 2017 12:14:41: 25000000 INFO @ Tue, 27 Jun 2017 12:14:42: 25000000 INFO @ Tue, 27 Jun 2017 12:14:44: 26000000 INFO @ Tue, 27 Jun 2017 12:14:47: 26000000 INFO @ Tue, 27 Jun 2017 12:14:50: 26000000 INFO @ Tue, 27 Jun 2017 12:14:52: 27000000 INFO @ Tue, 27 Jun 2017 12:14:54: 27000000 INFO @ Tue, 27 Jun 2017 12:14:58: 27000000 INFO @ Tue, 27 Jun 2017 12:14:59: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:14:59: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:14:59: #1 total tags in treatment: 27881639 INFO @ Tue, 27 Jun 2017 12:14:59: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:14:59: #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 12:15:00: #1 tags after filtering in treatment: 27881639 INFO @ Tue, 27 Jun 2017 12:15:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:15:00: #1 finished! INFO @ Tue, 27 Jun 2017 12:15:00: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:15:00: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:15:00: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:15:00: #1 total tags in treatment: 27881639 INFO @ Tue, 27 Jun 2017 12:15:00: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:15:00: #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 12:15:01: #1 tags after filtering in treatment: 27881639 INFO @ Tue, 27 Jun 2017 12:15:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:15:01: #1 finished! INFO @ Tue, 27 Jun 2017 12:15:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:15:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:15:02: #2 number of paired peaks: 186 WARNING @ Tue, 27 Jun 2017 12:15:02: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 27 Jun 2017 12:15:02: start model_add_line... INFO @ Tue, 27 Jun 2017 12:15:02: start X-correlation... INFO @ Tue, 27 Jun 2017 12:15:02: end of X-cor INFO @ Tue, 27 Jun 2017 12:15:02: #2 finished! INFO @ Tue, 27 Jun 2017 12:15:02: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:15:02: #2 alternative fragment length(s) may be 1,14,39,583 bps INFO @ Tue, 27 Jun 2017 12:15:02: #2.2 Generate R script for model : SRX1674086.20_model.r WARNING @ Tue, 27 Jun 2017 12:15:02: #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 12:15:02: #2 You may need to consider one of the other alternative d(s): 1,14,39,583 WARNING @ Tue, 27 Jun 2017 12:15:02: #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 12:15:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:15:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:15:02: #2 number of paired peaks: 186 WARNING @ Tue, 27 Jun 2017 12:15:02: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 27 Jun 2017 12:15:02: start model_add_line... INFO @ Tue, 27 Jun 2017 12:15:03: start X-correlation... INFO @ Tue, 27 Jun 2017 12:15:03: end of X-cor INFO @ Tue, 27 Jun 2017 12:15:03: #2 finished! INFO @ Tue, 27 Jun 2017 12:15:03: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:15:03: #2 alternative fragment length(s) may be 1,14,39,583 bps INFO @ Tue, 27 Jun 2017 12:15:03: #2.2 Generate R script for model : SRX1674086.10_model.r WARNING @ Tue, 27 Jun 2017 12:15:03: #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 12:15:03: #2 You may need to consider one of the other alternative d(s): 1,14,39,583 WARNING @ Tue, 27 Jun 2017 12:15:03: #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 12:15:03: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:15:05: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:15:05: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:15:05: #1 total tags in treatment: 27881639 INFO @ Tue, 27 Jun 2017 12:15:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:15:05: #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 12:15:05: #1 tags after filtering in treatment: 27881639 INFO @ Tue, 27 Jun 2017 12:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:15:05: #1 finished! INFO @ Tue, 27 Jun 2017 12:15:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:15:07: #2 number of paired peaks: 186 WARNING @ Tue, 27 Jun 2017 12:15:07: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 27 Jun 2017 12:15:07: start model_add_line... INFO @ Tue, 27 Jun 2017 12:15:08: start X-correlation... INFO @ Tue, 27 Jun 2017 12:15:08: end of X-cor INFO @ Tue, 27 Jun 2017 12:15:08: #2 finished! INFO @ Tue, 27 Jun 2017 12:15:08: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:15:08: #2 alternative fragment length(s) may be 1,14,39,583 bps INFO @ Tue, 27 Jun 2017 12:15:08: #2.2 Generate R script for model : SRX1674086.05_model.r WARNING @ Tue, 27 Jun 2017 12:15:08: #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 12:15:08: #2 You may need to consider one of the other alternative d(s): 1,14,39,583 WARNING @ Tue, 27 Jun 2017 12:15:08: #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 12:15:08: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:15:46: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:15:46: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:15:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:16:06: #4 Write output xls file... SRX1674086.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:16:06: #4 Write peak in narrowPeak format file... SRX1674086.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:16:06: #4 Write summits bed file... SRX1674086.10_summits.bed INFO @ Tue, 27 Jun 2017 12:16:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:16:08: #4 Write output xls file... SRX1674086.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:16:08: #4 Write peak in narrowPeak format file... SRX1674086.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:16:08: #4 Write summits bed file... SRX1674086.05_summits.bed INFO @ Tue, 27 Jun 2017 12:16:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:16:11: #4 Write output xls file... SRX1674086.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:16:11: #4 Write peak in narrowPeak format file... SRX1674086.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:16:11: #4 Write summits bed file... SRX1674086.20_summits.bed INFO @ Tue, 27 Jun 2017 12:16:11: 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。