Job ID = 9158489 sra ファイルのダウンロード中... Completed: 1886923K bytes transferred in 18 seconds (852800K 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 57671785 spots for /home/okishinya/chipatlas/results/dm3/SRX1361349/SRR2749787.sra Written 57671785 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: 00:26:43 57671785 reads; of these: 57671785 (100.00%) were unpaired; of these: 2519295 (4.37%) aligned 0 times 25245964 (43.78%) aligned exactly 1 time 29906526 (51.86%) aligned >1 times 95.63% overall alignment rate Time searching: 00:26:43 Overall time: 00:26:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 24762717 / 55152490 = 0.4490 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 17:46:09: # Command line: callpeak -t SRX1361349.bam -f BAM -g dm -n SRX1361349.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361349.10 # format = BAM # ChIP-seq file = ['SRX1361349.bam'] # control file = None # effective genome size = 1.20e+08 # 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 17:46:09: # Command line: callpeak -t SRX1361349.bam -f BAM -g dm -n SRX1361349.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361349.20 # format = BAM # ChIP-seq file = ['SRX1361349.bam'] # control file = None # effective genome size = 1.20e+08 # 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 17:46:09: # Command line: callpeak -t SRX1361349.bam -f BAM -g dm -n SRX1361349.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361349.05 # format = BAM # ChIP-seq file = ['SRX1361349.bam'] # control file = None # effective genome size = 1.20e+08 # 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 17:46:09: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:46:09: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:46:09: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:46:09: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:46:09: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:46:09: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:46:16: 1000000 INFO @ Tue, 27 Jun 2017 17:46:16: 1000000 INFO @ Tue, 27 Jun 2017 17:46:16: 1000000 INFO @ Tue, 27 Jun 2017 17:46:22: 2000000 INFO @ Tue, 27 Jun 2017 17:46:22: 2000000 INFO @ Tue, 27 Jun 2017 17:46:22: 2000000 INFO @ Tue, 27 Jun 2017 17:46:28: 3000000 INFO @ Tue, 27 Jun 2017 17:46:29: 3000000 INFO @ Tue, 27 Jun 2017 17:46:29: 3000000 INFO @ Tue, 27 Jun 2017 17:46:34: 4000000 INFO @ Tue, 27 Jun 2017 17:46:35: 4000000 INFO @ Tue, 27 Jun 2017 17:46:35: 4000000 INFO @ Tue, 27 Jun 2017 17:46:39: 5000000 INFO @ Tue, 27 Jun 2017 17:46:41: 5000000 INFO @ Tue, 27 Jun 2017 17:46:41: 5000000 INFO @ Tue, 27 Jun 2017 17:46:45: 6000000 INFO @ Tue, 27 Jun 2017 17:46:47: 6000000 INFO @ Tue, 27 Jun 2017 17:46:48: 6000000 INFO @ Tue, 27 Jun 2017 17:46:51: 7000000 INFO @ Tue, 27 Jun 2017 17:46:54: 7000000 INFO @ Tue, 27 Jun 2017 17:46:54: 7000000 INFO @ Tue, 27 Jun 2017 17:46:57: 8000000 INFO @ Tue, 27 Jun 2017 17:47:00: 8000000 INFO @ Tue, 27 Jun 2017 17:47:00: 8000000 INFO @ Tue, 27 Jun 2017 17:47:03: 9000000 INFO @ Tue, 27 Jun 2017 17:47:06: 9000000 INFO @ Tue, 27 Jun 2017 17:47:07: 9000000 INFO @ Tue, 27 Jun 2017 17:47:09: 10000000 INFO @ Tue, 27 Jun 2017 17:47:13: 10000000 INFO @ Tue, 27 Jun 2017 17:47:13: 10000000 INFO @ Tue, 27 Jun 2017 17:47:15: 11000000 INFO @ Tue, 27 Jun 2017 17:47:19: 11000000 INFO @ Tue, 27 Jun 2017 17:47:19: 11000000 INFO @ Tue, 27 Jun 2017 17:47:21: 12000000 INFO @ Tue, 27 Jun 2017 17:47:25: 12000000 INFO @ Tue, 27 Jun 2017 17:47:26: 12000000 INFO @ Tue, 27 Jun 2017 17:47:27: 13000000 INFO @ Tue, 27 Jun 2017 17:47:32: 13000000 INFO @ Tue, 27 Jun 2017 17:47:32: 13000000 INFO @ Tue, 27 Jun 2017 17:47:33: 14000000 INFO @ Tue, 27 Jun 2017 17:47:38: 14000000 INFO @ Tue, 27 Jun 2017 17:47:39: 14000000 INFO @ Tue, 27 Jun 2017 17:47:39: 15000000 INFO @ Tue, 27 Jun 2017 17:47:45: 15000000 INFO @ Tue, 27 Jun 2017 17:47:45: 16000000 INFO @ Tue, 27 Jun 2017 17:47:46: 15000000 INFO @ Tue, 27 Jun 2017 17:47:51: 17000000 INFO @ Tue, 27 Jun 2017 17:47:51: 16000000 INFO @ Tue, 27 Jun 2017 17:47:52: 16000000 INFO @ Tue, 27 Jun 2017 17:47:57: 18000000 INFO @ Tue, 27 Jun 2017 17:47:58: 17000000 INFO @ Tue, 27 Jun 2017 17:47:59: 17000000 INFO @ Tue, 27 Jun 2017 17:48:04: 19000000 INFO @ Tue, 27 Jun 2017 17:48:05: 18000000 INFO @ Tue, 27 Jun 2017 17:48:07: 18000000 INFO @ Tue, 27 Jun 2017 17:48:12: 20000000 INFO @ Tue, 27 Jun 2017 17:48:14: 19000000 INFO @ Tue, 27 Jun 2017 17:48:15: 19000000 INFO @ Tue, 27 Jun 2017 17:48:20: 21000000 INFO @ Tue, 27 Jun 2017 17:48:22: 20000000 INFO @ Tue, 27 Jun 2017 17:48:23: 20000000 INFO @ Tue, 27 Jun 2017 17:48:28: 22000000 INFO @ Tue, 27 Jun 2017 17:48:30: 21000000 INFO @ Tue, 27 Jun 2017 17:48:31: 21000000 INFO @ Tue, 27 Jun 2017 17:48:37: 23000000 INFO @ Tue, 27 Jun 2017 17:48:38: 22000000 INFO @ Tue, 27 Jun 2017 17:48:39: 22000000 INFO @ Tue, 27 Jun 2017 17:48:45: 24000000 INFO @ Tue, 27 Jun 2017 17:48:46: 23000000 INFO @ Tue, 27 Jun 2017 17:48:47: 23000000 INFO @ Tue, 27 Jun 2017 17:48:53: 25000000 INFO @ Tue, 27 Jun 2017 17:48:54: 24000000 INFO @ Tue, 27 Jun 2017 17:48:55: 24000000 INFO @ Tue, 27 Jun 2017 17:49:02: 26000000 INFO @ Tue, 27 Jun 2017 17:49:02: 25000000 INFO @ Tue, 27 Jun 2017 17:49:03: 25000000 INFO @ Tue, 27 Jun 2017 17:49:10: 26000000 INFO @ Tue, 27 Jun 2017 17:49:10: 27000000 INFO @ Tue, 27 Jun 2017 17:49:11: 26000000 INFO @ Tue, 27 Jun 2017 17:49:18: 27000000 INFO @ Tue, 27 Jun 2017 17:49:18: 28000000 INFO @ Tue, 27 Jun 2017 17:49:19: 27000000 INFO @ Tue, 27 Jun 2017 17:49:26: 28000000 INFO @ Tue, 27 Jun 2017 17:49:27: 29000000 INFO @ Tue, 27 Jun 2017 17:49:27: 28000000 INFO @ Tue, 27 Jun 2017 17:49:34: 29000000 INFO @ Tue, 27 Jun 2017 17:49:35: 29000000 INFO @ Tue, 27 Jun 2017 17:49:35: 30000000 INFO @ Tue, 27 Jun 2017 17:49:38: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:49:38: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:49:38: #1 total tags in treatment: 30389773 INFO @ Tue, 27 Jun 2017 17:49:38: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:49:38: #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 17:49:39: #1 tags after filtering in treatment: 30389773 INFO @ Tue, 27 Jun 2017 17:49:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:49:39: #1 finished! INFO @ Tue, 27 Jun 2017 17:49:39: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:49:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:49:41: #2 number of paired peaks: 857 WARNING @ Tue, 27 Jun 2017 17:49:41: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Tue, 27 Jun 2017 17:49:41: start model_add_line... INFO @ Tue, 27 Jun 2017 17:49:41: 30000000 INFO @ Tue, 27 Jun 2017 17:49:42: start X-correlation... INFO @ Tue, 27 Jun 2017 17:49:42: end of X-cor INFO @ Tue, 27 Jun 2017 17:49:42: #2 finished! INFO @ Tue, 27 Jun 2017 17:49:42: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 17:49:42: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 27 Jun 2017 17:49:42: #2.2 Generate R script for model : SRX1361349.05_model.r WARNING @ Tue, 27 Jun 2017 17:49:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:49:42: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 27 Jun 2017 17:49:42: #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 17:49:42: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:49:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:49:43: 30000000 INFO @ Tue, 27 Jun 2017 17:49:45: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:49:45: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:49:45: #1 total tags in treatment: 30389773 INFO @ Tue, 27 Jun 2017 17:49:45: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:49:45: #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 17:49:45: #1 tags after filtering in treatment: 30389773 INFO @ Tue, 27 Jun 2017 17:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:49:45: #1 finished! INFO @ Tue, 27 Jun 2017 17:49:45: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:49:46: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 17:49:46: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 17:49:46: #1 total tags in treatment: 30389773 INFO @ Tue, 27 Jun 2017 17:49:46: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:49:46: #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 17:49:47: #1 tags after filtering in treatment: 30389773 INFO @ Tue, 27 Jun 2017 17:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:49:47: #1 finished! INFO @ Tue, 27 Jun 2017 17:49:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:49:48: #2 number of paired peaks: 857 WARNING @ Tue, 27 Jun 2017 17:49:48: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Tue, 27 Jun 2017 17:49:48: start model_add_line... INFO @ Tue, 27 Jun 2017 17:49:48: start X-correlation... INFO @ Tue, 27 Jun 2017 17:49:48: end of X-cor INFO @ Tue, 27 Jun 2017 17:49:48: #2 finished! INFO @ Tue, 27 Jun 2017 17:49:48: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 17:49:48: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 27 Jun 2017 17:49:48: #2.2 Generate R script for model : SRX1361349.20_model.r WARNING @ Tue, 27 Jun 2017 17:49:48: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:49:48: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 27 Jun 2017 17:49:48: #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 17:49:48: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:49:49: #2 number of paired peaks: 857 WARNING @ Tue, 27 Jun 2017 17:49:49: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Tue, 27 Jun 2017 17:49:49: start model_add_line... INFO @ Tue, 27 Jun 2017 17:49:49: start X-correlation... INFO @ Tue, 27 Jun 2017 17:49:49: end of X-cor INFO @ Tue, 27 Jun 2017 17:49:49: #2 finished! INFO @ Tue, 27 Jun 2017 17:49:49: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 17:49:49: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 27 Jun 2017 17:49:49: #2.2 Generate R script for model : SRX1361349.10_model.r WARNING @ Tue, 27 Jun 2017 17:49:49: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:49:49: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 27 Jun 2017 17:49:49: #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 17:49:49: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:50:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:50:38: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:50:38: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:50:59: #4 Write output xls file... SRX1361349.05_peaks.xls INFO @ Tue, 27 Jun 2017 17:50:59: #4 Write peak in narrowPeak format file... SRX1361349.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:50:59: #4 Write summits bed file... SRX1361349.05_summits.bed INFO @ Tue, 27 Jun 2017 17:50:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:51:03: #4 Write output xls file... SRX1361349.10_peaks.xls INFO @ Tue, 27 Jun 2017 17:51:03: #4 Write peak in narrowPeak format file... SRX1361349.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:51:03: #4 Write summits bed file... SRX1361349.10_summits.bed INFO @ Tue, 27 Jun 2017 17:51:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:51:04: #4 Write output xls file... SRX1361349.20_peaks.xls INFO @ Tue, 27 Jun 2017 17:51:04: #4 Write peak in narrowPeak format file... SRX1361349.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:51:04: #4 Write summits bed file... SRX1361349.20_summits.bed INFO @ Tue, 27 Jun 2017 17:51:04: 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。