Job ID = 10194749 sra ファイルのダウンロード中... Completed: 526599K bytes transferred in 6 seconds (681461K 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... Written 38331192 spots for /home/okishinya/chipatlas/results/rn6/SRX1091087/SRR2095964.sra Written 38331192 spots total 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:59 38331192 reads; of these: 38331192 (100.00%) were unpaired; of these: 3304335 (8.62%) aligned 0 times 25481177 (66.48%) aligned exactly 1 time 9545680 (24.90%) aligned >1 times 91.38% overall alignment rate Time searching: 00:28:02 Overall time: 00:28:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 2168441 / 35026857 = 0.0619 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 @ Sat, 11 Nov 2017 00:49:24: # Command line: callpeak -t SRX1091087.bam -f BAM -g 2.15e9 -n SRX1091087.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1091087.05 # format = BAM # ChIP-seq file = ['SRX1091087.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 00:49:24: # Command line: callpeak -t SRX1091087.bam -f BAM -g 2.15e9 -n SRX1091087.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1091087.20 # format = BAM # ChIP-seq file = ['SRX1091087.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 00:49:24: # Command line: callpeak -t SRX1091087.bam -f BAM -g 2.15e9 -n SRX1091087.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1091087.10 # format = BAM # ChIP-seq file = ['SRX1091087.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 00:49:24: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:49:24: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:49:24: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:49:24: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:49:24: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:49:24: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:49:31: 1000000 INFO @ Sat, 11 Nov 2017 00:49:31: 1000000 INFO @ Sat, 11 Nov 2017 00:49:31: 1000000 INFO @ Sat, 11 Nov 2017 00:49:39: 2000000 INFO @ Sat, 11 Nov 2017 00:49:39: 2000000 INFO @ Sat, 11 Nov 2017 00:49:39: 2000000 INFO @ Sat, 11 Nov 2017 00:49:47: 3000000 INFO @ Sat, 11 Nov 2017 00:49:47: 3000000 INFO @ Sat, 11 Nov 2017 00:49:47: 3000000 INFO @ Sat, 11 Nov 2017 00:49:54: 4000000 INFO @ Sat, 11 Nov 2017 00:49:54: 4000000 INFO @ Sat, 11 Nov 2017 00:49:55: 4000000 INFO @ Sat, 11 Nov 2017 00:50:02: 5000000 INFO @ Sat, 11 Nov 2017 00:50:02: 5000000 INFO @ Sat, 11 Nov 2017 00:50:03: 5000000 INFO @ Sat, 11 Nov 2017 00:50:10: 6000000 INFO @ Sat, 11 Nov 2017 00:50:10: 6000000 INFO @ Sat, 11 Nov 2017 00:50:11: 6000000 INFO @ Sat, 11 Nov 2017 00:50:17: 7000000 INFO @ Sat, 11 Nov 2017 00:50:17: 7000000 INFO @ Sat, 11 Nov 2017 00:50:19: 7000000 INFO @ Sat, 11 Nov 2017 00:50:25: 8000000 INFO @ Sat, 11 Nov 2017 00:50:25: 8000000 INFO @ Sat, 11 Nov 2017 00:50:28: 8000000 INFO @ Sat, 11 Nov 2017 00:50:33: 9000000 INFO @ Sat, 11 Nov 2017 00:50:33: 9000000 INFO @ Sat, 11 Nov 2017 00:50:36: 9000000 INFO @ Sat, 11 Nov 2017 00:50:41: 10000000 INFO @ Sat, 11 Nov 2017 00:50:41: 10000000 INFO @ Sat, 11 Nov 2017 00:50:44: 10000000 INFO @ Sat, 11 Nov 2017 00:50:48: 11000000 INFO @ Sat, 11 Nov 2017 00:50:48: 11000000 INFO @ Sat, 11 Nov 2017 00:50:52: 11000000 INFO @ Sat, 11 Nov 2017 00:50:56: 12000000 INFO @ Sat, 11 Nov 2017 00:50:56: 12000000 INFO @ Sat, 11 Nov 2017 00:51:00: 12000000 INFO @ Sat, 11 Nov 2017 00:51:04: 13000000 INFO @ Sat, 11 Nov 2017 00:51:04: 13000000 INFO @ Sat, 11 Nov 2017 00:51:08: 13000000 INFO @ Sat, 11 Nov 2017 00:51:12: 14000000 INFO @ Sat, 11 Nov 2017 00:51:12: 14000000 INFO @ Sat, 11 Nov 2017 00:51:17: 14000000 INFO @ Sat, 11 Nov 2017 00:51:19: 15000000 INFO @ Sat, 11 Nov 2017 00:51:20: 15000000 INFO @ Sat, 11 Nov 2017 00:51:24: 15000000 INFO @ Sat, 11 Nov 2017 00:51:26: 16000000 INFO @ Sat, 11 Nov 2017 00:51:27: 16000000 INFO @ Sat, 11 Nov 2017 00:51:32: 16000000 INFO @ Sat, 11 Nov 2017 00:51:33: 17000000 INFO @ Sat, 11 Nov 2017 00:51:35: 17000000 INFO @ Sat, 11 Nov 2017 00:51:40: 17000000 INFO @ Sat, 11 Nov 2017 00:51:40: 18000000 INFO @ Sat, 11 Nov 2017 00:51:43: 18000000 INFO @ Sat, 11 Nov 2017 00:51:47: 19000000 INFO @ Sat, 11 Nov 2017 00:51:48: 18000000 INFO @ Sat, 11 Nov 2017 00:51:51: 19000000 INFO @ Sat, 11 Nov 2017 00:51:54: 20000000 INFO @ Sat, 11 Nov 2017 00:51:55: 19000000 INFO @ Sat, 11 Nov 2017 00:51:58: 20000000 INFO @ Sat, 11 Nov 2017 00:52:02: 21000000 INFO @ Sat, 11 Nov 2017 00:52:03: 20000000 INFO @ Sat, 11 Nov 2017 00:52:06: 21000000 INFO @ Sat, 11 Nov 2017 00:52:09: 22000000 INFO @ Sat, 11 Nov 2017 00:52:11: 21000000 INFO @ Sat, 11 Nov 2017 00:52:14: 22000000 INFO @ Sat, 11 Nov 2017 00:52:16: 23000000 INFO @ Sat, 11 Nov 2017 00:52:19: 22000000 INFO @ Sat, 11 Nov 2017 00:52:22: 23000000 INFO @ Sat, 11 Nov 2017 00:52:23: 24000000 INFO @ Sat, 11 Nov 2017 00:52:27: 23000000 INFO @ Sat, 11 Nov 2017 00:52:29: 24000000 INFO @ Sat, 11 Nov 2017 00:52:30: 25000000 INFO @ Sat, 11 Nov 2017 00:52:34: 24000000 INFO @ Sat, 11 Nov 2017 00:52:37: 25000000 INFO @ Sat, 11 Nov 2017 00:52:37: 26000000 INFO @ Sat, 11 Nov 2017 00:52:42: 25000000 INFO @ Sat, 11 Nov 2017 00:52:44: 27000000 INFO @ Sat, 11 Nov 2017 00:52:45: 26000000 INFO @ Sat, 11 Nov 2017 00:52:50: 26000000 INFO @ Sat, 11 Nov 2017 00:52:51: 28000000 INFO @ Sat, 11 Nov 2017 00:52:53: 27000000 INFO @ Sat, 11 Nov 2017 00:52:58: 27000000 INFO @ Sat, 11 Nov 2017 00:52:58: 29000000 INFO @ Sat, 11 Nov 2017 00:53:00: 28000000 INFO @ Sat, 11 Nov 2017 00:53:05: 30000000 INFO @ Sat, 11 Nov 2017 00:53:05: 28000000 INFO @ Sat, 11 Nov 2017 00:53:08: 29000000 INFO @ Sat, 11 Nov 2017 00:53:12: 31000000 INFO @ Sat, 11 Nov 2017 00:53:13: 29000000 INFO @ Sat, 11 Nov 2017 00:53:16: 30000000 INFO @ Sat, 11 Nov 2017 00:53:19: 32000000 INFO @ Sat, 11 Nov 2017 00:53:21: 30000000 INFO @ Sat, 11 Nov 2017 00:53:23: 31000000 INFO @ Sat, 11 Nov 2017 00:53:26: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:53:26: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:53:26: #1 total tags in treatment: 32858416 INFO @ Sat, 11 Nov 2017 00:53:26: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:53:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:53:26: #1 tags after filtering in treatment: 32858333 INFO @ Sat, 11 Nov 2017 00:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:53:26: #1 finished! INFO @ Sat, 11 Nov 2017 00:53:26: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:53:28: 31000000 INFO @ Sat, 11 Nov 2017 00:53:30: #2 number of paired peaks: 6439 INFO @ Sat, 11 Nov 2017 00:53:30: start model_add_line... INFO @ Sat, 11 Nov 2017 00:53:30: start X-correlation... INFO @ Sat, 11 Nov 2017 00:53:30: end of X-cor INFO @ Sat, 11 Nov 2017 00:53:30: #2 finished! INFO @ Sat, 11 Nov 2017 00:53:30: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Nov 2017 00:53:30: #2 alternative fragment length(s) may be 61,108 bps INFO @ Sat, 11 Nov 2017 00:53:30: #2.2 Generate R script for model : SRX1091087.20_model.r WARNING @ Sat, 11 Nov 2017 00:53:30: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:53:30: #2 You may need to consider one of the other alternative d(s): 61,108 WARNING @ Sat, 11 Nov 2017 00:53:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:53:30: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:53:31: 32000000 INFO @ Sat, 11 Nov 2017 00:53:36: 32000000 INFO @ Sat, 11 Nov 2017 00:53:38: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:53:38: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:53:38: #1 total tags in treatment: 32858416 INFO @ Sat, 11 Nov 2017 00:53:38: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:53:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:53:39: #1 tags after filtering in treatment: 32858333 INFO @ Sat, 11 Nov 2017 00:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:53:39: #1 finished! INFO @ Sat, 11 Nov 2017 00:53:39: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:53:42: #2 number of paired peaks: 6439 INFO @ Sat, 11 Nov 2017 00:53:42: start model_add_line... INFO @ Sat, 11 Nov 2017 00:53:43: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:53:43: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:53:43: #1 total tags in treatment: 32858416 INFO @ Sat, 11 Nov 2017 00:53:43: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:53:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:53:43: start X-correlation... INFO @ Sat, 11 Nov 2017 00:53:43: end of X-cor INFO @ Sat, 11 Nov 2017 00:53:43: #2 finished! INFO @ Sat, 11 Nov 2017 00:53:43: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Nov 2017 00:53:43: #2 alternative fragment length(s) may be 61,108 bps INFO @ Sat, 11 Nov 2017 00:53:43: #2.2 Generate R script for model : SRX1091087.05_model.r WARNING @ Sat, 11 Nov 2017 00:53:43: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:53:43: #2 You may need to consider one of the other alternative d(s): 61,108 WARNING @ Sat, 11 Nov 2017 00:53:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:53:43: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:53:44: #1 tags after filtering in treatment: 32858333 INFO @ Sat, 11 Nov 2017 00:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:53:44: #1 finished! INFO @ Sat, 11 Nov 2017 00:53:44: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:53:47: #2 number of paired peaks: 6439 INFO @ Sat, 11 Nov 2017 00:53:47: start model_add_line... INFO @ Sat, 11 Nov 2017 00:53:47: start X-correlation... INFO @ Sat, 11 Nov 2017 00:53:47: end of X-cor INFO @ Sat, 11 Nov 2017 00:53:47: #2 finished! INFO @ Sat, 11 Nov 2017 00:53:47: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Nov 2017 00:53:47: #2 alternative fragment length(s) may be 61,108 bps INFO @ Sat, 11 Nov 2017 00:53:47: #2.2 Generate R script for model : SRX1091087.10_model.r WARNING @ Sat, 11 Nov 2017 00:53:47: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:53:47: #2 You may need to consider one of the other alternative d(s): 61,108 WARNING @ Sat, 11 Nov 2017 00:53:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:53:47: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:54:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:55:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:55:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:55:36: #4 Write output xls file... SRX1091087.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:55:36: #4 Write peak in narrowPeak format file... SRX1091087.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:55:36: #4 Write summits bed file... SRX1091087.20_summits.bed INFO @ Sat, 11 Nov 2017 00:55:36: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (961 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:55:54: #4 Write output xls file... SRX1091087.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:55:54: #4 Write peak in narrowPeak format file... SRX1091087.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:55:54: #4 Write summits bed file... SRX1091087.05_summits.bed INFO @ Sat, 11 Nov 2017 00:55:54: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (3275 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:55:54: #4 Write output xls file... SRX1091087.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:55:54: #4 Write peak in narrowPeak format file... SRX1091087.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:55:54: #4 Write summits bed file... SRX1091087.10_summits.bed INFO @ Sat, 11 Nov 2017 00:55:54: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (2059 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。