Job ID = 10195034 sra ファイルのダウンロード中... Completed: 268042K bytes transferred in 7 seconds (280020K bits/sec), in 1 file. Completed: 1508658K bytes transferred in 26 seconds (458026K 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 11098343 spots for /home/okishinya/chipatlas/results/rn6/SRX913503/SRR1870943.sra Written 11098343 spots total Written 47884553 spots for /home/okishinya/chipatlas/results/rn6/SRX913503/SRR1870944.sra Written 47884553 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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:30:15 58982896 reads; of these: 58982896 (100.00%) were unpaired; of these: 16579041 (28.11%) aligned 0 times 31173204 (52.85%) aligned exactly 1 time 11230651 (19.04%) aligned >1 times 71.89% overall alignment rate Time searching: 00:30:19 Overall time: 00:30:19 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 20 files... [bam_rmdupse_core] 3891145 / 42403855 = 0.0918 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 07:24:04: # Command line: callpeak -t SRX913503.bam -f BAM -g 2.15e9 -n SRX913503.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913503.05 # format = BAM # ChIP-seq file = ['SRX913503.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 07:24:04: # Command line: callpeak -t SRX913503.bam -f BAM -g 2.15e9 -n SRX913503.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913503.20 # format = BAM # ChIP-seq file = ['SRX913503.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 07:24:04: # Command line: callpeak -t SRX913503.bam -f BAM -g 2.15e9 -n SRX913503.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913503.10 # format = BAM # ChIP-seq file = ['SRX913503.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 07:24:04: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:24:04: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:24:04: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:24:04: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:24:04: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:24:04: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:24:11: 1000000 INFO @ Sat, 11 Nov 2017 07:24:11: 1000000 INFO @ Sat, 11 Nov 2017 07:24:11: 1000000 INFO @ Sat, 11 Nov 2017 07:24:18: 2000000 INFO @ Sat, 11 Nov 2017 07:24:19: 2000000 INFO @ Sat, 11 Nov 2017 07:24:19: 2000000 INFO @ Sat, 11 Nov 2017 07:24:25: 3000000 INFO @ Sat, 11 Nov 2017 07:24:26: 3000000 INFO @ Sat, 11 Nov 2017 07:24:26: 3000000 INFO @ Sat, 11 Nov 2017 07:24:32: 4000000 INFO @ Sat, 11 Nov 2017 07:24:33: 4000000 INFO @ Sat, 11 Nov 2017 07:24:33: 4000000 INFO @ Sat, 11 Nov 2017 07:24:39: 5000000 INFO @ Sat, 11 Nov 2017 07:24:40: 5000000 INFO @ Sat, 11 Nov 2017 07:24:40: 5000000 INFO @ Sat, 11 Nov 2017 07:24:46: 6000000 INFO @ Sat, 11 Nov 2017 07:24:47: 6000000 INFO @ Sat, 11 Nov 2017 07:24:47: 6000000 INFO @ Sat, 11 Nov 2017 07:24:53: 7000000 INFO @ Sat, 11 Nov 2017 07:24:54: 7000000 INFO @ Sat, 11 Nov 2017 07:24:55: 7000000 INFO @ Sat, 11 Nov 2017 07:25:00: 8000000 INFO @ Sat, 11 Nov 2017 07:25:02: 8000000 INFO @ Sat, 11 Nov 2017 07:25:02: 8000000 INFO @ Sat, 11 Nov 2017 07:25:08: 9000000 INFO @ Sat, 11 Nov 2017 07:25:08: 9000000 INFO @ Sat, 11 Nov 2017 07:25:09: 9000000 INFO @ Sat, 11 Nov 2017 07:25:15: 10000000 INFO @ Sat, 11 Nov 2017 07:25:16: 10000000 INFO @ Sat, 11 Nov 2017 07:25:17: 10000000 INFO @ Sat, 11 Nov 2017 07:25:22: 11000000 INFO @ Sat, 11 Nov 2017 07:25:23: 11000000 INFO @ Sat, 11 Nov 2017 07:25:24: 11000000 INFO @ Sat, 11 Nov 2017 07:25:29: 12000000 INFO @ Sat, 11 Nov 2017 07:25:31: 12000000 INFO @ Sat, 11 Nov 2017 07:25:31: 12000000 INFO @ Sat, 11 Nov 2017 07:25:36: 13000000 INFO @ Sat, 11 Nov 2017 07:25:38: 13000000 INFO @ Sat, 11 Nov 2017 07:25:38: 13000000 INFO @ Sat, 11 Nov 2017 07:25:42: 14000000 INFO @ Sat, 11 Nov 2017 07:25:45: 14000000 INFO @ Sat, 11 Nov 2017 07:25:46: 14000000 INFO @ Sat, 11 Nov 2017 07:25:49: 15000000 INFO @ Sat, 11 Nov 2017 07:25:53: 15000000 INFO @ Sat, 11 Nov 2017 07:25:53: 15000000 INFO @ Sat, 11 Nov 2017 07:25:56: 16000000 INFO @ Sat, 11 Nov 2017 07:26:00: 16000000 INFO @ Sat, 11 Nov 2017 07:26:00: 16000000 INFO @ Sat, 11 Nov 2017 07:26:02: 17000000 INFO @ Sat, 11 Nov 2017 07:26:07: 17000000 INFO @ Sat, 11 Nov 2017 07:26:07: 17000000 INFO @ Sat, 11 Nov 2017 07:26:09: 18000000 INFO @ Sat, 11 Nov 2017 07:26:14: 18000000 INFO @ Sat, 11 Nov 2017 07:26:14: 18000000 INFO @ Sat, 11 Nov 2017 07:26:16: 19000000 INFO @ Sat, 11 Nov 2017 07:26:21: 19000000 INFO @ Sat, 11 Nov 2017 07:26:21: 19000000 INFO @ Sat, 11 Nov 2017 07:26:22: 20000000 INFO @ Sat, 11 Nov 2017 07:26:28: 20000000 INFO @ Sat, 11 Nov 2017 07:26:29: 20000000 INFO @ Sat, 11 Nov 2017 07:26:29: 21000000 INFO @ Sat, 11 Nov 2017 07:26:36: 21000000 INFO @ Sat, 11 Nov 2017 07:26:36: 22000000 INFO @ Sat, 11 Nov 2017 07:26:36: 21000000 INFO @ Sat, 11 Nov 2017 07:26:43: 22000000 INFO @ Sat, 11 Nov 2017 07:26:43: 23000000 INFO @ Sat, 11 Nov 2017 07:26:44: 22000000 INFO @ Sat, 11 Nov 2017 07:26:49: 23000000 INFO @ Sat, 11 Nov 2017 07:26:50: 24000000 INFO @ Sat, 11 Nov 2017 07:26:51: 23000000 INFO @ Sat, 11 Nov 2017 07:26:56: 24000000 INFO @ Sat, 11 Nov 2017 07:26:58: 25000000 INFO @ Sat, 11 Nov 2017 07:26:58: 24000000 INFO @ Sat, 11 Nov 2017 07:27:03: 25000000 INFO @ Sat, 11 Nov 2017 07:27:05: 26000000 INFO @ Sat, 11 Nov 2017 07:27:05: 25000000 INFO @ Sat, 11 Nov 2017 07:27:09: 26000000 INFO @ Sat, 11 Nov 2017 07:27:12: 27000000 INFO @ Sat, 11 Nov 2017 07:27:13: 26000000 INFO @ Sat, 11 Nov 2017 07:27:16: 27000000 INFO @ Sat, 11 Nov 2017 07:27:19: 28000000 INFO @ Sat, 11 Nov 2017 07:27:20: 27000000 INFO @ Sat, 11 Nov 2017 07:27:23: 28000000 INFO @ Sat, 11 Nov 2017 07:27:27: 29000000 INFO @ Sat, 11 Nov 2017 07:27:27: 28000000 INFO @ Sat, 11 Nov 2017 07:27:30: 29000000 INFO @ Sat, 11 Nov 2017 07:27:34: 30000000 INFO @ Sat, 11 Nov 2017 07:27:35: 29000000 INFO @ Sat, 11 Nov 2017 07:27:37: 30000000 INFO @ Sat, 11 Nov 2017 07:27:41: 31000000 INFO @ Sat, 11 Nov 2017 07:27:42: 30000000 INFO @ Sat, 11 Nov 2017 07:27:44: 31000000 INFO @ Sat, 11 Nov 2017 07:27:48: 32000000 INFO @ Sat, 11 Nov 2017 07:27:50: 31000000 INFO @ Sat, 11 Nov 2017 07:27:51: 32000000 INFO @ Sat, 11 Nov 2017 07:27:55: 33000000 INFO @ Sat, 11 Nov 2017 07:27:57: 32000000 INFO @ Sat, 11 Nov 2017 07:27:58: 33000000 INFO @ Sat, 11 Nov 2017 07:28:02: 34000000 INFO @ Sat, 11 Nov 2017 07:28:05: 33000000 INFO @ Sat, 11 Nov 2017 07:28:05: 34000000 INFO @ Sat, 11 Nov 2017 07:28:10: 35000000 INFO @ Sat, 11 Nov 2017 07:28:11: 35000000 INFO @ Sat, 11 Nov 2017 07:28:12: 34000000 INFO @ Sat, 11 Nov 2017 07:28:17: 36000000 INFO @ Sat, 11 Nov 2017 07:28:18: 36000000 INFO @ Sat, 11 Nov 2017 07:28:19: 35000000 INFO @ Sat, 11 Nov 2017 07:28:24: 37000000 INFO @ Sat, 11 Nov 2017 07:28:25: 37000000 INFO @ Sat, 11 Nov 2017 07:28:27: 36000000 INFO @ Sat, 11 Nov 2017 07:28:32: 38000000 INFO @ Sat, 11 Nov 2017 07:28:32: 38000000 INFO @ Sat, 11 Nov 2017 07:28:35: 37000000 INFO @ Sat, 11 Nov 2017 07:28:36: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:28:36: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:28:36: #1 total tags in treatment: 38512710 INFO @ Sat, 11 Nov 2017 07:28:36: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:28:36: #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 07:28:36: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:28:36: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:28:36: #1 total tags in treatment: 38512710 INFO @ Sat, 11 Nov 2017 07:28:36: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:28:36: #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 07:28:37: #1 tags after filtering in treatment: 38512625 INFO @ Sat, 11 Nov 2017 07:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:28:37: #1 finished! INFO @ Sat, 11 Nov 2017 07:28:37: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:28:37: #1 tags after filtering in treatment: 38512625 INFO @ Sat, 11 Nov 2017 07:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:28:37: #1 finished! INFO @ Sat, 11 Nov 2017 07:28:37: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:28:40: #2 number of paired peaks: 6902 INFO @ Sat, 11 Nov 2017 07:28:40: start model_add_line... INFO @ Sat, 11 Nov 2017 07:28:40: #2 number of paired peaks: 6902 INFO @ Sat, 11 Nov 2017 07:28:40: start model_add_line... INFO @ Sat, 11 Nov 2017 07:28:41: start X-correlation... INFO @ Sat, 11 Nov 2017 07:28:41: start X-correlation... INFO @ Sat, 11 Nov 2017 07:28:41: end of X-cor INFO @ Sat, 11 Nov 2017 07:28:41: end of X-cor INFO @ Sat, 11 Nov 2017 07:28:41: #2 finished! INFO @ Sat, 11 Nov 2017 07:28:41: #2 finished! INFO @ Sat, 11 Nov 2017 07:28:41: #2 predicted fragment length is 64 bps INFO @ Sat, 11 Nov 2017 07:28:41: #2 predicted fragment length is 64 bps INFO @ Sat, 11 Nov 2017 07:28:41: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 11 Nov 2017 07:28:41: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 11 Nov 2017 07:28:41: #2.2 Generate R script for model : SRX913503.05_model.r INFO @ Sat, 11 Nov 2017 07:28:41: #2.2 Generate R script for model : SRX913503.20_model.r WARNING @ Sat, 11 Nov 2017 07:28:41: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:28:41: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sat, 11 Nov 2017 07:28:41: #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 07:28:41: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:28:41: 38000000 WARNING @ Sat, 11 Nov 2017 07:28:41: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:28:41: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sat, 11 Nov 2017 07:28:41: #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 07:28:41: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:28:45: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:28:45: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:28:45: #1 total tags in treatment: 38512710 INFO @ Sat, 11 Nov 2017 07:28:45: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:28:45: #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 07:28:46: #1 tags after filtering in treatment: 38512625 INFO @ Sat, 11 Nov 2017 07:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:28:46: #1 finished! INFO @ Sat, 11 Nov 2017 07:28:46: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:28:50: #2 number of paired peaks: 6902 INFO @ Sat, 11 Nov 2017 07:28:50: start model_add_line... INFO @ Sat, 11 Nov 2017 07:28:51: start X-correlation... INFO @ Sat, 11 Nov 2017 07:28:51: end of X-cor INFO @ Sat, 11 Nov 2017 07:28:51: #2 finished! INFO @ Sat, 11 Nov 2017 07:28:51: #2 predicted fragment length is 64 bps INFO @ Sat, 11 Nov 2017 07:28:51: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 11 Nov 2017 07:28:51: #2.2 Generate R script for model : SRX913503.10_model.r WARNING @ Sat, 11 Nov 2017 07:28:51: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:28:51: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sat, 11 Nov 2017 07:28:51: #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 07:28:51: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:30:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:30:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:30:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:31:03: #4 Write output xls file... SRX913503.05_peaks.xls INFO @ Sat, 11 Nov 2017 07:31:03: #4 Write peak in narrowPeak format file... SRX913503.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:31:03: #4 Write summits bed file... SRX913503.05_summits.bed INFO @ Sat, 11 Nov 2017 07:31:03: Done! pass1 - making usageList (78 chroms): 1 millis pass2 - checking and writing primary data (1391 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:31:16: #4 Write output xls file... SRX913503.20_peaks.xls INFO @ Sat, 11 Nov 2017 07:31:16: #4 Write peak in narrowPeak format file... SRX913503.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:31:16: #4 Write summits bed file... SRX913503.20_summits.bed INFO @ Sat, 11 Nov 2017 07:31:16: Done! pass1 - making usageList (36 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:31:23: #4 Write output xls file... SRX913503.10_peaks.xls INFO @ Sat, 11 Nov 2017 07:31:23: #4 Write peak in narrowPeak format file... SRX913503.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:31:23: #4 Write summits bed file... SRX913503.10_summits.bed INFO @ Sat, 11 Nov 2017 07:31:23: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。