Job ID = 10487606 sra ファイルのダウンロード中... Completed: 1522409K bytes transferred in 32 seconds (385601K 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 57477721 spots for /home/okishinya/chipatlas/results/rn6/SRX3087686/SRR5927322.sra Written 57477721 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:13:16 57477721 reads; of these: 57477721 (100.00%) were unpaired; of these: 2259012 (3.93%) aligned 0 times 40041164 (69.66%) aligned exactly 1 time 15177545 (26.41%) aligned >1 times 96.07% overall alignment rate Time searching: 01:13:20 Overall time: 01:13:20 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 24 files... [bam_rmdupse_core] 3063293 / 55218709 = 0.0555 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 @ Sun, 18 Mar 2018 11:24:55: # Command line: callpeak -t SRX3087686.bam -f BAM -g 2.15e9 -n SRX3087686.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087686.20 # format = BAM # ChIP-seq file = ['SRX3087686.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 @ Sun, 18 Mar 2018 11:24:55: # Command line: callpeak -t SRX3087686.bam -f BAM -g 2.15e9 -n SRX3087686.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087686.05 # format = BAM # ChIP-seq file = ['SRX3087686.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 @ Sun, 18 Mar 2018 11:24:55: # Command line: callpeak -t SRX3087686.bam -f BAM -g 2.15e9 -n SRX3087686.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087686.10 # format = BAM # ChIP-seq file = ['SRX3087686.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 @ Sun, 18 Mar 2018 11:24:55: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:24:55: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:24:55: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:24:55: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:24:55: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:24:55: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:25:06: 1000000 INFO @ Sun, 18 Mar 2018 11:25:06: 1000000 INFO @ Sun, 18 Mar 2018 11:25:06: 1000000 INFO @ Sun, 18 Mar 2018 11:25:16: 2000000 INFO @ Sun, 18 Mar 2018 11:25:16: 2000000 INFO @ Sun, 18 Mar 2018 11:25:16: 2000000 INFO @ Sun, 18 Mar 2018 11:25:26: 3000000 INFO @ Sun, 18 Mar 2018 11:25:26: 3000000 INFO @ Sun, 18 Mar 2018 11:25:26: 3000000 INFO @ Sun, 18 Mar 2018 11:25:36: 4000000 INFO @ Sun, 18 Mar 2018 11:25:36: 4000000 INFO @ Sun, 18 Mar 2018 11:25:36: 4000000 INFO @ Sun, 18 Mar 2018 11:25:47: 5000000 INFO @ Sun, 18 Mar 2018 11:25:47: 5000000 INFO @ Sun, 18 Mar 2018 11:25:47: 5000000 INFO @ Sun, 18 Mar 2018 11:25:57: 6000000 INFO @ Sun, 18 Mar 2018 11:25:57: 6000000 INFO @ Sun, 18 Mar 2018 11:25:57: 6000000 INFO @ Sun, 18 Mar 2018 11:26:07: 7000000 INFO @ Sun, 18 Mar 2018 11:26:07: 7000000 INFO @ Sun, 18 Mar 2018 11:26:07: 7000000 INFO @ Sun, 18 Mar 2018 11:26:17: 8000000 INFO @ Sun, 18 Mar 2018 11:26:17: 8000000 INFO @ Sun, 18 Mar 2018 11:26:17: 8000000 INFO @ Sun, 18 Mar 2018 11:26:27: 9000000 INFO @ Sun, 18 Mar 2018 11:26:27: 9000000 INFO @ Sun, 18 Mar 2018 11:26:27: 9000000 INFO @ Sun, 18 Mar 2018 11:26:37: 10000000 INFO @ Sun, 18 Mar 2018 11:26:37: 10000000 INFO @ Sun, 18 Mar 2018 11:26:37: 10000000 INFO @ Sun, 18 Mar 2018 11:26:47: 11000000 INFO @ Sun, 18 Mar 2018 11:26:47: 11000000 INFO @ Sun, 18 Mar 2018 11:26:47: 11000000 INFO @ Sun, 18 Mar 2018 11:26:57: 12000000 INFO @ Sun, 18 Mar 2018 11:26:57: 12000000 INFO @ Sun, 18 Mar 2018 11:26:57: 12000000 INFO @ Sun, 18 Mar 2018 11:27:07: 13000000 INFO @ Sun, 18 Mar 2018 11:27:07: 13000000 INFO @ Sun, 18 Mar 2018 11:27:07: 13000000 INFO @ Sun, 18 Mar 2018 11:27:17: 14000000 INFO @ Sun, 18 Mar 2018 11:27:17: 14000000 INFO @ Sun, 18 Mar 2018 11:27:17: 14000000 INFO @ Sun, 18 Mar 2018 11:27:28: 15000000 INFO @ Sun, 18 Mar 2018 11:27:28: 15000000 INFO @ Sun, 18 Mar 2018 11:27:28: 15000000 INFO @ Sun, 18 Mar 2018 11:27:38: 16000000 INFO @ Sun, 18 Mar 2018 11:27:38: 16000000 INFO @ Sun, 18 Mar 2018 11:27:38: 16000000 INFO @ Sun, 18 Mar 2018 11:27:48: 17000000 INFO @ Sun, 18 Mar 2018 11:27:48: 17000000 INFO @ Sun, 18 Mar 2018 11:27:48: 17000000 INFO @ Sun, 18 Mar 2018 11:27:58: 18000000 INFO @ Sun, 18 Mar 2018 11:27:58: 18000000 INFO @ Sun, 18 Mar 2018 11:27:58: 18000000 INFO @ Sun, 18 Mar 2018 11:28:08: 19000000 INFO @ Sun, 18 Mar 2018 11:28:08: 19000000 INFO @ Sun, 18 Mar 2018 11:28:08: 19000000 INFO @ Sun, 18 Mar 2018 11:28:18: 20000000 INFO @ Sun, 18 Mar 2018 11:28:18: 20000000 INFO @ Sun, 18 Mar 2018 11:28:18: 20000000 INFO @ Sun, 18 Mar 2018 11:28:28: 21000000 INFO @ Sun, 18 Mar 2018 11:28:28: 21000000 INFO @ Sun, 18 Mar 2018 11:28:28: 21000000 INFO @ Sun, 18 Mar 2018 11:28:38: 22000000 INFO @ Sun, 18 Mar 2018 11:28:38: 22000000 INFO @ Sun, 18 Mar 2018 11:28:38: 22000000 INFO @ Sun, 18 Mar 2018 11:28:48: 23000000 INFO @ Sun, 18 Mar 2018 11:28:48: 23000000 INFO @ Sun, 18 Mar 2018 11:28:48: 23000000 INFO @ Sun, 18 Mar 2018 11:28:58: 24000000 INFO @ Sun, 18 Mar 2018 11:28:58: 24000000 INFO @ Sun, 18 Mar 2018 11:28:58: 24000000 INFO @ Sun, 18 Mar 2018 11:29:08: 25000000 INFO @ Sun, 18 Mar 2018 11:29:08: 25000000 INFO @ Sun, 18 Mar 2018 11:29:08: 25000000 INFO @ Sun, 18 Mar 2018 11:29:19: 26000000 INFO @ Sun, 18 Mar 2018 11:29:19: 26000000 INFO @ Sun, 18 Mar 2018 11:29:19: 26000000 INFO @ Sun, 18 Mar 2018 11:29:29: 27000000 INFO @ Sun, 18 Mar 2018 11:29:29: 27000000 INFO @ Sun, 18 Mar 2018 11:29:29: 27000000 INFO @ Sun, 18 Mar 2018 11:29:40: 28000000 INFO @ Sun, 18 Mar 2018 11:29:40: 28000000 INFO @ Sun, 18 Mar 2018 11:29:40: 28000000 INFO @ Sun, 18 Mar 2018 11:29:51: 29000000 INFO @ Sun, 18 Mar 2018 11:29:51: 29000000 INFO @ Sun, 18 Mar 2018 11:29:51: 29000000 INFO @ Sun, 18 Mar 2018 11:30:02: 30000000 INFO @ Sun, 18 Mar 2018 11:30:02: 30000000 INFO @ Sun, 18 Mar 2018 11:30:02: 30000000 INFO @ Sun, 18 Mar 2018 11:30:13: 31000000 INFO @ Sun, 18 Mar 2018 11:30:13: 31000000 INFO @ Sun, 18 Mar 2018 11:30:13: 31000000 INFO @ Sun, 18 Mar 2018 11:30:23: 32000000 INFO @ Sun, 18 Mar 2018 11:30:23: 32000000 INFO @ Sun, 18 Mar 2018 11:30:23: 32000000 INFO @ Sun, 18 Mar 2018 11:30:34: 33000000 INFO @ Sun, 18 Mar 2018 11:30:34: 33000000 INFO @ Sun, 18 Mar 2018 11:30:34: 33000000 INFO @ Sun, 18 Mar 2018 11:30:45: 34000000 INFO @ Sun, 18 Mar 2018 11:30:45: 34000000 INFO @ Sun, 18 Mar 2018 11:30:45: 34000000 INFO @ Sun, 18 Mar 2018 11:30:56: 35000000 INFO @ Sun, 18 Mar 2018 11:30:56: 35000000 INFO @ Sun, 18 Mar 2018 11:30:56: 35000000 INFO @ Sun, 18 Mar 2018 11:31:07: 36000000 INFO @ Sun, 18 Mar 2018 11:31:07: 36000000 INFO @ Sun, 18 Mar 2018 11:31:07: 36000000 INFO @ Sun, 18 Mar 2018 11:31:17: 37000000 INFO @ Sun, 18 Mar 2018 11:31:17: 37000000 INFO @ Sun, 18 Mar 2018 11:31:17: 37000000 INFO @ Sun, 18 Mar 2018 11:31:28: 38000000 INFO @ Sun, 18 Mar 2018 11:31:28: 38000000 INFO @ Sun, 18 Mar 2018 11:31:28: 38000000 INFO @ Sun, 18 Mar 2018 11:31:39: 39000000 INFO @ Sun, 18 Mar 2018 11:31:39: 39000000 INFO @ Sun, 18 Mar 2018 11:31:39: 39000000 INFO @ Sun, 18 Mar 2018 11:31:50: 40000000 INFO @ Sun, 18 Mar 2018 11:31:50: 40000000 INFO @ Sun, 18 Mar 2018 11:31:50: 40000000 INFO @ Sun, 18 Mar 2018 11:32:00: 41000000 INFO @ Sun, 18 Mar 2018 11:32:00: 41000000 INFO @ Sun, 18 Mar 2018 11:32:00: 41000000 INFO @ Sun, 18 Mar 2018 11:32:11: 42000000 INFO @ Sun, 18 Mar 2018 11:32:11: 42000000 INFO @ Sun, 18 Mar 2018 11:32:11: 42000000 INFO @ Sun, 18 Mar 2018 11:32:22: 43000000 INFO @ Sun, 18 Mar 2018 11:32:22: 43000000 INFO @ Sun, 18 Mar 2018 11:32:22: 43000000 INFO @ Sun, 18 Mar 2018 11:32:32: 44000000 INFO @ Sun, 18 Mar 2018 11:32:32: 44000000 INFO @ Sun, 18 Mar 2018 11:32:32: 44000000 INFO @ Sun, 18 Mar 2018 11:32:42: 45000000 INFO @ Sun, 18 Mar 2018 11:32:42: 45000000 INFO @ Sun, 18 Mar 2018 11:32:42: 45000000 INFO @ Sun, 18 Mar 2018 11:32:52: 46000000 INFO @ Sun, 18 Mar 2018 11:32:52: 46000000 INFO @ Sun, 18 Mar 2018 11:32:52: 46000000 INFO @ Sun, 18 Mar 2018 11:33:03: 47000000 INFO @ Sun, 18 Mar 2018 11:33:03: 47000000 INFO @ Sun, 18 Mar 2018 11:33:03: 47000000 INFO @ Sun, 18 Mar 2018 11:33:13: 48000000 INFO @ Sun, 18 Mar 2018 11:33:13: 48000000 INFO @ Sun, 18 Mar 2018 11:33:13: 48000000 INFO @ Sun, 18 Mar 2018 11:33:23: 49000000 INFO @ Sun, 18 Mar 2018 11:33:23: 49000000 INFO @ Sun, 18 Mar 2018 11:33:23: 49000000 INFO @ Sun, 18 Mar 2018 11:33:34: 50000000 INFO @ Sun, 18 Mar 2018 11:33:34: 50000000 INFO @ Sun, 18 Mar 2018 11:33:34: 50000000 INFO @ Sun, 18 Mar 2018 11:33:44: 51000000 INFO @ Sun, 18 Mar 2018 11:33:44: 51000000 INFO @ Sun, 18 Mar 2018 11:33:44: 51000000 INFO @ Sun, 18 Mar 2018 11:33:54: 52000000 INFO @ Sun, 18 Mar 2018 11:33:54: 52000000 INFO @ Sun, 18 Mar 2018 11:33:54: 52000000 INFO @ Sun, 18 Mar 2018 11:33:56: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:33:56: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:33:56: #1 total tags in treatment: 52155416 INFO @ Sun, 18 Mar 2018 11:33:56: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:33:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:33:56: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:33:56: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:33:56: #1 total tags in treatment: 52155416 INFO @ Sun, 18 Mar 2018 11:33:56: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:33:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:33:56: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:33:56: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:33:56: #1 total tags in treatment: 52155416 INFO @ Sun, 18 Mar 2018 11:33:56: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:33:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:33:57: #1 tags after filtering in treatment: 52155364 INFO @ Sun, 18 Mar 2018 11:33:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:33:57: #1 finished! INFO @ Sun, 18 Mar 2018 11:33:57: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:33:57: #1 tags after filtering in treatment: 52155364 INFO @ Sun, 18 Mar 2018 11:33:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:33:57: #1 finished! INFO @ Sun, 18 Mar 2018 11:33:57: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:33:57: #1 tags after filtering in treatment: 52155364 INFO @ Sun, 18 Mar 2018 11:33:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:33:57: #1 finished! INFO @ Sun, 18 Mar 2018 11:33:57: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:34:02: #2 number of paired peaks: 5718 INFO @ Sun, 18 Mar 2018 11:34:02: start model_add_line... INFO @ Sun, 18 Mar 2018 11:34:02: #2 number of paired peaks: 5718 INFO @ Sun, 18 Mar 2018 11:34:02: start model_add_line... INFO @ Sun, 18 Mar 2018 11:34:02: #2 number of paired peaks: 5718 INFO @ Sun, 18 Mar 2018 11:34:02: start model_add_line... INFO @ Sun, 18 Mar 2018 11:34:02: start X-correlation... INFO @ Sun, 18 Mar 2018 11:34:02: end of X-cor INFO @ Sun, 18 Mar 2018 11:34:02: #2 finished! INFO @ Sun, 18 Mar 2018 11:34:02: #2 predicted fragment length is 60 bps INFO @ Sun, 18 Mar 2018 11:34:02: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 18 Mar 2018 11:34:02: #2.2 Generate R script for model : SRX3087686.20_model.r WARNING @ Sun, 18 Mar 2018 11:34:02: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:34:02: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 18 Mar 2018 11:34:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:34:02: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:34:02: start X-correlation... INFO @ Sun, 18 Mar 2018 11:34:02: end of X-cor INFO @ Sun, 18 Mar 2018 11:34:02: #2 finished! INFO @ Sun, 18 Mar 2018 11:34:02: #2 predicted fragment length is 60 bps INFO @ Sun, 18 Mar 2018 11:34:02: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 18 Mar 2018 11:34:02: #2.2 Generate R script for model : SRX3087686.10_model.r WARNING @ Sun, 18 Mar 2018 11:34:02: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:34:02: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 18 Mar 2018 11:34:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:34:02: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:34:03: start X-correlation... INFO @ Sun, 18 Mar 2018 11:34:03: end of X-cor INFO @ Sun, 18 Mar 2018 11:34:03: #2 finished! INFO @ Sun, 18 Mar 2018 11:34:03: #2 predicted fragment length is 60 bps INFO @ Sun, 18 Mar 2018 11:34:03: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 18 Mar 2018 11:34:03: #2.2 Generate R script for model : SRX3087686.05_model.r WARNING @ Sun, 18 Mar 2018 11:34:03: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:34:03: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 18 Mar 2018 11:34:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:34:03: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:34:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:35:59: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:36:02: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:36:17: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:37:08: #4 Write output xls file... SRX3087686.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:37:08: #4 Write peak in narrowPeak format file... SRX3087686.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:37:08: #4 Write summits bed file... SRX3087686.20_summits.bed INFO @ Sun, 18 Mar 2018 11:37:08: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (659 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:37:17: #4 Write output xls file... SRX3087686.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:37:17: #4 Write peak in narrowPeak format file... SRX3087686.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:37:17: #4 Write summits bed file... SRX3087686.10_summits.bed INFO @ Sun, 18 Mar 2018 11:37:17: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1378 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:37:27: #4 Write output xls file... SRX3087686.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:37:27: #4 Write peak in narrowPeak format file... SRX3087686.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:37:27: #4 Write summits bed file... SRX3087686.05_summits.bed INFO @ Sun, 18 Mar 2018 11:37:27: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (2567 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。