Job ID = 10851040 sra ファイルのダウンロード中... Completed: 1079779K bytes transferred in 25 seconds (345634K 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... Read 31579144 spots for /home/okishinya/chipatlas/results/rn6/SRX3461656/SRR6366134.sra Written 31579144 spots for /home/okishinya/chipatlas/results/rn6/SRX3461656/SRR6366134.sra 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:44:41 31579144 reads; of these: 31579144 (100.00%) were unpaired; of these: 1098280 (3.48%) aligned 0 times 23106228 (73.17%) aligned exactly 1 time 7374636 (23.35%) aligned >1 times 96.52% overall alignment rate Time searching: 00:44:45 Overall time: 00:44:45 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] 1066051 / 30480864 = 0.0350 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 @ Thu, 05 Jul 2018 23:00:29: # Command line: callpeak -t SRX3461656.bam -f BAM -g 2.15e9 -n SRX3461656.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3461656.05 # format = BAM # ChIP-seq file = ['SRX3461656.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 @ Thu, 05 Jul 2018 23:00:29: #1 read tag files... INFO @ Thu, 05 Jul 2018 23:00:29: #1 read treatment tags... INFO @ Thu, 05 Jul 2018 23:00:29: # Command line: callpeak -t SRX3461656.bam -f BAM -g 2.15e9 -n SRX3461656.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3461656.20 # format = BAM # ChIP-seq file = ['SRX3461656.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 @ Thu, 05 Jul 2018 23:00:29: #1 read tag files... INFO @ Thu, 05 Jul 2018 23:00:29: #1 read treatment tags... INFO @ Thu, 05 Jul 2018 23:00:29: # Command line: callpeak -t SRX3461656.bam -f BAM -g 2.15e9 -n SRX3461656.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3461656.10 # format = BAM # ChIP-seq file = ['SRX3461656.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 @ Thu, 05 Jul 2018 23:00:29: #1 read tag files... INFO @ Thu, 05 Jul 2018 23:00:29: #1 read treatment tags... INFO @ Thu, 05 Jul 2018 23:00:37: 1000000 INFO @ Thu, 05 Jul 2018 23:00:37: 1000000 INFO @ Thu, 05 Jul 2018 23:00:38: 1000000 INFO @ Thu, 05 Jul 2018 23:00:46: 2000000 INFO @ Thu, 05 Jul 2018 23:00:46: 2000000 INFO @ Thu, 05 Jul 2018 23:00:48: 2000000 INFO @ Thu, 05 Jul 2018 23:00:54: 3000000 INFO @ Thu, 05 Jul 2018 23:00:54: 3000000 INFO @ Thu, 05 Jul 2018 23:00:57: 3000000 INFO @ Thu, 05 Jul 2018 23:01:03: 4000000 INFO @ Thu, 05 Jul 2018 23:01:03: 4000000 INFO @ Thu, 05 Jul 2018 23:01:06: 4000000 INFO @ Thu, 05 Jul 2018 23:01:11: 5000000 INFO @ Thu, 05 Jul 2018 23:01:11: 5000000 INFO @ Thu, 05 Jul 2018 23:01:16: 5000000 INFO @ Thu, 05 Jul 2018 23:01:20: 6000000 INFO @ Thu, 05 Jul 2018 23:01:20: 6000000 INFO @ Thu, 05 Jul 2018 23:01:25: 6000000 INFO @ Thu, 05 Jul 2018 23:01:28: 7000000 INFO @ Thu, 05 Jul 2018 23:01:28: 7000000 INFO @ Thu, 05 Jul 2018 23:01:35: 7000000 INFO @ Thu, 05 Jul 2018 23:01:36: 8000000 INFO @ Thu, 05 Jul 2018 23:01:36: 8000000 INFO @ Thu, 05 Jul 2018 23:01:44: 9000000 INFO @ Thu, 05 Jul 2018 23:01:44: 9000000 INFO @ Thu, 05 Jul 2018 23:01:45: 8000000 INFO @ Thu, 05 Jul 2018 23:01:53: 10000000 INFO @ Thu, 05 Jul 2018 23:01:53: 10000000 INFO @ Thu, 05 Jul 2018 23:01:54: 9000000 INFO @ Thu, 05 Jul 2018 23:02:01: 11000000 INFO @ Thu, 05 Jul 2018 23:02:01: 11000000 INFO @ Thu, 05 Jul 2018 23:02:04: 10000000 INFO @ Thu, 05 Jul 2018 23:02:09: 12000000 INFO @ Thu, 05 Jul 2018 23:02:09: 12000000 INFO @ Thu, 05 Jul 2018 23:02:14: 11000000 INFO @ Thu, 05 Jul 2018 23:02:18: 13000000 INFO @ Thu, 05 Jul 2018 23:02:18: 13000000 INFO @ Thu, 05 Jul 2018 23:02:23: 12000000 INFO @ Thu, 05 Jul 2018 23:02:26: 14000000 INFO @ Thu, 05 Jul 2018 23:02:26: 14000000 INFO @ Thu, 05 Jul 2018 23:02:33: 13000000 INFO @ Thu, 05 Jul 2018 23:02:34: 15000000 INFO @ Thu, 05 Jul 2018 23:02:34: 15000000 INFO @ Thu, 05 Jul 2018 23:02:43: 14000000 INFO @ Thu, 05 Jul 2018 23:02:43: 16000000 INFO @ Thu, 05 Jul 2018 23:02:43: 16000000 INFO @ Thu, 05 Jul 2018 23:02:51: 17000000 INFO @ Thu, 05 Jul 2018 23:02:51: 17000000 INFO @ Thu, 05 Jul 2018 23:02:52: 15000000 INFO @ Thu, 05 Jul 2018 23:03:00: 18000000 INFO @ Thu, 05 Jul 2018 23:03:00: 18000000 INFO @ Thu, 05 Jul 2018 23:03:02: 16000000 INFO @ Thu, 05 Jul 2018 23:03:08: 19000000 INFO @ Thu, 05 Jul 2018 23:03:08: 19000000 INFO @ Thu, 05 Jul 2018 23:03:12: 17000000 INFO @ Thu, 05 Jul 2018 23:03:16: 20000000 INFO @ Thu, 05 Jul 2018 23:03:16: 20000000 INFO @ Thu, 05 Jul 2018 23:03:21: 18000000 INFO @ Thu, 05 Jul 2018 23:03:25: 21000000 INFO @ Thu, 05 Jul 2018 23:03:25: 21000000 INFO @ Thu, 05 Jul 2018 23:03:31: 19000000 INFO @ Thu, 05 Jul 2018 23:03:33: 22000000 INFO @ Thu, 05 Jul 2018 23:03:33: 22000000 INFO @ Thu, 05 Jul 2018 23:03:40: 20000000 INFO @ Thu, 05 Jul 2018 23:03:42: 23000000 INFO @ Thu, 05 Jul 2018 23:03:42: 23000000 INFO @ Thu, 05 Jul 2018 23:03:50: 24000000 INFO @ Thu, 05 Jul 2018 23:03:50: 24000000 INFO @ Thu, 05 Jul 2018 23:03:50: 21000000 INFO @ Thu, 05 Jul 2018 23:03:58: 25000000 INFO @ Thu, 05 Jul 2018 23:03:58: 25000000 INFO @ Thu, 05 Jul 2018 23:04:00: 22000000 INFO @ Thu, 05 Jul 2018 23:04:07: 26000000 INFO @ Thu, 05 Jul 2018 23:04:07: 26000000 INFO @ Thu, 05 Jul 2018 23:04:09: 23000000 INFO @ Thu, 05 Jul 2018 23:04:15: 27000000 INFO @ Thu, 05 Jul 2018 23:04:15: 27000000 INFO @ Thu, 05 Jul 2018 23:04:19: 24000000 INFO @ Thu, 05 Jul 2018 23:04:24: 28000000 INFO @ Thu, 05 Jul 2018 23:04:24: 28000000 INFO @ Thu, 05 Jul 2018 23:04:28: 25000000 INFO @ Thu, 05 Jul 2018 23:04:32: 29000000 INFO @ Thu, 05 Jul 2018 23:04:32: 29000000 INFO @ Thu, 05 Jul 2018 23:04:36: #1 tag size is determined as 75 bps INFO @ Thu, 05 Jul 2018 23:04:36: #1 tag size = 75 INFO @ Thu, 05 Jul 2018 23:04:36: #1 total tags in treatment: 29414813 INFO @ Thu, 05 Jul 2018 23:04:36: #1 user defined the maximum tags... INFO @ Thu, 05 Jul 2018 23:04:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Jul 2018 23:04:36: #1 tag size is determined as 75 bps INFO @ Thu, 05 Jul 2018 23:04:36: #1 tag size = 75 INFO @ Thu, 05 Jul 2018 23:04:36: #1 total tags in treatment: 29414813 INFO @ Thu, 05 Jul 2018 23:04:36: #1 user defined the maximum tags... INFO @ Thu, 05 Jul 2018 23:04:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Jul 2018 23:04:37: #1 tags after filtering in treatment: 29414714 INFO @ Thu, 05 Jul 2018 23:04:37: #1 tags after filtering in treatment: 29414714 INFO @ Thu, 05 Jul 2018 23:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Jul 2018 23:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Jul 2018 23:04:37: #1 finished! INFO @ Thu, 05 Jul 2018 23:04:37: #1 finished! INFO @ Thu, 05 Jul 2018 23:04:37: #2 Build Peak Model... INFO @ Thu, 05 Jul 2018 23:04:37: #2 Build Peak Model... INFO @ Thu, 05 Jul 2018 23:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Jul 2018 23:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Jul 2018 23:04:38: 26000000 INFO @ Thu, 05 Jul 2018 23:04:40: #2 number of paired peaks: 18119 INFO @ Thu, 05 Jul 2018 23:04:40: start model_add_line... INFO @ Thu, 05 Jul 2018 23:04:40: #2 number of paired peaks: 18119 INFO @ Thu, 05 Jul 2018 23:04:40: start model_add_line... INFO @ Thu, 05 Jul 2018 23:04:40: start X-correlation... INFO @ Thu, 05 Jul 2018 23:04:40: end of X-cor INFO @ Thu, 05 Jul 2018 23:04:40: #2 finished! INFO @ Thu, 05 Jul 2018 23:04:40: #2 predicted fragment length is 156 bps INFO @ Thu, 05 Jul 2018 23:04:40: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 05 Jul 2018 23:04:40: #2.2 Generate R script for model : SRX3461656.05_model.r INFO @ Thu, 05 Jul 2018 23:04:40: #3 Call peaks... INFO @ Thu, 05 Jul 2018 23:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Jul 2018 23:04:41: start X-correlation... INFO @ Thu, 05 Jul 2018 23:04:41: end of X-cor INFO @ Thu, 05 Jul 2018 23:04:41: #2 finished! INFO @ Thu, 05 Jul 2018 23:04:41: #2 predicted fragment length is 156 bps INFO @ Thu, 05 Jul 2018 23:04:41: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 05 Jul 2018 23:04:41: #2.2 Generate R script for model : SRX3461656.20_model.r INFO @ Thu, 05 Jul 2018 23:04:41: #3 Call peaks... INFO @ Thu, 05 Jul 2018 23:04:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Jul 2018 23:04:48: 27000000 INFO @ Thu, 05 Jul 2018 23:04:58: 28000000 INFO @ Thu, 05 Jul 2018 23:05:07: 29000000 INFO @ Thu, 05 Jul 2018 23:05:12: #1 tag size is determined as 75 bps INFO @ Thu, 05 Jul 2018 23:05:12: #1 tag size = 75 INFO @ Thu, 05 Jul 2018 23:05:12: #1 total tags in treatment: 29414813 INFO @ Thu, 05 Jul 2018 23:05:12: #1 user defined the maximum tags... INFO @ Thu, 05 Jul 2018 23:05:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Jul 2018 23:05:13: #1 tags after filtering in treatment: 29414714 INFO @ Thu, 05 Jul 2018 23:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Jul 2018 23:05:13: #1 finished! INFO @ Thu, 05 Jul 2018 23:05:13: #2 Build Peak Model... INFO @ Thu, 05 Jul 2018 23:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Jul 2018 23:05:16: #2 number of paired peaks: 18119 INFO @ Thu, 05 Jul 2018 23:05:16: start model_add_line... INFO @ Thu, 05 Jul 2018 23:05:16: start X-correlation... INFO @ Thu, 05 Jul 2018 23:05:16: end of X-cor INFO @ Thu, 05 Jul 2018 23:05:16: #2 finished! INFO @ Thu, 05 Jul 2018 23:05:16: #2 predicted fragment length is 156 bps INFO @ Thu, 05 Jul 2018 23:05:16: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 05 Jul 2018 23:05:16: #2.2 Generate R script for model : SRX3461656.10_model.r INFO @ Thu, 05 Jul 2018 23:05:16: #3 Call peaks... INFO @ Thu, 05 Jul 2018 23:05:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Jul 2018 23:05:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Jul 2018 23:05:56: #3 Call peaks for each chromosome... INFO @ Thu, 05 Jul 2018 23:06:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Jul 2018 23:06:36: #4 Write output xls file... SRX3461656.20_peaks.xls INFO @ Thu, 05 Jul 2018 23:06:36: #4 Write peak in narrowPeak format file... SRX3461656.20_peaks.narrowPeak INFO @ Thu, 05 Jul 2018 23:06:36: #4 Write summits bed file... SRX3461656.20_summits.bed INFO @ Thu, 05 Jul 2018 23:06:36: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (2650 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 05 Jul 2018 23:06:37: #4 Write output xls file... SRX3461656.05_peaks.xls INFO @ Thu, 05 Jul 2018 23:06:37: #4 Write peak in narrowPeak format file... SRX3461656.05_peaks.narrowPeak INFO @ Thu, 05 Jul 2018 23:06:37: #4 Write summits bed file... SRX3461656.05_summits.bed INFO @ Thu, 05 Jul 2018 23:06:37: Done! pass1 - making usageList (96 chroms): 3 millis pass2 - checking and writing primary data (12242 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 05 Jul 2018 23:07:09: #4 Write output xls file... SRX3461656.10_peaks.xls INFO @ Thu, 05 Jul 2018 23:07:09: #4 Write peak in narrowPeak format file... SRX3461656.10_peaks.narrowPeak INFO @ Thu, 05 Jul 2018 23:07:09: #4 Write summits bed file... SRX3461656.10_summits.bed INFO @ Thu, 05 Jul 2018 23:07:09: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (6480 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。