Job ID = 11192579 sra ファイルのダウンロード中... Completed: 1029611K bytes transferred in 9 seconds (875273K 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 32291701 spots for /home/okishinya/chipatlas/results/rn6/SRX2226591/SRR4374841.sra Written 32291701 spots for /home/okishinya/chipatlas/results/rn6/SRX2226591/SRR4374841.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:00 32291701 reads; of these: 32291701 (100.00%) were unpaired; of these: 886479 (2.75%) aligned 0 times 22815503 (70.65%) aligned exactly 1 time 8589719 (26.60%) aligned >1 times 97.25% overall alignment rate Time searching: 00:25:03 Overall time: 00:25:03 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] 1901369 / 31405222 = 0.0605 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, 15 Sep 2018 09:41:36: # Command line: callpeak -t SRX2226591.bam -f BAM -g 2.15e9 -n SRX2226591.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226591.05 # format = BAM # ChIP-seq file = ['SRX2226591.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, 15 Sep 2018 09:41:36: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:41:36: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:41:36: # Command line: callpeak -t SRX2226591.bam -f BAM -g 2.15e9 -n SRX2226591.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226591.20 # format = BAM # ChIP-seq file = ['SRX2226591.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, 15 Sep 2018 09:41:36: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:41:36: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:41:36: # Command line: callpeak -t SRX2226591.bam -f BAM -g 2.15e9 -n SRX2226591.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226591.10 # format = BAM # ChIP-seq file = ['SRX2226591.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, 15 Sep 2018 09:41:36: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:41:36: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:41:43: 1000000 INFO @ Sat, 15 Sep 2018 09:41:43: 1000000 INFO @ Sat, 15 Sep 2018 09:41:43: 1000000 INFO @ Sat, 15 Sep 2018 09:41:49: 2000000 INFO @ Sat, 15 Sep 2018 09:41:50: 2000000 INFO @ Sat, 15 Sep 2018 09:41:50: 2000000 INFO @ Sat, 15 Sep 2018 09:41:56: 3000000 INFO @ Sat, 15 Sep 2018 09:41:57: 3000000 INFO @ Sat, 15 Sep 2018 09:41:57: 3000000 INFO @ Sat, 15 Sep 2018 09:42:03: 4000000 INFO @ Sat, 15 Sep 2018 09:42:03: 4000000 INFO @ Sat, 15 Sep 2018 09:42:04: 4000000 INFO @ Sat, 15 Sep 2018 09:42:09: 5000000 INFO @ Sat, 15 Sep 2018 09:42:10: 5000000 INFO @ Sat, 15 Sep 2018 09:42:10: 5000000 INFO @ Sat, 15 Sep 2018 09:42:16: 6000000 INFO @ Sat, 15 Sep 2018 09:42:16: 6000000 INFO @ Sat, 15 Sep 2018 09:42:17: 6000000 INFO @ Sat, 15 Sep 2018 09:42:23: 7000000 INFO @ Sat, 15 Sep 2018 09:42:23: 7000000 INFO @ Sat, 15 Sep 2018 09:42:24: 7000000 INFO @ Sat, 15 Sep 2018 09:42:29: 8000000 INFO @ Sat, 15 Sep 2018 09:42:30: 8000000 INFO @ Sat, 15 Sep 2018 09:42:31: 8000000 INFO @ Sat, 15 Sep 2018 09:42:36: 9000000 INFO @ Sat, 15 Sep 2018 09:42:36: 9000000 INFO @ Sat, 15 Sep 2018 09:42:37: 9000000 INFO @ Sat, 15 Sep 2018 09:42:42: 10000000 INFO @ Sat, 15 Sep 2018 09:42:43: 10000000 INFO @ Sat, 15 Sep 2018 09:42:44: 10000000 INFO @ Sat, 15 Sep 2018 09:42:49: 11000000 INFO @ Sat, 15 Sep 2018 09:42:49: 11000000 INFO @ Sat, 15 Sep 2018 09:42:51: 11000000 INFO @ Sat, 15 Sep 2018 09:42:55: 12000000 INFO @ Sat, 15 Sep 2018 09:42:56: 12000000 INFO @ Sat, 15 Sep 2018 09:42:58: 12000000 INFO @ Sat, 15 Sep 2018 09:43:02: 13000000 INFO @ Sat, 15 Sep 2018 09:43:02: 13000000 INFO @ Sat, 15 Sep 2018 09:43:04: 13000000 INFO @ Sat, 15 Sep 2018 09:43:08: 14000000 INFO @ Sat, 15 Sep 2018 09:43:09: 14000000 INFO @ Sat, 15 Sep 2018 09:43:11: 14000000 INFO @ Sat, 15 Sep 2018 09:43:15: 15000000 INFO @ Sat, 15 Sep 2018 09:43:16: 15000000 INFO @ Sat, 15 Sep 2018 09:43:18: 15000000 INFO @ Sat, 15 Sep 2018 09:43:22: 16000000 INFO @ Sat, 15 Sep 2018 09:43:22: 16000000 INFO @ Sat, 15 Sep 2018 09:43:25: 16000000 INFO @ Sat, 15 Sep 2018 09:43:28: 17000000 INFO @ Sat, 15 Sep 2018 09:43:29: 17000000 INFO @ Sat, 15 Sep 2018 09:43:31: 17000000 INFO @ Sat, 15 Sep 2018 09:43:35: 18000000 INFO @ Sat, 15 Sep 2018 09:43:35: 18000000 INFO @ Sat, 15 Sep 2018 09:43:38: 18000000 INFO @ Sat, 15 Sep 2018 09:43:41: 19000000 INFO @ Sat, 15 Sep 2018 09:43:42: 19000000 INFO @ Sat, 15 Sep 2018 09:43:45: 19000000 INFO @ Sat, 15 Sep 2018 09:43:48: 20000000 INFO @ Sat, 15 Sep 2018 09:43:48: 20000000 INFO @ Sat, 15 Sep 2018 09:43:52: 20000000 INFO @ Sat, 15 Sep 2018 09:43:55: 21000000 INFO @ Sat, 15 Sep 2018 09:43:55: 21000000 INFO @ Sat, 15 Sep 2018 09:43:59: 21000000 INFO @ Sat, 15 Sep 2018 09:44:01: 22000000 INFO @ Sat, 15 Sep 2018 09:44:01: 22000000 INFO @ Sat, 15 Sep 2018 09:44:06: 22000000 INFO @ Sat, 15 Sep 2018 09:44:08: 23000000 INFO @ Sat, 15 Sep 2018 09:44:08: 23000000 INFO @ Sat, 15 Sep 2018 09:44:12: 23000000 INFO @ Sat, 15 Sep 2018 09:44:15: 24000000 INFO @ Sat, 15 Sep 2018 09:44:15: 24000000 INFO @ Sat, 15 Sep 2018 09:44:19: 24000000 INFO @ Sat, 15 Sep 2018 09:44:21: 25000000 INFO @ Sat, 15 Sep 2018 09:44:21: 25000000 INFO @ Sat, 15 Sep 2018 09:44:26: 25000000 INFO @ Sat, 15 Sep 2018 09:44:28: 26000000 INFO @ Sat, 15 Sep 2018 09:44:28: 26000000 INFO @ Sat, 15 Sep 2018 09:44:32: 26000000 INFO @ Sat, 15 Sep 2018 09:44:34: 27000000 INFO @ Sat, 15 Sep 2018 09:44:34: 27000000 INFO @ Sat, 15 Sep 2018 09:44:39: 27000000 INFO @ Sat, 15 Sep 2018 09:44:41: 28000000 INFO @ Sat, 15 Sep 2018 09:44:41: 28000000 INFO @ Sat, 15 Sep 2018 09:44:46: 28000000 INFO @ Sat, 15 Sep 2018 09:44:47: 29000000 INFO @ Sat, 15 Sep 2018 09:44:48: 29000000 INFO @ Sat, 15 Sep 2018 09:44:51: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:44:51: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:44:51: #1 total tags in treatment: 29503853 INFO @ Sat, 15 Sep 2018 09:44:51: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:44:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:44:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:44:52: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:44:52: #1 total tags in treatment: 29503853 INFO @ Sat, 15 Sep 2018 09:44:52: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:44:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:44:52: #1 tags after filtering in treatment: 29503754 INFO @ Sat, 15 Sep 2018 09:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:44:52: #1 finished! INFO @ Sat, 15 Sep 2018 09:44:52: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:44:52: #1 tags after filtering in treatment: 29503754 INFO @ Sat, 15 Sep 2018 09:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:44:52: #1 finished! INFO @ Sat, 15 Sep 2018 09:44:52: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:44:53: 29000000 INFO @ Sat, 15 Sep 2018 09:44:55: #2 number of paired peaks: 4977 INFO @ Sat, 15 Sep 2018 09:44:55: start model_add_line... INFO @ Sat, 15 Sep 2018 09:44:55: start X-correlation... INFO @ Sat, 15 Sep 2018 09:44:55: end of X-cor INFO @ Sat, 15 Sep 2018 09:44:55: #2 finished! INFO @ Sat, 15 Sep 2018 09:44:55: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Sep 2018 09:44:55: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 15 Sep 2018 09:44:55: #2.2 Generate R script for model : SRX2226591.10_model.r WARNING @ Sat, 15 Sep 2018 09:44:55: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 09:44:55: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 15 Sep 2018 09:44:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 09:44:55: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:44:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:44:55: #2 number of paired peaks: 4977 INFO @ Sat, 15 Sep 2018 09:44:55: start model_add_line... INFO @ Sat, 15 Sep 2018 09:44:56: start X-correlation... INFO @ Sat, 15 Sep 2018 09:44:56: end of X-cor INFO @ Sat, 15 Sep 2018 09:44:56: #2 finished! INFO @ Sat, 15 Sep 2018 09:44:56: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Sep 2018 09:44:56: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 15 Sep 2018 09:44:56: #2.2 Generate R script for model : SRX2226591.05_model.r WARNING @ Sat, 15 Sep 2018 09:44:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 09:44:56: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 15 Sep 2018 09:44:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 09:44:56: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:44:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:44:56: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:44:56: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:44:56: #1 total tags in treatment: 29503853 INFO @ Sat, 15 Sep 2018 09:44:56: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:44:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:44:57: #1 tags after filtering in treatment: 29503754 INFO @ Sat, 15 Sep 2018 09:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:44:57: #1 finished! INFO @ Sat, 15 Sep 2018 09:44:57: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:45:00: #2 number of paired peaks: 4977 INFO @ Sat, 15 Sep 2018 09:45:00: start model_add_line... INFO @ Sat, 15 Sep 2018 09:45:01: start X-correlation... INFO @ Sat, 15 Sep 2018 09:45:01: end of X-cor INFO @ Sat, 15 Sep 2018 09:45:01: #2 finished! INFO @ Sat, 15 Sep 2018 09:45:01: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Sep 2018 09:45:01: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 15 Sep 2018 09:45:01: #2.2 Generate R script for model : SRX2226591.20_model.r WARNING @ Sat, 15 Sep 2018 09:45:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 09:45:01: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 15 Sep 2018 09:45:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 09:45:01: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:46:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:46:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:46:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:46:42: #4 Write output xls file... SRX2226591.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:46:42: #4 Write peak in narrowPeak format file... SRX2226591.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:46:42: #4 Write summits bed file... SRX2226591.05_summits.bed INFO @ Sat, 15 Sep 2018 09:46:42: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (1982 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:46:52: #4 Write output xls file... SRX2226591.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:46:52: #4 Write peak in narrowPeak format file... SRX2226591.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:46:52: #4 Write summits bed file... SRX2226591.20_summits.bed INFO @ Sat, 15 Sep 2018 09:46:52: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (521 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:46:53: #4 Write output xls file... SRX2226591.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:46:53: #4 Write peak in narrowPeak format file... SRX2226591.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:46:53: #4 Write summits bed file... SRX2226591.10_summits.bed INFO @ Sat, 15 Sep 2018 09:46:53: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1092 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。