Job ID = 11192580 sra ファイルのダウンロード中... Completed: 583464K bytes transferred in 8 seconds (585456K 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 45617249 spots for /home/okishinya/chipatlas/results/rn6/SRX4014801/SRR7085050.sra Written 45617249 spots for /home/okishinya/chipatlas/results/rn6/SRX4014801/SRR7085050.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: 00:50:36 45617249 reads; of these: 45617249 (100.00%) were unpaired; of these: 1728777 (3.79%) aligned 0 times 32576926 (71.41%) aligned exactly 1 time 11311546 (24.80%) aligned >1 times 96.21% overall alignment rate Time searching: 00:50:39 Overall time: 00:50:39 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] 3501598 / 43888472 = 0.0798 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 11:56:35: # Command line: callpeak -t SRX4014801.bam -f BAM -g 2.15e9 -n SRX4014801.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014801.10 # format = BAM # ChIP-seq file = ['SRX4014801.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 11:56:35: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:56:35: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:56:35: # Command line: callpeak -t SRX4014801.bam -f BAM -g 2.15e9 -n SRX4014801.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014801.20 # format = BAM # ChIP-seq file = ['SRX4014801.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 11:56:35: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:56:35: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:56:35: # Command line: callpeak -t SRX4014801.bam -f BAM -g 2.15e9 -n SRX4014801.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014801.05 # format = BAM # ChIP-seq file = ['SRX4014801.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 11:56:35: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:56:35: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:56:42: 1000000 INFO @ Sat, 15 Sep 2018 11:56:42: 1000000 INFO @ Sat, 15 Sep 2018 11:56:42: 1000000 INFO @ Sat, 15 Sep 2018 11:56:48: 2000000 INFO @ Sat, 15 Sep 2018 11:56:50: 2000000 INFO @ Sat, 15 Sep 2018 11:56:50: 2000000 INFO @ Sat, 15 Sep 2018 11:56:55: 3000000 INFO @ Sat, 15 Sep 2018 11:56:57: 3000000 INFO @ Sat, 15 Sep 2018 11:56:58: 3000000 INFO @ Sat, 15 Sep 2018 11:57:02: 4000000 INFO @ Sat, 15 Sep 2018 11:57:05: 4000000 INFO @ Sat, 15 Sep 2018 11:57:06: 4000000 INFO @ Sat, 15 Sep 2018 11:57:08: 5000000 INFO @ Sat, 15 Sep 2018 11:57:13: 5000000 INFO @ Sat, 15 Sep 2018 11:57:14: 5000000 INFO @ Sat, 15 Sep 2018 11:57:15: 6000000 INFO @ Sat, 15 Sep 2018 11:57:20: 6000000 INFO @ Sat, 15 Sep 2018 11:57:22: 7000000 INFO @ Sat, 15 Sep 2018 11:57:23: 6000000 INFO @ Sat, 15 Sep 2018 11:57:28: 8000000 INFO @ Sat, 15 Sep 2018 11:57:28: 7000000 INFO @ Sat, 15 Sep 2018 11:57:31: 7000000 INFO @ Sat, 15 Sep 2018 11:57:35: 9000000 INFO @ Sat, 15 Sep 2018 11:57:36: 8000000 INFO @ Sat, 15 Sep 2018 11:57:39: 8000000 INFO @ Sat, 15 Sep 2018 11:57:41: 10000000 INFO @ Sat, 15 Sep 2018 11:57:44: 9000000 INFO @ Sat, 15 Sep 2018 11:57:47: 9000000 INFO @ Sat, 15 Sep 2018 11:57:48: 11000000 INFO @ Sat, 15 Sep 2018 11:57:51: 10000000 INFO @ Sat, 15 Sep 2018 11:57:55: 10000000 INFO @ Sat, 15 Sep 2018 11:57:55: 12000000 INFO @ Sat, 15 Sep 2018 11:57:59: 11000000 INFO @ Sat, 15 Sep 2018 11:58:01: 13000000 INFO @ Sat, 15 Sep 2018 11:58:03: 11000000 INFO @ Sat, 15 Sep 2018 11:58:07: 12000000 INFO @ Sat, 15 Sep 2018 11:58:08: 14000000 INFO @ Sat, 15 Sep 2018 11:58:11: 12000000 INFO @ Sat, 15 Sep 2018 11:58:14: 15000000 INFO @ Sat, 15 Sep 2018 11:58:15: 13000000 INFO @ Sat, 15 Sep 2018 11:58:20: 13000000 INFO @ Sat, 15 Sep 2018 11:58:21: 16000000 INFO @ Sat, 15 Sep 2018 11:58:22: 14000000 INFO @ Sat, 15 Sep 2018 11:58:27: 14000000 INFO @ Sat, 15 Sep 2018 11:58:28: 17000000 INFO @ Sat, 15 Sep 2018 11:58:30: 15000000 INFO @ Sat, 15 Sep 2018 11:58:35: 18000000 INFO @ Sat, 15 Sep 2018 11:58:35: 15000000 INFO @ Sat, 15 Sep 2018 11:58:37: 16000000 INFO @ Sat, 15 Sep 2018 11:58:42: 19000000 INFO @ Sat, 15 Sep 2018 11:58:43: 16000000 INFO @ Sat, 15 Sep 2018 11:58:44: 17000000 INFO @ Sat, 15 Sep 2018 11:58:49: 20000000 INFO @ Sat, 15 Sep 2018 11:58:50: 17000000 INFO @ Sat, 15 Sep 2018 11:58:51: 18000000 INFO @ Sat, 15 Sep 2018 11:58:57: 21000000 INFO @ Sat, 15 Sep 2018 11:58:57: 18000000 INFO @ Sat, 15 Sep 2018 11:58:58: 19000000 INFO @ Sat, 15 Sep 2018 11:59:03: 22000000 INFO @ Sat, 15 Sep 2018 11:59:05: 19000000 INFO @ Sat, 15 Sep 2018 11:59:05: 20000000 INFO @ Sat, 15 Sep 2018 11:59:10: 23000000 INFO @ Sat, 15 Sep 2018 11:59:12: 21000000 INFO @ Sat, 15 Sep 2018 11:59:13: 20000000 INFO @ Sat, 15 Sep 2018 11:59:17: 24000000 INFO @ Sat, 15 Sep 2018 11:59:20: 22000000 INFO @ Sat, 15 Sep 2018 11:59:20: 21000000 INFO @ Sat, 15 Sep 2018 11:59:24: 25000000 INFO @ Sat, 15 Sep 2018 11:59:27: 23000000 INFO @ Sat, 15 Sep 2018 11:59:28: 22000000 INFO @ Sat, 15 Sep 2018 11:59:31: 26000000 INFO @ Sat, 15 Sep 2018 11:59:35: 24000000 INFO @ Sat, 15 Sep 2018 11:59:36: 23000000 INFO @ Sat, 15 Sep 2018 11:59:38: 27000000 INFO @ Sat, 15 Sep 2018 11:59:42: 25000000 INFO @ Sat, 15 Sep 2018 11:59:43: 24000000 INFO @ Sat, 15 Sep 2018 11:59:45: 28000000 INFO @ Sat, 15 Sep 2018 11:59:49: 26000000 INFO @ Sat, 15 Sep 2018 11:59:51: 25000000 INFO @ Sat, 15 Sep 2018 11:59:51: 29000000 INFO @ Sat, 15 Sep 2018 11:59:57: 27000000 INFO @ Sat, 15 Sep 2018 11:59:58: 30000000 INFO @ Sat, 15 Sep 2018 11:59:59: 26000000 INFO @ Sat, 15 Sep 2018 12:00:04: 31000000 INFO @ Sat, 15 Sep 2018 12:00:05: 28000000 INFO @ Sat, 15 Sep 2018 12:00:08: 27000000 INFO @ Sat, 15 Sep 2018 12:00:11: 32000000 INFO @ Sat, 15 Sep 2018 12:00:13: 29000000 INFO @ Sat, 15 Sep 2018 12:00:16: 28000000 INFO @ Sat, 15 Sep 2018 12:00:18: 33000000 INFO @ Sat, 15 Sep 2018 12:00:20: 30000000 INFO @ Sat, 15 Sep 2018 12:00:24: 29000000 INFO @ Sat, 15 Sep 2018 12:00:24: 34000000 INFO @ Sat, 15 Sep 2018 12:00:28: 31000000 INFO @ Sat, 15 Sep 2018 12:00:31: 35000000 INFO @ Sat, 15 Sep 2018 12:00:32: 30000000 INFO @ Sat, 15 Sep 2018 12:00:36: 32000000 INFO @ Sat, 15 Sep 2018 12:00:38: 36000000 INFO @ Sat, 15 Sep 2018 12:00:40: 31000000 INFO @ Sat, 15 Sep 2018 12:00:43: 33000000 INFO @ Sat, 15 Sep 2018 12:00:45: 37000000 INFO @ Sat, 15 Sep 2018 12:00:47: 32000000 INFO @ Sat, 15 Sep 2018 12:00:50: 34000000 INFO @ Sat, 15 Sep 2018 12:00:52: 38000000 INFO @ Sat, 15 Sep 2018 12:00:54: 33000000 INFO @ Sat, 15 Sep 2018 12:00:56: 35000000 INFO @ Sat, 15 Sep 2018 12:01:00: 39000000 INFO @ Sat, 15 Sep 2018 12:01:02: 34000000 INFO @ Sat, 15 Sep 2018 12:01:04: 36000000 INFO @ Sat, 15 Sep 2018 12:01:07: 40000000 INFO @ Sat, 15 Sep 2018 12:01:10: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 12:01:10: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 12:01:10: #1 total tags in treatment: 40386874 INFO @ Sat, 15 Sep 2018 12:01:10: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 12:01:10: #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 12:01:10: 35000000 INFO @ Sat, 15 Sep 2018 12:01:11: #1 tags after filtering in treatment: 40386796 INFO @ Sat, 15 Sep 2018 12:01:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 12:01:11: #1 finished! INFO @ Sat, 15 Sep 2018 12:01:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 12:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 12:01:12: 37000000 INFO @ Sat, 15 Sep 2018 12:01:14: #2 number of paired peaks: 5746 INFO @ Sat, 15 Sep 2018 12:01:14: start model_add_line... INFO @ Sat, 15 Sep 2018 12:01:15: start X-correlation... INFO @ Sat, 15 Sep 2018 12:01:15: end of X-cor INFO @ Sat, 15 Sep 2018 12:01:15: #2 finished! INFO @ Sat, 15 Sep 2018 12:01:15: #2 predicted fragment length is 76 bps INFO @ Sat, 15 Sep 2018 12:01:15: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 15 Sep 2018 12:01:15: #2.2 Generate R script for model : SRX4014801.10_model.r WARNING @ Sat, 15 Sep 2018 12:01:15: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 12:01:15: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 15 Sep 2018 12:01:15: #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 12:01:15: #3 Call peaks... INFO @ Sat, 15 Sep 2018 12:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 12:01:18: 36000000 INFO @ Sat, 15 Sep 2018 12:01:20: 38000000 INFO @ Sat, 15 Sep 2018 12:01:26: 37000000 INFO @ Sat, 15 Sep 2018 12:01:27: 39000000 INFO @ Sat, 15 Sep 2018 12:01:34: 38000000 INFO @ Sat, 15 Sep 2018 12:01:35: 40000000 INFO @ Sat, 15 Sep 2018 12:01:38: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 12:01:38: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 12:01:38: #1 total tags in treatment: 40386874 INFO @ Sat, 15 Sep 2018 12:01:38: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 12:01:38: #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 12:01:39: #1 tags after filtering in treatment: 40386796 INFO @ Sat, 15 Sep 2018 12:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 12:01:39: #1 finished! INFO @ Sat, 15 Sep 2018 12:01:39: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 12:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 12:01:42: 39000000 INFO @ Sat, 15 Sep 2018 12:01:43: #2 number of paired peaks: 5746 INFO @ Sat, 15 Sep 2018 12:01:43: start model_add_line... INFO @ Sat, 15 Sep 2018 12:01:43: start X-correlation... INFO @ Sat, 15 Sep 2018 12:01:43: end of X-cor INFO @ Sat, 15 Sep 2018 12:01:43: #2 finished! INFO @ Sat, 15 Sep 2018 12:01:43: #2 predicted fragment length is 76 bps INFO @ Sat, 15 Sep 2018 12:01:43: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 15 Sep 2018 12:01:43: #2.2 Generate R script for model : SRX4014801.05_model.r WARNING @ Sat, 15 Sep 2018 12:01:43: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 12:01:43: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 15 Sep 2018 12:01:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 12:01:43: #3 Call peaks... INFO @ Sat, 15 Sep 2018 12:01:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 12:01:50: 40000000 INFO @ Sat, 15 Sep 2018 12:01:53: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 12:01:53: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 12:01:53: #1 total tags in treatment: 40386874 INFO @ Sat, 15 Sep 2018 12:01:53: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 12:01:53: #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 12:01:54: #1 tags after filtering in treatment: 40386796 INFO @ Sat, 15 Sep 2018 12:01:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 12:01:54: #1 finished! INFO @ Sat, 15 Sep 2018 12:01:54: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 12:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 12:01:58: #2 number of paired peaks: 5746 INFO @ Sat, 15 Sep 2018 12:01:58: start model_add_line... INFO @ Sat, 15 Sep 2018 12:01:58: start X-correlation... INFO @ Sat, 15 Sep 2018 12:01:58: end of X-cor INFO @ Sat, 15 Sep 2018 12:01:58: #2 finished! INFO @ Sat, 15 Sep 2018 12:01:58: #2 predicted fragment length is 76 bps INFO @ Sat, 15 Sep 2018 12:01:58: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 15 Sep 2018 12:01:58: #2.2 Generate R script for model : SRX4014801.20_model.r WARNING @ Sat, 15 Sep 2018 12:01:58: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 12:01:58: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 15 Sep 2018 12:01:58: #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 12:01:58: #3 Call peaks... INFO @ Sat, 15 Sep 2018 12:01:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 12:02:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 12:03:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 12:03:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 12:03:50: #4 Write output xls file... SRX4014801.10_peaks.xls INFO @ Sat, 15 Sep 2018 12:03:50: #4 Write peak in narrowPeak format file... SRX4014801.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 12:03:50: #4 Write summits bed file... SRX4014801.10_summits.bed INFO @ Sat, 15 Sep 2018 12:03:50: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (1247 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 12:04:29: #4 Write output xls file... SRX4014801.05_peaks.xls INFO @ Sat, 15 Sep 2018 12:04:29: #4 Write peak in narrowPeak format file... SRX4014801.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 12:04:29: #4 Write summits bed file... SRX4014801.05_summits.bed INFO @ Sat, 15 Sep 2018 12:04:29: Done! pass1 - making usageList (65 chroms): 1 millis pass2 - checking and writing primary data (2481 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 12:05:02: #4 Write output xls file... SRX4014801.20_peaks.xls INFO @ Sat, 15 Sep 2018 12:05:02: #4 Write peak in narrowPeak format file... SRX4014801.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 12:05:02: #4 Write summits bed file... SRX4014801.20_summits.bed INFO @ Sat, 15 Sep 2018 12:05:02: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (605 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。