Job ID = 11388790 sra ファイルのダウンロード中... Completed: 1439559K bytes transferred in 21 seconds (537018K 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 48866027 spots for /home/okishinya/chipatlas/results/rn6/SRX1453554/SRR2962630.sra Written 48866027 spots for /home/okishinya/chipatlas/results/rn6/SRX1453554/SRR2962630.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:30:21 48866027 reads; of these: 48866027 (100.00%) were unpaired; of these: 1263597 (2.59%) aligned 0 times 33904923 (69.38%) aligned exactly 1 time 13697507 (28.03%) aligned >1 times 97.41% overall alignment rate Time searching: 01:30:25 Overall time: 01:30:26 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] 5043546 / 47602430 = 0.1060 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, 13 Dec 2018 00:28:19: # Command line: callpeak -t SRX1453554.bam -f BAM -g 2.15e9 -n SRX1453554.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453554.05 # format = BAM # ChIP-seq file = ['SRX1453554.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, 13 Dec 2018 00:28:19: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:28:19: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:28:19: # Command line: callpeak -t SRX1453554.bam -f BAM -g 2.15e9 -n SRX1453554.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453554.10 # format = BAM # ChIP-seq file = ['SRX1453554.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, 13 Dec 2018 00:28:19: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:28:19: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:28:19: # Command line: callpeak -t SRX1453554.bam -f BAM -g 2.15e9 -n SRX1453554.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453554.20 # format = BAM # ChIP-seq file = ['SRX1453554.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, 13 Dec 2018 00:28:19: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:28:19: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:28:31: 1000000 INFO @ Thu, 13 Dec 2018 00:28:31: 1000000 INFO @ Thu, 13 Dec 2018 00:28:31: 1000000 INFO @ Thu, 13 Dec 2018 00:28:43: 2000000 INFO @ Thu, 13 Dec 2018 00:28:44: 2000000 INFO @ Thu, 13 Dec 2018 00:28:47: 2000000 INFO @ Thu, 13 Dec 2018 00:28:55: 3000000 INFO @ Thu, 13 Dec 2018 00:28:56: 3000000 INFO @ Thu, 13 Dec 2018 00:29:05: 3000000 INFO @ Thu, 13 Dec 2018 00:29:07: 4000000 INFO @ Thu, 13 Dec 2018 00:29:08: 4000000 INFO @ Thu, 13 Dec 2018 00:29:18: 4000000 INFO @ Thu, 13 Dec 2018 00:29:18: 5000000 INFO @ Thu, 13 Dec 2018 00:29:24: 5000000 INFO @ Thu, 13 Dec 2018 00:29:27: 6000000 INFO @ Thu, 13 Dec 2018 00:29:30: 5000000 INFO @ Thu, 13 Dec 2018 00:29:37: 7000000 INFO @ Thu, 13 Dec 2018 00:29:39: 6000000 INFO @ Thu, 13 Dec 2018 00:29:44: 6000000 INFO @ Thu, 13 Dec 2018 00:29:50: 8000000 INFO @ Thu, 13 Dec 2018 00:29:56: 7000000 INFO @ Thu, 13 Dec 2018 00:29:59: 7000000 INFO @ Thu, 13 Dec 2018 00:30:03: 9000000 INFO @ Thu, 13 Dec 2018 00:30:14: 8000000 INFO @ Thu, 13 Dec 2018 00:30:15: 8000000 INFO @ Thu, 13 Dec 2018 00:30:15: 10000000 INFO @ Thu, 13 Dec 2018 00:30:28: 11000000 INFO @ Thu, 13 Dec 2018 00:30:28: 9000000 INFO @ Thu, 13 Dec 2018 00:30:33: 9000000 INFO @ Thu, 13 Dec 2018 00:30:42: 12000000 INFO @ Thu, 13 Dec 2018 00:30:43: 10000000 INFO @ Thu, 13 Dec 2018 00:30:47: 10000000 INFO @ Thu, 13 Dec 2018 00:30:56: 13000000 INFO @ Thu, 13 Dec 2018 00:30:57: 11000000 INFO @ Thu, 13 Dec 2018 00:31:01: 11000000 INFO @ Thu, 13 Dec 2018 00:31:11: 12000000 INFO @ Thu, 13 Dec 2018 00:31:11: 14000000 INFO @ Thu, 13 Dec 2018 00:31:13: 12000000 INFO @ Thu, 13 Dec 2018 00:31:23: 15000000 INFO @ Thu, 13 Dec 2018 00:31:25: 13000000 INFO @ Thu, 13 Dec 2018 00:31:26: 13000000 INFO @ Thu, 13 Dec 2018 00:31:36: 14000000 INFO @ Thu, 13 Dec 2018 00:31:37: 16000000 INFO @ Thu, 13 Dec 2018 00:31:42: 14000000 INFO @ Thu, 13 Dec 2018 00:31:46: 15000000 INFO @ Thu, 13 Dec 2018 00:31:50: 17000000 INFO @ Thu, 13 Dec 2018 00:31:56: 16000000 INFO @ Thu, 13 Dec 2018 00:31:57: 15000000 INFO @ Thu, 13 Dec 2018 00:32:05: 18000000 INFO @ Thu, 13 Dec 2018 00:32:05: 17000000 INFO @ Thu, 13 Dec 2018 00:32:14: 16000000 INFO @ Thu, 13 Dec 2018 00:32:17: 18000000 INFO @ Thu, 13 Dec 2018 00:32:20: 19000000 INFO @ Thu, 13 Dec 2018 00:32:29: 19000000 INFO @ Thu, 13 Dec 2018 00:32:30: 17000000 INFO @ Thu, 13 Dec 2018 00:32:34: 20000000 INFO @ Thu, 13 Dec 2018 00:32:42: 20000000 INFO @ Thu, 13 Dec 2018 00:32:46: 21000000 INFO @ Thu, 13 Dec 2018 00:32:49: 18000000 INFO @ Thu, 13 Dec 2018 00:32:57: 21000000 INFO @ Thu, 13 Dec 2018 00:32:58: 22000000 INFO @ Thu, 13 Dec 2018 00:33:09: 19000000 INFO @ Thu, 13 Dec 2018 00:33:09: 23000000 INFO @ Thu, 13 Dec 2018 00:33:13: 22000000 INFO @ Thu, 13 Dec 2018 00:33:21: 24000000 INFO @ Thu, 13 Dec 2018 00:33:28: 20000000 INFO @ Thu, 13 Dec 2018 00:33:29: 23000000 INFO @ Thu, 13 Dec 2018 00:33:34: 25000000 INFO @ Thu, 13 Dec 2018 00:33:42: 21000000 INFO @ Thu, 13 Dec 2018 00:33:45: 24000000 INFO @ Thu, 13 Dec 2018 00:33:47: 26000000 INFO @ Thu, 13 Dec 2018 00:33:56: 22000000 INFO @ Thu, 13 Dec 2018 00:34:01: 27000000 INFO @ Thu, 13 Dec 2018 00:34:04: 25000000 INFO @ Thu, 13 Dec 2018 00:34:10: 23000000 INFO @ Thu, 13 Dec 2018 00:34:14: 28000000 INFO @ Thu, 13 Dec 2018 00:34:21: 26000000 INFO @ Thu, 13 Dec 2018 00:34:27: 29000000 INFO @ Thu, 13 Dec 2018 00:34:28: 24000000 INFO @ Thu, 13 Dec 2018 00:34:36: 27000000 INFO @ Thu, 13 Dec 2018 00:34:41: 30000000 INFO @ Thu, 13 Dec 2018 00:34:44: 25000000 INFO @ Thu, 13 Dec 2018 00:34:53: 28000000 INFO @ Thu, 13 Dec 2018 00:34:56: 31000000 INFO @ Thu, 13 Dec 2018 00:34:58: 26000000 INFO @ Thu, 13 Dec 2018 00:35:09: 29000000 INFO @ Thu, 13 Dec 2018 00:35:10: 32000000 INFO @ Thu, 13 Dec 2018 00:35:12: 27000000 INFO @ Thu, 13 Dec 2018 00:35:24: 33000000 INFO @ Thu, 13 Dec 2018 00:35:25: 30000000 INFO @ Thu, 13 Dec 2018 00:35:32: 28000000 INFO @ Thu, 13 Dec 2018 00:35:39: 34000000 INFO @ Thu, 13 Dec 2018 00:35:41: 31000000 INFO @ Thu, 13 Dec 2018 00:35:47: 29000000 INFO @ Thu, 13 Dec 2018 00:35:57: 35000000 INFO @ Thu, 13 Dec 2018 00:35:59: 32000000 INFO @ Thu, 13 Dec 2018 00:36:03: 30000000 INFO @ Thu, 13 Dec 2018 00:36:14: 33000000 INFO @ Thu, 13 Dec 2018 00:36:14: 36000000 INFO @ Thu, 13 Dec 2018 00:36:19: 31000000 INFO @ Thu, 13 Dec 2018 00:36:28: 34000000 INFO @ Thu, 13 Dec 2018 00:36:32: 32000000 INFO @ Thu, 13 Dec 2018 00:36:32: 37000000 INFO @ Thu, 13 Dec 2018 00:36:43: 35000000 INFO @ Thu, 13 Dec 2018 00:36:45: 33000000 INFO @ Thu, 13 Dec 2018 00:36:52: 38000000 INFO @ Thu, 13 Dec 2018 00:36:56: 36000000 INFO @ Thu, 13 Dec 2018 00:36:59: 34000000 INFO @ Thu, 13 Dec 2018 00:37:06: 39000000 INFO @ Thu, 13 Dec 2018 00:37:07: 37000000 INFO @ Thu, 13 Dec 2018 00:37:12: 35000000 INFO @ Thu, 13 Dec 2018 00:37:18: 40000000 INFO @ Thu, 13 Dec 2018 00:37:18: 38000000 INFO @ Thu, 13 Dec 2018 00:37:26: 36000000 INFO @ Thu, 13 Dec 2018 00:37:30: 41000000 INFO @ Thu, 13 Dec 2018 00:37:32: 39000000 INFO @ Thu, 13 Dec 2018 00:37:39: 37000000 INFO @ Thu, 13 Dec 2018 00:37:41: 42000000 INFO @ Thu, 13 Dec 2018 00:37:48: 40000000 INFO @ Thu, 13 Dec 2018 00:37:48: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 00:37:48: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 00:37:48: #1 total tags in treatment: 42558884 INFO @ Thu, 13 Dec 2018 00:37:48: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:37:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:37:50: #1 tags after filtering in treatment: 42558828 INFO @ Thu, 13 Dec 2018 00:37:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 00:37:50: #1 finished! INFO @ Thu, 13 Dec 2018 00:37:50: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:37:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:37:53: 38000000 INFO @ Thu, 13 Dec 2018 00:37:55: #2 number of paired peaks: 4772 INFO @ Thu, 13 Dec 2018 00:37:55: start model_add_line... INFO @ Thu, 13 Dec 2018 00:37:55: start X-correlation... INFO @ Thu, 13 Dec 2018 00:37:55: end of X-cor INFO @ Thu, 13 Dec 2018 00:37:55: #2 finished! INFO @ Thu, 13 Dec 2018 00:37:55: #2 predicted fragment length is 51 bps INFO @ Thu, 13 Dec 2018 00:37:55: #2 alternative fragment length(s) may be 51,206 bps INFO @ Thu, 13 Dec 2018 00:37:55: #2.2 Generate R script for model : SRX1453554.20_model.r WARNING @ Thu, 13 Dec 2018 00:37:55: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 00:37:55: #2 You may need to consider one of the other alternative d(s): 51,206 WARNING @ Thu, 13 Dec 2018 00:37:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 00:37:55: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:37:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:38:04: 41000000 INFO @ Thu, 13 Dec 2018 00:38:07: 39000000 INFO @ Thu, 13 Dec 2018 00:38:19: 42000000 INFO @ Thu, 13 Dec 2018 00:38:24: 40000000 INFO @ Thu, 13 Dec 2018 00:38:28: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 00:38:28: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 00:38:28: #1 total tags in treatment: 42558884 INFO @ Thu, 13 Dec 2018 00:38:28: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:38:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:38:30: #1 tags after filtering in treatment: 42558828 INFO @ Thu, 13 Dec 2018 00:38:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 00:38:30: #1 finished! INFO @ Thu, 13 Dec 2018 00:38:30: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:38:35: #2 number of paired peaks: 4772 INFO @ Thu, 13 Dec 2018 00:38:35: start model_add_line... INFO @ Thu, 13 Dec 2018 00:38:36: start X-correlation... INFO @ Thu, 13 Dec 2018 00:38:36: end of X-cor INFO @ Thu, 13 Dec 2018 00:38:36: #2 finished! INFO @ Thu, 13 Dec 2018 00:38:36: #2 predicted fragment length is 51 bps INFO @ Thu, 13 Dec 2018 00:38:36: #2 alternative fragment length(s) may be 51,206 bps INFO @ Thu, 13 Dec 2018 00:38:36: #2.2 Generate R script for model : SRX1453554.10_model.r WARNING @ Thu, 13 Dec 2018 00:38:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 00:38:36: #2 You may need to consider one of the other alternative d(s): 51,206 WARNING @ Thu, 13 Dec 2018 00:38:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 00:38:36: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:38:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:38:40: 41000000 INFO @ Thu, 13 Dec 2018 00:38:57: 42000000 INFO @ Thu, 13 Dec 2018 00:39:09: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 00:39:09: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 00:39:09: #1 total tags in treatment: 42558884 INFO @ Thu, 13 Dec 2018 00:39:09: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:39:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:39:11: #1 tags after filtering in treatment: 42558828 INFO @ Thu, 13 Dec 2018 00:39:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 00:39:11: #1 finished! INFO @ Thu, 13 Dec 2018 00:39:11: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:39:16: #2 number of paired peaks: 4772 INFO @ Thu, 13 Dec 2018 00:39:16: start model_add_line... INFO @ Thu, 13 Dec 2018 00:39:16: start X-correlation... INFO @ Thu, 13 Dec 2018 00:39:16: end of X-cor INFO @ Thu, 13 Dec 2018 00:39:16: #2 finished! INFO @ Thu, 13 Dec 2018 00:39:16: #2 predicted fragment length is 51 bps INFO @ Thu, 13 Dec 2018 00:39:16: #2 alternative fragment length(s) may be 51,206 bps INFO @ Thu, 13 Dec 2018 00:39:16: #2.2 Generate R script for model : SRX1453554.05_model.r WARNING @ Thu, 13 Dec 2018 00:39:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 00:39:16: #2 You may need to consider one of the other alternative d(s): 51,206 WARNING @ Thu, 13 Dec 2018 00:39:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 00:39:16: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:39:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:40:03: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:40:43: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:41:12: #4 Write output xls file... SRX1453554.20_peaks.xls INFO @ Thu, 13 Dec 2018 00:41:12: #4 Write peak in narrowPeak format file... SRX1453554.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:41:12: #4 Write summits bed file... SRX1453554.20_summits.bed INFO @ Thu, 13 Dec 2018 00:41:12: Done! pass1 - making usageList (40 chroms): 5 millis pass2 - checking and writing primary data (675 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 00:41:22: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:41:59: #4 Write output xls file... SRX1453554.10_peaks.xls INFO @ Thu, 13 Dec 2018 00:41:59: #4 Write peak in narrowPeak format file... SRX1453554.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:41:59: #4 Write summits bed file... SRX1453554.10_summits.bed INFO @ Thu, 13 Dec 2018 00:41:59: Done! pass1 - making usageList (50 chroms): 3 millis pass2 - checking and writing primary data (1363 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 00:42:33: #4 Write output xls file... SRX1453554.05_peaks.xls INFO @ Thu, 13 Dec 2018 00:42:33: #4 Write peak in narrowPeak format file... SRX1453554.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:42:33: #4 Write summits bed file... SRX1453554.05_summits.bed INFO @ Thu, 13 Dec 2018 00:42:33: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (2357 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。