Job ID = 2003484 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 75,806,276 reads read : 75,806,276 reads written : 75,806,276 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:10 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:34:07 75806276 reads; of these: 75806276 (100.00%) were unpaired; of these: 22323230 (29.45%) aligned 0 times 30239098 (39.89%) aligned exactly 1 time 23243948 (30.66%) aligned >1 times 70.55% overall alignment rate Time searching: 01:34:20 Overall time: 01:34:22 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] 4845990 / 53483046 = 0.0906 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 @ Fri, 05 Jul 2019 15:54:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.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 @ Fri, 05 Jul 2019 15:54:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:54:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.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 @ Fri, 05 Jul 2019 15:54:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:54:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:54:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.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 @ Fri, 05 Jul 2019 15:54:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:54:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:54:38: 1000000 INFO @ Fri, 05 Jul 2019 15:54:39: 1000000 INFO @ Fri, 05 Jul 2019 15:54:40: 1000000 INFO @ Fri, 05 Jul 2019 15:54:50: 2000000 INFO @ Fri, 05 Jul 2019 15:54:50: 2000000 INFO @ Fri, 05 Jul 2019 15:54:52: 2000000 INFO @ Fri, 05 Jul 2019 15:55:01: 3000000 INFO @ Fri, 05 Jul 2019 15:55:02: 3000000 INFO @ Fri, 05 Jul 2019 15:55:03: 3000000 INFO @ Fri, 05 Jul 2019 15:55:11: 4000000 INFO @ Fri, 05 Jul 2019 15:55:13: 4000000 INFO @ Fri, 05 Jul 2019 15:55:13: 4000000 INFO @ Fri, 05 Jul 2019 15:55:21: 5000000 INFO @ Fri, 05 Jul 2019 15:55:24: 5000000 INFO @ Fri, 05 Jul 2019 15:55:25: 5000000 INFO @ Fri, 05 Jul 2019 15:55:31: 6000000 INFO @ Fri, 05 Jul 2019 15:55:36: 6000000 INFO @ Fri, 05 Jul 2019 15:55:36: 6000000 INFO @ Fri, 05 Jul 2019 15:55:40: 7000000 INFO @ Fri, 05 Jul 2019 15:55:47: 7000000 INFO @ Fri, 05 Jul 2019 15:55:48: 7000000 INFO @ Fri, 05 Jul 2019 15:55:50: 8000000 INFO @ Fri, 05 Jul 2019 15:55:58: 8000000 INFO @ Fri, 05 Jul 2019 15:55:59: 8000000 INFO @ Fri, 05 Jul 2019 15:55:59: 9000000 INFO @ Fri, 05 Jul 2019 15:56:09: 10000000 INFO @ Fri, 05 Jul 2019 15:56:10: 9000000 INFO @ Fri, 05 Jul 2019 15:56:10: 9000000 INFO @ Fri, 05 Jul 2019 15:56:18: 11000000 INFO @ Fri, 05 Jul 2019 15:56:21: 10000000 INFO @ Fri, 05 Jul 2019 15:56:21: 10000000 INFO @ Fri, 05 Jul 2019 15:56:27: 12000000 INFO @ Fri, 05 Jul 2019 15:56:32: 11000000 INFO @ Fri, 05 Jul 2019 15:56:32: 11000000 INFO @ Fri, 05 Jul 2019 15:56:36: 13000000 INFO @ Fri, 05 Jul 2019 15:56:43: 12000000 INFO @ Fri, 05 Jul 2019 15:56:43: 12000000 INFO @ Fri, 05 Jul 2019 15:56:46: 14000000 INFO @ Fri, 05 Jul 2019 15:56:54: 13000000 INFO @ Fri, 05 Jul 2019 15:56:54: 13000000 INFO @ Fri, 05 Jul 2019 15:56:55: 15000000 INFO @ Fri, 05 Jul 2019 15:57:05: 16000000 INFO @ Fri, 05 Jul 2019 15:57:05: 14000000 INFO @ Fri, 05 Jul 2019 15:57:06: 14000000 INFO @ Fri, 05 Jul 2019 15:57:14: 17000000 INFO @ Fri, 05 Jul 2019 15:57:16: 15000000 INFO @ Fri, 05 Jul 2019 15:57:17: 15000000 INFO @ Fri, 05 Jul 2019 15:57:23: 18000000 INFO @ Fri, 05 Jul 2019 15:57:27: 16000000 INFO @ Fri, 05 Jul 2019 15:57:28: 16000000 INFO @ Fri, 05 Jul 2019 15:57:33: 19000000 INFO @ Fri, 05 Jul 2019 15:57:41: 17000000 INFO @ Fri, 05 Jul 2019 15:57:41: 17000000 INFO @ Fri, 05 Jul 2019 15:57:42: 20000000 INFO @ Fri, 05 Jul 2019 15:57:59: 21000000 INFO @ Fri, 05 Jul 2019 15:58:00: 18000000 INFO @ Fri, 05 Jul 2019 15:58:00: 18000000 INFO @ Fri, 05 Jul 2019 15:58:09: 22000000 INFO @ Fri, 05 Jul 2019 15:58:11: 19000000 INFO @ Fri, 05 Jul 2019 15:58:11: 19000000 INFO @ Fri, 05 Jul 2019 15:58:20: 23000000 INFO @ Fri, 05 Jul 2019 15:58:22: 20000000 INFO @ Fri, 05 Jul 2019 15:58:22: 20000000 INFO @ Fri, 05 Jul 2019 15:58:29: 24000000 INFO @ Fri, 05 Jul 2019 15:58:33: 21000000 INFO @ Fri, 05 Jul 2019 15:58:34: 21000000 INFO @ Fri, 05 Jul 2019 15:58:46: 25000000 INFO @ Fri, 05 Jul 2019 15:58:51: 22000000 INFO @ Fri, 05 Jul 2019 15:58:52: 22000000 INFO @ Fri, 05 Jul 2019 15:58:55: 26000000 INFO @ Fri, 05 Jul 2019 15:59:02: 23000000 INFO @ Fri, 05 Jul 2019 15:59:03: 23000000 INFO @ Fri, 05 Jul 2019 15:59:06: 27000000 INFO @ Fri, 05 Jul 2019 15:59:13: 24000000 INFO @ Fri, 05 Jul 2019 15:59:15: 24000000 INFO @ Fri, 05 Jul 2019 15:59:15: 28000000 INFO @ Fri, 05 Jul 2019 15:59:25: 25000000 INFO @ Fri, 05 Jul 2019 15:59:25: 29000000 INFO @ Fri, 05 Jul 2019 15:59:26: 25000000 INFO @ Fri, 05 Jul 2019 15:59:34: 30000000 INFO @ Fri, 05 Jul 2019 15:59:36: 26000000 INFO @ Fri, 05 Jul 2019 15:59:37: 26000000 INFO @ Fri, 05 Jul 2019 15:59:44: 31000000 INFO @ Fri, 05 Jul 2019 15:59:47: 27000000 INFO @ Fri, 05 Jul 2019 15:59:48: 27000000 INFO @ Fri, 05 Jul 2019 15:59:53: 32000000 INFO @ Fri, 05 Jul 2019 15:59:58: 28000000 INFO @ Fri, 05 Jul 2019 16:00:00: 28000000 INFO @ Fri, 05 Jul 2019 16:00:03: 33000000 INFO @ Fri, 05 Jul 2019 16:00:10: 29000000 INFO @ Fri, 05 Jul 2019 16:00:11: 29000000 INFO @ Fri, 05 Jul 2019 16:00:13: 34000000 INFO @ Fri, 05 Jul 2019 16:00:21: 30000000 INFO @ Fri, 05 Jul 2019 16:00:22: 30000000 INFO @ Fri, 05 Jul 2019 16:00:22: 35000000 INFO @ Fri, 05 Jul 2019 16:00:32: 31000000 INFO @ Fri, 05 Jul 2019 16:00:32: 36000000 INFO @ Fri, 05 Jul 2019 16:00:33: 31000000 INFO @ Fri, 05 Jul 2019 16:00:44: 37000000 INFO @ Fri, 05 Jul 2019 16:00:46: 32000000 INFO @ Fri, 05 Jul 2019 16:00:46: 32000000 INFO @ Fri, 05 Jul 2019 16:00:54: 38000000 INFO @ Fri, 05 Jul 2019 16:00:56: 33000000 INFO @ Fri, 05 Jul 2019 16:00:58: 33000000 INFO @ Fri, 05 Jul 2019 16:01:03: 39000000 INFO @ Fri, 05 Jul 2019 16:01:06: 34000000 INFO @ Fri, 05 Jul 2019 16:01:10: 34000000 INFO @ Fri, 05 Jul 2019 16:01:12: 40000000 INFO @ Fri, 05 Jul 2019 16:01:16: 35000000 INFO @ Fri, 05 Jul 2019 16:01:22: 41000000 INFO @ Fri, 05 Jul 2019 16:01:22: 35000000 INFO @ Fri, 05 Jul 2019 16:01:26: 36000000 INFO @ Fri, 05 Jul 2019 16:01:31: 42000000 INFO @ Fri, 05 Jul 2019 16:01:34: 36000000 INFO @ Fri, 05 Jul 2019 16:01:36: 37000000 INFO @ Fri, 05 Jul 2019 16:01:40: 43000000 INFO @ Fri, 05 Jul 2019 16:01:45: 38000000 INFO @ Fri, 05 Jul 2019 16:01:46: 37000000 INFO @ Fri, 05 Jul 2019 16:01:50: 44000000 INFO @ Fri, 05 Jul 2019 16:01:55: 39000000 INFO @ Fri, 05 Jul 2019 16:01:57: 38000000 INFO @ Fri, 05 Jul 2019 16:01:59: 45000000 INFO @ Fri, 05 Jul 2019 16:02:04: 40000000 INFO @ Fri, 05 Jul 2019 16:02:08: 39000000 INFO @ Fri, 05 Jul 2019 16:02:08: 46000000 INFO @ Fri, 05 Jul 2019 16:02:14: 41000000 INFO @ Fri, 05 Jul 2019 16:02:18: 47000000 INFO @ Fri, 05 Jul 2019 16:02:20: 40000000 INFO @ Fri, 05 Jul 2019 16:02:24: 42000000 INFO @ Fri, 05 Jul 2019 16:02:28: 48000000 INFO @ Fri, 05 Jul 2019 16:02:31: 41000000 INFO @ Fri, 05 Jul 2019 16:02:33: 43000000 INFO @ Fri, 05 Jul 2019 16:02:34: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 16:02:34: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 16:02:34: #1 total tags in treatment: 48637056 INFO @ Fri, 05 Jul 2019 16:02:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:02:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:02:35: #1 tags after filtering in treatment: 48636975 INFO @ Fri, 05 Jul 2019 16:02:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:02:35: #1 finished! INFO @ Fri, 05 Jul 2019 16:02:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:02:42: 42000000 INFO @ Fri, 05 Jul 2019 16:02:42: #2 number of paired peaks: 24114 INFO @ Fri, 05 Jul 2019 16:02:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:02:43: 44000000 INFO @ Fri, 05 Jul 2019 16:02:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:02:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:02:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:02:43: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 16:02:43: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 05 Jul 2019 16:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.10_model.r WARNING @ Fri, 05 Jul 2019 16:02:43: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:02:43: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 05 Jul 2019 16:02:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:02:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:02:52: 45000000 INFO @ Fri, 05 Jul 2019 16:02:54: 43000000 INFO @ Fri, 05 Jul 2019 16:03:02: 46000000 INFO @ Fri, 05 Jul 2019 16:03:05: 44000000 INFO @ Fri, 05 Jul 2019 16:03:11: 47000000 INFO @ Fri, 05 Jul 2019 16:03:16: 45000000 INFO @ Fri, 05 Jul 2019 16:03:21: 48000000 INFO @ Fri, 05 Jul 2019 16:03:27: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 16:03:28: 46000000 INFO @ Fri, 05 Jul 2019 16:03:28: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 16:03:28: #1 total tags in treatment: 48637056 INFO @ Fri, 05 Jul 2019 16:03:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:03:30: #1 tags after filtering in treatment: 48636975 INFO @ Fri, 05 Jul 2019 16:03:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:30: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:37: #2 number of paired peaks: 24114 INFO @ Fri, 05 Jul 2019 16:03:37: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:37: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:37: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:37: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:37: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 16:03:37: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 05 Jul 2019 16:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.20_model.r WARNING @ Fri, 05 Jul 2019 16:03:37: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:03:37: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 05 Jul 2019 16:03:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:03:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:03:39: 47000000 INFO @ Fri, 05 Jul 2019 16:03:51: 48000000 INFO @ Fri, 05 Jul 2019 16:03:58: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 16:03:58: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 16:03:58: #1 total tags in treatment: 48637056 INFO @ Fri, 05 Jul 2019 16:03:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:03:59: #1 tags after filtering in treatment: 48636975 INFO @ Fri, 05 Jul 2019 16:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:59: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:04:06: #2 number of paired peaks: 24114 INFO @ Fri, 05 Jul 2019 16:04:06: start model_add_line... INFO @ Fri, 05 Jul 2019 16:04:07: start X-correlation... INFO @ Fri, 05 Jul 2019 16:04:07: end of X-cor INFO @ Fri, 05 Jul 2019 16:04:07: #2 finished! INFO @ Fri, 05 Jul 2019 16:04:07: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 16:04:07: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 05 Jul 2019 16:04:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.05_model.r WARNING @ Fri, 05 Jul 2019 16:04:07: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:04:07: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 05 Jul 2019 16:04:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:04:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:04:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:05:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:06:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:06:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.10_summits.bed INFO @ Fri, 05 Jul 2019 16:06:41: Done! pass1 - making usageList (93 chroms): 3 millis pass2 - checking and writing primary data (6031 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.20_summits.bed INFO @ Fri, 05 Jul 2019 16:07:19: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (1645 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:07:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX189937/SRX189937.05_summits.bed INFO @ Fri, 05 Jul 2019 16:07:49: Done! pass1 - making usageList (131 chroms): 9 millis pass2 - checking and writing primary data (19576 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。