Job ID = 2003700 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 82,126,863 reads read : 164,253,726 reads written : 82,126,863 reads 0-length : 82,126,863 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:34:21 82126863 reads; of these: 82126863 (100.00%) were unpaired; of these: 3253879 (3.96%) aligned 0 times 55610117 (67.71%) aligned exactly 1 time 23262867 (28.33%) aligned >1 times 96.04% overall alignment rate Time searching: 01:34:27 Overall time: 01:34:28 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 36 files... [bam_rmdupse_core] 31681565 / 78872984 = 0.4017 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 16:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.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 16:54:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:54:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.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 16:54:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:54:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.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 16:54:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:54:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:45: 1000000 INFO @ Fri, 05 Jul 2019 16:54:46: 1000000 INFO @ Fri, 05 Jul 2019 16:54:46: 1000000 INFO @ Fri, 05 Jul 2019 16:54:53: 2000000 INFO @ Fri, 05 Jul 2019 16:54:54: 2000000 INFO @ Fri, 05 Jul 2019 16:54:54: 2000000 INFO @ Fri, 05 Jul 2019 16:55:00: 3000000 INFO @ Fri, 05 Jul 2019 16:55:01: 3000000 INFO @ Fri, 05 Jul 2019 16:55:02: 3000000 INFO @ Fri, 05 Jul 2019 16:55:08: 4000000 INFO @ Fri, 05 Jul 2019 16:55:09: 4000000 INFO @ Fri, 05 Jul 2019 16:55:10: 4000000 INFO @ Fri, 05 Jul 2019 16:55:16: 5000000 INFO @ Fri, 05 Jul 2019 16:55:18: 5000000 INFO @ Fri, 05 Jul 2019 16:55:19: 5000000 INFO @ Fri, 05 Jul 2019 16:55:24: 6000000 INFO @ Fri, 05 Jul 2019 16:55:27: 6000000 INFO @ Fri, 05 Jul 2019 16:55:27: 6000000 INFO @ Fri, 05 Jul 2019 16:55:31: 7000000 INFO @ Fri, 05 Jul 2019 16:55:35: 7000000 INFO @ Fri, 05 Jul 2019 16:55:37: 7000000 INFO @ Fri, 05 Jul 2019 16:55:39: 8000000 INFO @ Fri, 05 Jul 2019 16:55:43: 8000000 INFO @ Fri, 05 Jul 2019 16:55:46: 9000000 INFO @ Fri, 05 Jul 2019 16:55:46: 8000000 INFO @ Fri, 05 Jul 2019 16:55:54: 10000000 INFO @ Fri, 05 Jul 2019 16:55:54: 9000000 INFO @ Fri, 05 Jul 2019 16:55:56: 9000000 INFO @ Fri, 05 Jul 2019 16:56:01: 11000000 INFO @ Fri, 05 Jul 2019 16:56:02: 10000000 INFO @ Fri, 05 Jul 2019 16:56:05: 10000000 INFO @ Fri, 05 Jul 2019 16:56:09: 12000000 INFO @ Fri, 05 Jul 2019 16:56:10: 11000000 INFO @ Fri, 05 Jul 2019 16:56:15: 11000000 INFO @ Fri, 05 Jul 2019 16:56:16: 13000000 INFO @ Fri, 05 Jul 2019 16:56:19: 12000000 INFO @ Fri, 05 Jul 2019 16:56:24: 14000000 INFO @ Fri, 05 Jul 2019 16:56:24: 12000000 INFO @ Fri, 05 Jul 2019 16:56:27: 13000000 INFO @ Fri, 05 Jul 2019 16:56:31: 15000000 INFO @ Fri, 05 Jul 2019 16:56:33: 13000000 INFO @ Fri, 05 Jul 2019 16:56:35: 14000000 INFO @ Fri, 05 Jul 2019 16:56:39: 16000000 INFO @ Fri, 05 Jul 2019 16:56:42: 15000000 INFO @ Fri, 05 Jul 2019 16:56:43: 14000000 INFO @ Fri, 05 Jul 2019 16:56:46: 17000000 INFO @ Fri, 05 Jul 2019 16:56:50: 16000000 INFO @ Fri, 05 Jul 2019 16:56:52: 15000000 INFO @ Fri, 05 Jul 2019 16:56:54: 18000000 INFO @ Fri, 05 Jul 2019 16:56:58: 17000000 INFO @ Fri, 05 Jul 2019 16:57:01: 16000000 INFO @ Fri, 05 Jul 2019 16:57:04: 19000000 INFO @ Fri, 05 Jul 2019 16:57:06: 18000000 INFO @ Fri, 05 Jul 2019 16:57:10: 17000000 INFO @ Fri, 05 Jul 2019 16:57:12: 20000000 INFO @ Fri, 05 Jul 2019 16:57:14: 19000000 INFO @ Fri, 05 Jul 2019 16:57:19: 18000000 INFO @ Fri, 05 Jul 2019 16:57:20: 21000000 INFO @ Fri, 05 Jul 2019 16:57:22: 20000000 INFO @ Fri, 05 Jul 2019 16:57:28: 22000000 INFO @ Fri, 05 Jul 2019 16:57:29: 19000000 INFO @ Fri, 05 Jul 2019 16:57:31: 21000000 INFO @ Fri, 05 Jul 2019 16:57:38: 23000000 INFO @ Fri, 05 Jul 2019 16:57:39: 22000000 INFO @ Fri, 05 Jul 2019 16:57:39: 20000000 INFO @ Fri, 05 Jul 2019 16:57:46: 24000000 INFO @ Fri, 05 Jul 2019 16:57:46: 23000000 INFO @ Fri, 05 Jul 2019 16:57:49: 21000000 INFO @ Fri, 05 Jul 2019 16:57:53: 25000000 INFO @ Fri, 05 Jul 2019 16:57:54: 24000000 INFO @ Fri, 05 Jul 2019 16:57:58: 22000000 INFO @ Fri, 05 Jul 2019 16:58:01: 26000000 INFO @ Fri, 05 Jul 2019 16:58:02: 25000000 INFO @ Fri, 05 Jul 2019 16:58:08: 23000000 INFO @ Fri, 05 Jul 2019 16:58:09: 27000000 INFO @ Fri, 05 Jul 2019 16:58:10: 26000000 INFO @ Fri, 05 Jul 2019 16:58:16: 28000000 INFO @ Fri, 05 Jul 2019 16:58:17: 24000000 INFO @ Fri, 05 Jul 2019 16:58:18: 27000000 INFO @ Fri, 05 Jul 2019 16:58:24: 29000000 INFO @ Fri, 05 Jul 2019 16:58:26: 25000000 INFO @ Fri, 05 Jul 2019 16:58:26: 28000000 INFO @ Fri, 05 Jul 2019 16:58:32: 30000000 INFO @ Fri, 05 Jul 2019 16:58:34: 29000000 INFO @ Fri, 05 Jul 2019 16:58:35: 26000000 INFO @ Fri, 05 Jul 2019 16:58:39: 31000000 INFO @ Fri, 05 Jul 2019 16:58:42: 30000000 INFO @ Fri, 05 Jul 2019 16:58:44: 27000000 INFO @ Fri, 05 Jul 2019 16:58:46: 32000000 INFO @ Fri, 05 Jul 2019 16:58:50: 31000000 INFO @ Fri, 05 Jul 2019 16:58:53: 28000000 INFO @ Fri, 05 Jul 2019 16:58:54: 33000000 INFO @ Fri, 05 Jul 2019 16:58:57: 32000000 INFO @ Fri, 05 Jul 2019 16:59:01: 34000000 INFO @ Fri, 05 Jul 2019 16:59:01: 29000000 INFO @ Fri, 05 Jul 2019 16:59:05: 33000000 INFO @ Fri, 05 Jul 2019 16:59:08: 35000000 INFO @ Fri, 05 Jul 2019 16:59:10: 30000000 INFO @ Fri, 05 Jul 2019 16:59:13: 34000000 INFO @ Fri, 05 Jul 2019 16:59:16: 36000000 INFO @ Fri, 05 Jul 2019 16:59:19: 31000000 INFO @ Fri, 05 Jul 2019 16:59:21: 35000000 INFO @ Fri, 05 Jul 2019 16:59:23: 37000000 INFO @ Fri, 05 Jul 2019 16:59:28: 32000000 INFO @ Fri, 05 Jul 2019 16:59:29: 36000000 INFO @ Fri, 05 Jul 2019 16:59:31: 38000000 INFO @ Fri, 05 Jul 2019 16:59:37: 37000000 INFO @ Fri, 05 Jul 2019 16:59:37: 33000000 INFO @ Fri, 05 Jul 2019 16:59:38: 39000000 INFO @ Fri, 05 Jul 2019 16:59:45: 38000000 INFO @ Fri, 05 Jul 2019 16:59:45: 40000000 INFO @ Fri, 05 Jul 2019 16:59:46: 34000000 INFO @ Fri, 05 Jul 2019 16:59:52: 39000000 INFO @ Fri, 05 Jul 2019 16:59:53: 41000000 INFO @ Fri, 05 Jul 2019 16:59:55: 35000000 INFO @ Fri, 05 Jul 2019 17:00:00: 42000000 INFO @ Fri, 05 Jul 2019 17:00:00: 40000000 INFO @ Fri, 05 Jul 2019 17:00:04: 36000000 INFO @ Fri, 05 Jul 2019 17:00:07: 43000000 INFO @ Fri, 05 Jul 2019 17:00:08: 41000000 INFO @ Fri, 05 Jul 2019 17:00:13: 37000000 INFO @ Fri, 05 Jul 2019 17:00:15: 44000000 INFO @ Fri, 05 Jul 2019 17:00:16: 42000000 INFO @ Fri, 05 Jul 2019 17:00:22: 38000000 INFO @ Fri, 05 Jul 2019 17:00:22: 45000000 INFO @ Fri, 05 Jul 2019 17:00:24: 43000000 INFO @ Fri, 05 Jul 2019 17:00:30: 46000000 INFO @ Fri, 05 Jul 2019 17:00:31: 39000000 INFO @ Fri, 05 Jul 2019 17:00:32: 44000000 INFO @ Fri, 05 Jul 2019 17:00:37: 47000000 INFO @ Fri, 05 Jul 2019 17:00:39: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 17:00:39: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 17:00:39: #1 total tags in treatment: 47191419 INFO @ Fri, 05 Jul 2019 17:00:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:00:39: #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 17:00:40: 45000000 INFO @ Fri, 05 Jul 2019 17:00:40: 40000000 INFO @ Fri, 05 Jul 2019 17:00:40: #1 tags after filtering in treatment: 47191371 INFO @ Fri, 05 Jul 2019 17:00:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 17:00:40: #1 finished! INFO @ Fri, 05 Jul 2019 17:00:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:00:46: #2 number of paired peaks: 11060 INFO @ Fri, 05 Jul 2019 17:00:46: start model_add_line... INFO @ Fri, 05 Jul 2019 17:00:46: start X-correlation... INFO @ Fri, 05 Jul 2019 17:00:46: end of X-cor INFO @ Fri, 05 Jul 2019 17:00:46: #2 finished! INFO @ Fri, 05 Jul 2019 17:00:46: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 17:00:46: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 05 Jul 2019 17:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.20_model.r WARNING @ Fri, 05 Jul 2019 17:00:46: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:00:46: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 05 Jul 2019 17:00:46: #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 17:00:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:00:47: 46000000 INFO @ Fri, 05 Jul 2019 17:00:49: 41000000 INFO @ Fri, 05 Jul 2019 17:00:55: 47000000 INFO @ Fri, 05 Jul 2019 17:00:57: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 17:00:57: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 17:00:57: #1 total tags in treatment: 47191419 INFO @ Fri, 05 Jul 2019 17:00:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:00:57: #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 17:00:58: 42000000 INFO @ Fri, 05 Jul 2019 17:00:58: #1 tags after filtering in treatment: 47191371 INFO @ Fri, 05 Jul 2019 17:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 17:00:59: #1 finished! INFO @ Fri, 05 Jul 2019 17:00:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:01:05: #2 number of paired peaks: 11060 INFO @ Fri, 05 Jul 2019 17:01:05: start model_add_line... INFO @ Fri, 05 Jul 2019 17:01:05: start X-correlation... INFO @ Fri, 05 Jul 2019 17:01:05: end of X-cor INFO @ Fri, 05 Jul 2019 17:01:05: #2 finished! INFO @ Fri, 05 Jul 2019 17:01:05: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 17:01:05: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 05 Jul 2019 17:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.05_model.r WARNING @ Fri, 05 Jul 2019 17:01:05: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:01:05: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 05 Jul 2019 17:01:05: #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 17:01:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:01:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:01:08: 43000000 INFO @ Fri, 05 Jul 2019 17:01:17: 44000000 INFO @ Fri, 05 Jul 2019 17:01:26: 45000000 INFO @ Fri, 05 Jul 2019 17:01:35: 46000000 INFO @ Fri, 05 Jul 2019 17:01:44: 47000000 INFO @ Fri, 05 Jul 2019 17:01:46: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 17:01:46: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 17:01:46: #1 total tags in treatment: 47191419 INFO @ Fri, 05 Jul 2019 17:01:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:01:46: #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 17:01:47: #1 tags after filtering in treatment: 47191371 INFO @ Fri, 05 Jul 2019 17:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 17:01:47: #1 finished! INFO @ Fri, 05 Jul 2019 17:01:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:01:53: #2 number of paired peaks: 11060 INFO @ Fri, 05 Jul 2019 17:01:53: start model_add_line... INFO @ Fri, 05 Jul 2019 17:01:53: start X-correlation... INFO @ Fri, 05 Jul 2019 17:01:53: end of X-cor INFO @ Fri, 05 Jul 2019 17:01:53: #2 finished! INFO @ Fri, 05 Jul 2019 17:01:53: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 17:01:53: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 05 Jul 2019 17:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.10_model.r WARNING @ Fri, 05 Jul 2019 17:01:53: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:01:53: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 05 Jul 2019 17:01:53: #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 17:01:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:03:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:03:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:04:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.20_summits.bed INFO @ Fri, 05 Jul 2019 17:04:35: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (817 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.05_summits.bed INFO @ Fri, 05 Jul 2019 17:04:50: Done! pass1 - making usageList (102 chroms): 5 millis pass2 - checking and writing primary data (7721 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:05:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:05:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:05:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370839/SRX4370839.10_summits.bed INFO @ Fri, 05 Jul 2019 17:05:49: Done! pass1 - making usageList (64 chroms): 2 millis pass2 - checking and writing primary data (2157 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。