Job ID = 3805920 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,832,062 reads read : 67,664,124 reads written : 33,832,062 reads 0-length : 33,832,062 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: 00:00:04 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:49:20 33832062 reads; of these: 33832062 (100.00%) were unpaired; of these: 1430246 (4.23%) aligned 0 times 24334685 (71.93%) aligned exactly 1 time 8067131 (23.84%) aligned >1 times 95.77% overall alignment rate Time searching: 00:49:26 Overall time: 00:49:26 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 16 files... [bam_rmdupse_core] 1962363 / 32401816 = 0.0606 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Mon, 04 Nov 2019 03:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.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 @ Mon, 04 Nov 2019 03:11:34: #1 read tag files... INFO @ Mon, 04 Nov 2019 03:11:34: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 03:11:45: 1000000 INFO @ Mon, 04 Nov 2019 03:11:56: 2000000 INFO @ Mon, 04 Nov 2019 03:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.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 @ Mon, 04 Nov 2019 03:12:04: #1 read tag files... INFO @ Mon, 04 Nov 2019 03:12:04: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 03:12:07: 3000000 INFO @ Mon, 04 Nov 2019 03:12:16: 1000000 INFO @ Mon, 04 Nov 2019 03:12:18: 4000000 INFO @ Mon, 04 Nov 2019 03:12:27: 2000000 INFO @ Mon, 04 Nov 2019 03:12:29: 5000000 BedGraph に変換中... INFO @ Mon, 04 Nov 2019 03:12:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.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 @ Mon, 04 Nov 2019 03:12:34: #1 read tag files... INFO @ Mon, 04 Nov 2019 03:12:34: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 03:12:40: 3000000 INFO @ Mon, 04 Nov 2019 03:12:40: 6000000 INFO @ Mon, 04 Nov 2019 03:12:47: 1000000 INFO @ Mon, 04 Nov 2019 03:12:51: 7000000 INFO @ Mon, 04 Nov 2019 03:12:53: 4000000 INFO @ Mon, 04 Nov 2019 03:13:00: 2000000 INFO @ Mon, 04 Nov 2019 03:13:02: 8000000 INFO @ Mon, 04 Nov 2019 03:13:04: 5000000 INFO @ Mon, 04 Nov 2019 03:13:13: 3000000 INFO @ Mon, 04 Nov 2019 03:13:13: 9000000 INFO @ Mon, 04 Nov 2019 03:13:17: 6000000 INFO @ Mon, 04 Nov 2019 03:13:24: 10000000 INFO @ Mon, 04 Nov 2019 03:13:26: 4000000 INFO @ Mon, 04 Nov 2019 03:13:29: 7000000 INFO @ Mon, 04 Nov 2019 03:13:35: 11000000 INFO @ Mon, 04 Nov 2019 03:13:39: 5000000 INFO @ Mon, 04 Nov 2019 03:13:41: 8000000 INFO @ Mon, 04 Nov 2019 03:13:46: 12000000 INFO @ Mon, 04 Nov 2019 03:13:52: 6000000 INFO @ Mon, 04 Nov 2019 03:13:53: 9000000 INFO @ Mon, 04 Nov 2019 03:13:58: 13000000 INFO @ Mon, 04 Nov 2019 03:14:05: 7000000 INFO @ Mon, 04 Nov 2019 03:14:05: 10000000 INFO @ Mon, 04 Nov 2019 03:14:09: 14000000 INFO @ Mon, 04 Nov 2019 03:14:17: 11000000 INFO @ Mon, 04 Nov 2019 03:14:18: 8000000 INFO @ Mon, 04 Nov 2019 03:14:20: 15000000 INFO @ Mon, 04 Nov 2019 03:14:29: 12000000 INFO @ Mon, 04 Nov 2019 03:14:30: 9000000 INFO @ Mon, 04 Nov 2019 03:14:32: 16000000 INFO @ Mon, 04 Nov 2019 03:14:40: 13000000 INFO @ Mon, 04 Nov 2019 03:14:42: 10000000 INFO @ Mon, 04 Nov 2019 03:14:42: 17000000 INFO @ Mon, 04 Nov 2019 03:14:53: 14000000 INFO @ Mon, 04 Nov 2019 03:14:54: 18000000 INFO @ Mon, 04 Nov 2019 03:14:55: 11000000 INFO @ Mon, 04 Nov 2019 03:15:05: 15000000 INFO @ Mon, 04 Nov 2019 03:15:05: 19000000 INFO @ Mon, 04 Nov 2019 03:15:07: 12000000 INFO @ Mon, 04 Nov 2019 03:15:16: 20000000 INFO @ Mon, 04 Nov 2019 03:15:17: 16000000 INFO @ Mon, 04 Nov 2019 03:15:20: 13000000 INFO @ Mon, 04 Nov 2019 03:15:27: 21000000 INFO @ Mon, 04 Nov 2019 03:15:29: 17000000 INFO @ Mon, 04 Nov 2019 03:15:33: 14000000 INFO @ Mon, 04 Nov 2019 03:15:39: 22000000 INFO @ Mon, 04 Nov 2019 03:15:41: 18000000 INFO @ Mon, 04 Nov 2019 03:15:45: 15000000 INFO @ Mon, 04 Nov 2019 03:15:50: 23000000 INFO @ Mon, 04 Nov 2019 03:15:53: 19000000 INFO @ Mon, 04 Nov 2019 03:15:59: 16000000 INFO @ Mon, 04 Nov 2019 03:16:00: 24000000 INFO @ Mon, 04 Nov 2019 03:16:05: 20000000 INFO @ Mon, 04 Nov 2019 03:16:11: 25000000 INFO @ Mon, 04 Nov 2019 03:16:12: 17000000 INFO @ Mon, 04 Nov 2019 03:16:17: 21000000 INFO @ Mon, 04 Nov 2019 03:16:22: 26000000 INFO @ Mon, 04 Nov 2019 03:16:25: 18000000 INFO @ Mon, 04 Nov 2019 03:16:29: 22000000 INFO @ Mon, 04 Nov 2019 03:16:34: 27000000 INFO @ Mon, 04 Nov 2019 03:16:37: 19000000 INFO @ Mon, 04 Nov 2019 03:16:41: 23000000 INFO @ Mon, 04 Nov 2019 03:16:45: 28000000 INFO @ Mon, 04 Nov 2019 03:16:49: 20000000 INFO @ Mon, 04 Nov 2019 03:16:53: 24000000 INFO @ Mon, 04 Nov 2019 03:16:56: 29000000 INFO @ Mon, 04 Nov 2019 03:17:02: 21000000 INFO @ Mon, 04 Nov 2019 03:17:06: 25000000 INFO @ Mon, 04 Nov 2019 03:17:07: 30000000 INFO @ Mon, 04 Nov 2019 03:17:13: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 03:17:13: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 03:17:13: #1 total tags in treatment: 30439453 INFO @ Mon, 04 Nov 2019 03:17:13: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 03:17:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 03:17:14: #1 tags after filtering in treatment: 30439359 INFO @ Mon, 04 Nov 2019 03:17:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 03:17:14: #1 finished! INFO @ Mon, 04 Nov 2019 03:17:14: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 03:17:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 03:17:15: 22000000 INFO @ Mon, 04 Nov 2019 03:17:18: #2 number of paired peaks: 6373 INFO @ Mon, 04 Nov 2019 03:17:18: start model_add_line... INFO @ Mon, 04 Nov 2019 03:17:18: 26000000 INFO @ Mon, 04 Nov 2019 03:17:18: start X-correlation... INFO @ Mon, 04 Nov 2019 03:17:18: end of X-cor INFO @ Mon, 04 Nov 2019 03:17:18: #2 finished! INFO @ Mon, 04 Nov 2019 03:17:18: #2 predicted fragment length is 78 bps INFO @ Mon, 04 Nov 2019 03:17:18: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 04 Nov 2019 03:17:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.05_model.r WARNING @ Mon, 04 Nov 2019 03:17:18: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 04 Nov 2019 03:17:18: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Mon, 04 Nov 2019 03:17:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 04 Nov 2019 03:17:18: #3 Call peaks... INFO @ Mon, 04 Nov 2019 03:17:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 03:17:27: 23000000 INFO @ Mon, 04 Nov 2019 03:17:30: 27000000 INFO @ Mon, 04 Nov 2019 03:17:39: 24000000 INFO @ Mon, 04 Nov 2019 03:17:42: 28000000 INFO @ Mon, 04 Nov 2019 03:17:52: 25000000 INFO @ Mon, 04 Nov 2019 03:17:54: 29000000 INFO @ Mon, 04 Nov 2019 03:18:05: 26000000 INFO @ Mon, 04 Nov 2019 03:18:06: 30000000 INFO @ Mon, 04 Nov 2019 03:18:12: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 03:18:12: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 03:18:12: #1 total tags in treatment: 30439453 INFO @ Mon, 04 Nov 2019 03:18:12: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 03:18:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 03:18:13: #1 tags after filtering in treatment: 30439359 INFO @ Mon, 04 Nov 2019 03:18:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 03:18:13: #1 finished! INFO @ Mon, 04 Nov 2019 03:18:13: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 03:18:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 03:18:17: #2 number of paired peaks: 6373 INFO @ Mon, 04 Nov 2019 03:18:17: start model_add_line... INFO @ Mon, 04 Nov 2019 03:18:17: start X-correlation... INFO @ Mon, 04 Nov 2019 03:18:17: end of X-cor INFO @ Mon, 04 Nov 2019 03:18:17: #2 finished! INFO @ Mon, 04 Nov 2019 03:18:17: #2 predicted fragment length is 78 bps INFO @ Mon, 04 Nov 2019 03:18:17: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 04 Nov 2019 03:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.10_model.r WARNING @ Mon, 04 Nov 2019 03:18:17: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 04 Nov 2019 03:18:17: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Mon, 04 Nov 2019 03:18:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 04 Nov 2019 03:18:17: #3 Call peaks... INFO @ Mon, 04 Nov 2019 03:18:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 03:18:18: 27000000 INFO @ Mon, 04 Nov 2019 03:18:31: 28000000 INFO @ Mon, 04 Nov 2019 03:18:44: 29000000 INFO @ Mon, 04 Nov 2019 03:18:57: 30000000 INFO @ Mon, 04 Nov 2019 03:19:03: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 03:19:03: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 03:19:03: #1 total tags in treatment: 30439453 INFO @ Mon, 04 Nov 2019 03:19:03: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 03:19:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 03:19:04: #1 tags after filtering in treatment: 30439359 INFO @ Mon, 04 Nov 2019 03:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 03:19:04: #1 finished! INFO @ Mon, 04 Nov 2019 03:19:04: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 03:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 03:19:08: #2 number of paired peaks: 6373 INFO @ Mon, 04 Nov 2019 03:19:08: start model_add_line... INFO @ Mon, 04 Nov 2019 03:19:08: start X-correlation... INFO @ Mon, 04 Nov 2019 03:19:08: end of X-cor INFO @ Mon, 04 Nov 2019 03:19:08: #2 finished! INFO @ Mon, 04 Nov 2019 03:19:08: #2 predicted fragment length is 78 bps INFO @ Mon, 04 Nov 2019 03:19:08: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 04 Nov 2019 03:19:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.20_model.r WARNING @ Mon, 04 Nov 2019 03:19:08: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 04 Nov 2019 03:19:08: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Mon, 04 Nov 2019 03:19:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 04 Nov 2019 03:19:08: #3 Call peaks... INFO @ Mon, 04 Nov 2019 03:19:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 03:19:10: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 03:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.05_peaks.xls INFO @ Mon, 04 Nov 2019 03:20:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.05_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 03:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.05_summits.bed INFO @ Mon, 04 Nov 2019 03:20:01: Done! pass1 - making usageList (63 chroms): 2 millis pass2 - checking and writing primary data (2660 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 04 Nov 2019 03:20:06: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 03:20:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.10_peaks.xls INFO @ Mon, 04 Nov 2019 03:20:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.10_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 03:20:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.10_summits.bed INFO @ Mon, 04 Nov 2019 03:20:57: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1273 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 04 Nov 2019 03:20:58: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 03:21:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.20_peaks.xls INFO @ Mon, 04 Nov 2019 03:21:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.20_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 03:21:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098376/SRX4098376.20_summits.bed INFO @ Mon, 04 Nov 2019 03:21:48: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (596 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。