Job ID = 2590373 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,393,863 reads read : 28,787,726 reads written : 14,393,863 reads 0-length : 14,393,863 spots read : 14,277,122 reads read : 28,554,244 reads written : 14,277,122 reads 0-length : 14,277,122 spots read : 14,254,931 reads read : 28,509,862 reads written : 14,254,931 reads 0-length : 14,254,931 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:30 42925916 reads; of these: 42925916 (100.00%) were unpaired; of these: 1519966 (3.54%) aligned 0 times 35224494 (82.06%) aligned exactly 1 time 6181456 (14.40%) aligned >1 times 96.46% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 9103053 / 41405950 = 0.2198 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 @ Mon, 12 Aug 2019 21:41:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 12 Aug 2019 21:41:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:41:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 12 Aug 2019 21:41:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:41:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:41:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 12 Aug 2019 21:41:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:41:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:42:00: 1000000 INFO @ Mon, 12 Aug 2019 21:42:02: 1000000 INFO @ Mon, 12 Aug 2019 21:42:04: 1000000 INFO @ Mon, 12 Aug 2019 21:42:07: 2000000 INFO @ Mon, 12 Aug 2019 21:42:11: 2000000 INFO @ Mon, 12 Aug 2019 21:42:13: 3000000 INFO @ Mon, 12 Aug 2019 21:42:13: 2000000 INFO @ Mon, 12 Aug 2019 21:42:20: 4000000 INFO @ Mon, 12 Aug 2019 21:42:21: 3000000 INFO @ Mon, 12 Aug 2019 21:42:23: 3000000 INFO @ Mon, 12 Aug 2019 21:42:27: 5000000 INFO @ Mon, 12 Aug 2019 21:42:31: 4000000 INFO @ Mon, 12 Aug 2019 21:42:33: 4000000 INFO @ Mon, 12 Aug 2019 21:42:34: 6000000 INFO @ Mon, 12 Aug 2019 21:42:40: 5000000 INFO @ Mon, 12 Aug 2019 21:42:41: 7000000 INFO @ Mon, 12 Aug 2019 21:42:43: 5000000 INFO @ Mon, 12 Aug 2019 21:42:47: 8000000 INFO @ Mon, 12 Aug 2019 21:42:50: 6000000 INFO @ Mon, 12 Aug 2019 21:42:52: 6000000 INFO @ Mon, 12 Aug 2019 21:42:54: 9000000 INFO @ Mon, 12 Aug 2019 21:43:00: 7000000 INFO @ Mon, 12 Aug 2019 21:43:01: 10000000 INFO @ Mon, 12 Aug 2019 21:43:02: 7000000 INFO @ Mon, 12 Aug 2019 21:43:08: 11000000 INFO @ Mon, 12 Aug 2019 21:43:09: 8000000 INFO @ Mon, 12 Aug 2019 21:43:12: 8000000 INFO @ Mon, 12 Aug 2019 21:43:14: 12000000 INFO @ Mon, 12 Aug 2019 21:43:19: 9000000 INFO @ Mon, 12 Aug 2019 21:43:21: 13000000 INFO @ Mon, 12 Aug 2019 21:43:21: 9000000 INFO @ Mon, 12 Aug 2019 21:43:28: 14000000 INFO @ Mon, 12 Aug 2019 21:43:29: 10000000 INFO @ Mon, 12 Aug 2019 21:43:31: 10000000 INFO @ Mon, 12 Aug 2019 21:43:34: 15000000 INFO @ Mon, 12 Aug 2019 21:43:38: 11000000 INFO @ Mon, 12 Aug 2019 21:43:41: 11000000 INFO @ Mon, 12 Aug 2019 21:43:41: 16000000 INFO @ Mon, 12 Aug 2019 21:43:48: 17000000 INFO @ Mon, 12 Aug 2019 21:43:48: 12000000 INFO @ Mon, 12 Aug 2019 21:43:50: 12000000 INFO @ Mon, 12 Aug 2019 21:43:54: 18000000 INFO @ Mon, 12 Aug 2019 21:43:58: 13000000 INFO @ Mon, 12 Aug 2019 21:44:00: 13000000 INFO @ Mon, 12 Aug 2019 21:44:01: 19000000 INFO @ Mon, 12 Aug 2019 21:44:07: 14000000 INFO @ Mon, 12 Aug 2019 21:44:08: 20000000 INFO @ Mon, 12 Aug 2019 21:44:09: 14000000 INFO @ Mon, 12 Aug 2019 21:44:14: 21000000 INFO @ Mon, 12 Aug 2019 21:44:17: 15000000 INFO @ Mon, 12 Aug 2019 21:44:19: 15000000 INFO @ Mon, 12 Aug 2019 21:44:21: 22000000 INFO @ Mon, 12 Aug 2019 21:44:26: 16000000 INFO @ Mon, 12 Aug 2019 21:44:28: 23000000 INFO @ Mon, 12 Aug 2019 21:44:29: 16000000 INFO @ Mon, 12 Aug 2019 21:44:34: 24000000 INFO @ Mon, 12 Aug 2019 21:44:36: 17000000 INFO @ Mon, 12 Aug 2019 21:44:38: 17000000 INFO @ Mon, 12 Aug 2019 21:44:41: 25000000 INFO @ Mon, 12 Aug 2019 21:44:45: 18000000 INFO @ Mon, 12 Aug 2019 21:44:48: 18000000 INFO @ Mon, 12 Aug 2019 21:44:48: 26000000 INFO @ Mon, 12 Aug 2019 21:44:54: 27000000 INFO @ Mon, 12 Aug 2019 21:44:55: 19000000 INFO @ Mon, 12 Aug 2019 21:44:57: 19000000 INFO @ Mon, 12 Aug 2019 21:45:01: 28000000 INFO @ Mon, 12 Aug 2019 21:45:04: 20000000 INFO @ Mon, 12 Aug 2019 21:45:07: 20000000 INFO @ Mon, 12 Aug 2019 21:45:08: 29000000 INFO @ Mon, 12 Aug 2019 21:45:14: 21000000 INFO @ Mon, 12 Aug 2019 21:45:15: 30000000 INFO @ Mon, 12 Aug 2019 21:45:16: 21000000 INFO @ Mon, 12 Aug 2019 21:45:21: 31000000 INFO @ Mon, 12 Aug 2019 21:45:23: 22000000 INFO @ Mon, 12 Aug 2019 21:45:26: 22000000 INFO @ Mon, 12 Aug 2019 21:45:28: 32000000 INFO @ Mon, 12 Aug 2019 21:45:30: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:45:30: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:45:30: #1 total tags in treatment: 32302897 INFO @ Mon, 12 Aug 2019 21:45:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:45:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:45:31: #1 tags after filtering in treatment: 32302897 INFO @ Mon, 12 Aug 2019 21:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:45:31: #1 finished! INFO @ Mon, 12 Aug 2019 21:45:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:45:33: 23000000 INFO @ Mon, 12 Aug 2019 21:45:34: #2 number of paired peaks: 701 WARNING @ Mon, 12 Aug 2019 21:45:34: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Mon, 12 Aug 2019 21:45:34: start model_add_line... INFO @ Mon, 12 Aug 2019 21:45:34: start X-correlation... INFO @ Mon, 12 Aug 2019 21:45:34: end of X-cor INFO @ Mon, 12 Aug 2019 21:45:34: #2 finished! INFO @ Mon, 12 Aug 2019 21:45:34: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 21:45:34: #2 alternative fragment length(s) may be 2,53,62,86 bps INFO @ Mon, 12 Aug 2019 21:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.10_model.r WARNING @ Mon, 12 Aug 2019 21:45:34: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:45:34: #2 You may need to consider one of the other alternative d(s): 2,53,62,86 WARNING @ Mon, 12 Aug 2019 21:45:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:45:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:45:35: 23000000 INFO @ Mon, 12 Aug 2019 21:45:42: 24000000 INFO @ Mon, 12 Aug 2019 21:45:44: 24000000 INFO @ Mon, 12 Aug 2019 21:45:52: 25000000 INFO @ Mon, 12 Aug 2019 21:45:54: 25000000 INFO @ Mon, 12 Aug 2019 21:46:01: 26000000 INFO @ Mon, 12 Aug 2019 21:46:03: 26000000 INFO @ Mon, 12 Aug 2019 21:46:11: 27000000 INFO @ Mon, 12 Aug 2019 21:46:13: 27000000 INFO @ Mon, 12 Aug 2019 21:46:20: 28000000 INFO @ Mon, 12 Aug 2019 21:46:22: 28000000 INFO @ Mon, 12 Aug 2019 21:46:30: 29000000 INFO @ Mon, 12 Aug 2019 21:46:32: 29000000 INFO @ Mon, 12 Aug 2019 21:46:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:46:39: 30000000 INFO @ Mon, 12 Aug 2019 21:46:41: 30000000 INFO @ Mon, 12 Aug 2019 21:46:48: 31000000 INFO @ Mon, 12 Aug 2019 21:46:51: 31000000 INFO @ Mon, 12 Aug 2019 21:46:58: 32000000 INFO @ Mon, 12 Aug 2019 21:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.10_summits.bed INFO @ Mon, 12 Aug 2019 21:46:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:47:00: 32000000 INFO @ Mon, 12 Aug 2019 21:47:01: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:47:01: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:47:01: #1 total tags in treatment: 32302897 INFO @ Mon, 12 Aug 2019 21:47:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:47:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:47:02: #1 tags after filtering in treatment: 32302897 INFO @ Mon, 12 Aug 2019 21:47:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:47:02: #1 finished! INFO @ Mon, 12 Aug 2019 21:47:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:47:03: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:47:03: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:47:03: #1 total tags in treatment: 32302897 INFO @ Mon, 12 Aug 2019 21:47:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:47:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:47:04: #1 tags after filtering in treatment: 32302897 INFO @ Mon, 12 Aug 2019 21:47:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:47:04: #1 finished! INFO @ Mon, 12 Aug 2019 21:47:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:47:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:47:05: #2 number of paired peaks: 701 WARNING @ Mon, 12 Aug 2019 21:47:05: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Mon, 12 Aug 2019 21:47:05: start model_add_line... INFO @ Mon, 12 Aug 2019 21:47:05: start X-correlation... INFO @ Mon, 12 Aug 2019 21:47:05: end of X-cor INFO @ Mon, 12 Aug 2019 21:47:05: #2 finished! INFO @ Mon, 12 Aug 2019 21:47:05: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 21:47:05: #2 alternative fragment length(s) may be 2,53,62,86 bps INFO @ Mon, 12 Aug 2019 21:47:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.05_model.r WARNING @ Mon, 12 Aug 2019 21:47:05: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:47:05: #2 You may need to consider one of the other alternative d(s): 2,53,62,86 WARNING @ Mon, 12 Aug 2019 21:47:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:47:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:47:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:47:07: #2 number of paired peaks: 701 WARNING @ Mon, 12 Aug 2019 21:47:07: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Mon, 12 Aug 2019 21:47:07: start model_add_line... INFO @ Mon, 12 Aug 2019 21:47:07: start X-correlation... INFO @ Mon, 12 Aug 2019 21:47:07: end of X-cor INFO @ Mon, 12 Aug 2019 21:47:07: #2 finished! INFO @ Mon, 12 Aug 2019 21:47:07: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 21:47:07: #2 alternative fragment length(s) may be 2,53,62,86 bps INFO @ Mon, 12 Aug 2019 21:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.20_model.r WARNING @ Mon, 12 Aug 2019 21:47:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:47:07: #2 You may need to consider one of the other alternative d(s): 2,53,62,86 WARNING @ Mon, 12 Aug 2019 21:47:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:47:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:48:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:48:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.05_summits.bed INFO @ Mon, 12 Aug 2019 21:48:30: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981645/SRX3981645.20_summits.bed INFO @ Mon, 12 Aug 2019 21:48:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。