Job ID = 2590798 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,754,938 reads read : 77,509,876 reads written : 38,754,938 reads 0-length : 38,754,938 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:42 38754938 reads; of these: 38754938 (100.00%) were unpaired; of these: 3762037 (9.71%) aligned 0 times 26240784 (67.71%) aligned exactly 1 time 8752117 (22.58%) aligned >1 times 90.29% overall alignment rate Time searching: 00:13:42 Overall time: 00:13:42 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 16 files... [bam_rmdupse_core] 15609073 / 34992901 = 0.4461 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 23:43:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.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 23:43:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:43:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:43:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.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 23:43:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:43:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.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 23:43:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:43:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:44:03: 1000000 INFO @ Mon, 12 Aug 2019 23:44:05: 1000000 INFO @ Mon, 12 Aug 2019 23:44:05: 1000000 INFO @ Mon, 12 Aug 2019 23:44:15: 2000000 INFO @ Mon, 12 Aug 2019 23:44:15: 2000000 INFO @ Mon, 12 Aug 2019 23:44:17: 2000000 INFO @ Mon, 12 Aug 2019 23:44:24: 3000000 INFO @ Mon, 12 Aug 2019 23:44:26: 3000000 INFO @ Mon, 12 Aug 2019 23:44:28: 3000000 INFO @ Mon, 12 Aug 2019 23:44:34: 4000000 INFO @ Mon, 12 Aug 2019 23:44:37: 4000000 INFO @ Mon, 12 Aug 2019 23:44:39: 4000000 INFO @ Mon, 12 Aug 2019 23:44:43: 5000000 INFO @ Mon, 12 Aug 2019 23:44:48: 5000000 INFO @ Mon, 12 Aug 2019 23:44:50: 5000000 INFO @ Mon, 12 Aug 2019 23:44:52: 6000000 INFO @ Mon, 12 Aug 2019 23:44:59: 6000000 INFO @ Mon, 12 Aug 2019 23:45:01: 6000000 INFO @ Mon, 12 Aug 2019 23:45:02: 7000000 INFO @ Mon, 12 Aug 2019 23:45:11: 7000000 INFO @ Mon, 12 Aug 2019 23:45:11: 8000000 INFO @ Mon, 12 Aug 2019 23:45:12: 7000000 INFO @ Mon, 12 Aug 2019 23:45:20: 9000000 INFO @ Mon, 12 Aug 2019 23:45:21: 8000000 INFO @ Mon, 12 Aug 2019 23:45:23: 8000000 INFO @ Mon, 12 Aug 2019 23:45:30: 10000000 INFO @ Mon, 12 Aug 2019 23:45:33: 9000000 INFO @ Mon, 12 Aug 2019 23:45:34: 9000000 INFO @ Mon, 12 Aug 2019 23:45:39: 11000000 INFO @ Mon, 12 Aug 2019 23:45:43: 10000000 INFO @ Mon, 12 Aug 2019 23:45:44: 10000000 INFO @ Mon, 12 Aug 2019 23:45:48: 12000000 INFO @ Mon, 12 Aug 2019 23:45:52: 11000000 INFO @ Mon, 12 Aug 2019 23:45:54: 11000000 INFO @ Mon, 12 Aug 2019 23:45:58: 13000000 INFO @ Mon, 12 Aug 2019 23:46:02: 12000000 INFO @ Mon, 12 Aug 2019 23:46:03: 12000000 INFO @ Mon, 12 Aug 2019 23:46:07: 14000000 INFO @ Mon, 12 Aug 2019 23:46:10: 13000000 INFO @ Mon, 12 Aug 2019 23:46:12: 13000000 INFO @ Mon, 12 Aug 2019 23:46:16: 15000000 INFO @ Mon, 12 Aug 2019 23:46:19: 14000000 INFO @ Mon, 12 Aug 2019 23:46:20: 14000000 INFO @ Mon, 12 Aug 2019 23:46:25: 16000000 INFO @ Mon, 12 Aug 2019 23:46:27: 15000000 INFO @ Mon, 12 Aug 2019 23:46:29: 15000000 INFO @ Mon, 12 Aug 2019 23:46:35: 17000000 INFO @ Mon, 12 Aug 2019 23:46:36: 16000000 INFO @ Mon, 12 Aug 2019 23:46:37: 16000000 INFO @ Mon, 12 Aug 2019 23:46:44: 18000000 INFO @ Mon, 12 Aug 2019 23:46:44: 17000000 INFO @ Mon, 12 Aug 2019 23:46:46: 17000000 INFO @ Mon, 12 Aug 2019 23:46:53: 18000000 INFO @ Mon, 12 Aug 2019 23:46:53: 19000000 INFO @ Mon, 12 Aug 2019 23:46:54: 18000000 INFO @ Mon, 12 Aug 2019 23:46:56: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:46:56: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:46:56: #1 total tags in treatment: 19383828 INFO @ Mon, 12 Aug 2019 23:46:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:46:56: #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 23:46:57: #1 tags after filtering in treatment: 19383828 INFO @ Mon, 12 Aug 2019 23:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:46:57: #1 finished! INFO @ Mon, 12 Aug 2019 23:46:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:46:58: #2 number of paired peaks: 782 WARNING @ Mon, 12 Aug 2019 23:46:58: Fewer paired peaks (782) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 782 pairs to build model! INFO @ Mon, 12 Aug 2019 23:46:58: start model_add_line... INFO @ Mon, 12 Aug 2019 23:46:59: start X-correlation... INFO @ Mon, 12 Aug 2019 23:46:59: end of X-cor INFO @ Mon, 12 Aug 2019 23:46:59: #2 finished! INFO @ Mon, 12 Aug 2019 23:46:59: #2 predicted fragment length is 210 bps INFO @ Mon, 12 Aug 2019 23:46:59: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 12 Aug 2019 23:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.20_model.r INFO @ Mon, 12 Aug 2019 23:46:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:47:01: 19000000 INFO @ Mon, 12 Aug 2019 23:47:02: 19000000 INFO @ Mon, 12 Aug 2019 23:47:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:47:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:47:04: #1 total tags in treatment: 19383828 INFO @ Mon, 12 Aug 2019 23:47:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:47:04: #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 23:47:05: #1 tags after filtering in treatment: 19383828 INFO @ Mon, 12 Aug 2019 23:47:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:47:05: #1 finished! INFO @ Mon, 12 Aug 2019 23:47:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:47:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:47:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:47:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:47:05: #1 total tags in treatment: 19383828 INFO @ Mon, 12 Aug 2019 23:47:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:47:05: #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 23:47:06: #1 tags after filtering in treatment: 19383828 INFO @ Mon, 12 Aug 2019 23:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:47:06: #1 finished! INFO @ Mon, 12 Aug 2019 23:47:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:47:06: #2 number of paired peaks: 782 WARNING @ Mon, 12 Aug 2019 23:47:06: Fewer paired peaks (782) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 782 pairs to build model! INFO @ Mon, 12 Aug 2019 23:47:06: start model_add_line... INFO @ Mon, 12 Aug 2019 23:47:07: start X-correlation... INFO @ Mon, 12 Aug 2019 23:47:07: end of X-cor INFO @ Mon, 12 Aug 2019 23:47:07: #2 finished! INFO @ Mon, 12 Aug 2019 23:47:07: #2 predicted fragment length is 210 bps INFO @ Mon, 12 Aug 2019 23:47:07: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 12 Aug 2019 23:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.05_model.r INFO @ Mon, 12 Aug 2019 23:47:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:47:07: #2 number of paired peaks: 782 WARNING @ Mon, 12 Aug 2019 23:47:07: Fewer paired peaks (782) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 782 pairs to build model! INFO @ Mon, 12 Aug 2019 23:47:07: start model_add_line... INFO @ Mon, 12 Aug 2019 23:47:08: start X-correlation... INFO @ Mon, 12 Aug 2019 23:47:08: end of X-cor INFO @ Mon, 12 Aug 2019 23:47:08: #2 finished! INFO @ Mon, 12 Aug 2019 23:47:08: #2 predicted fragment length is 210 bps INFO @ Mon, 12 Aug 2019 23:47:08: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 12 Aug 2019 23:47:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.10_model.r INFO @ Mon, 12 Aug 2019 23:47:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:47:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:48:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.20_summits.bed INFO @ Mon, 12 Aug 2019 23:48:20: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4913 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:48:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.05_summits.bed INFO @ Mon, 12 Aug 2019 23:48:29: Done! INFO @ Mon, 12 Aug 2019 23:48:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.10_peaks.narrowPeak pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (11345 records, 4 fields): 17 millis INFO @ Mon, 12 Aug 2019 23:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011040/SRX5011040.10_summits.bed CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:48:29: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7966 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。