Job ID = 1294976 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,734,451 reads read : 24,734,451 reads written : 24,734,451 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:08:11 24734451 reads; of these: 24734451 (100.00%) were unpaired; of these: 2098337 (8.48%) aligned 0 times 17257832 (69.77%) aligned exactly 1 time 5378282 (21.74%) aligned >1 times 91.52% overall alignment rate Time searching: 00:08:11 Overall time: 00:08:11 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 12 files... [bam_rmdupse_core] 3551578 / 22636114 = 0.1569 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, 03 Jun 2019 11:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.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, 03 Jun 2019 11:27:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:27:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.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, 03 Jun 2019 11:27:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:27:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.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, 03 Jun 2019 11:27:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:27:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:27:42: 1000000 INFO @ Mon, 03 Jun 2019 11:27:43: 1000000 INFO @ Mon, 03 Jun 2019 11:27:44: 1000000 INFO @ Mon, 03 Jun 2019 11:27:50: 2000000 INFO @ Mon, 03 Jun 2019 11:27:51: 2000000 INFO @ Mon, 03 Jun 2019 11:27:54: 2000000 INFO @ Mon, 03 Jun 2019 11:27:57: 3000000 INFO @ Mon, 03 Jun 2019 11:27:59: 3000000 INFO @ Mon, 03 Jun 2019 11:28:03: 3000000 INFO @ Mon, 03 Jun 2019 11:28:05: 4000000 INFO @ Mon, 03 Jun 2019 11:28:07: 4000000 INFO @ Mon, 03 Jun 2019 11:28:12: 4000000 INFO @ Mon, 03 Jun 2019 11:28:12: 5000000 INFO @ Mon, 03 Jun 2019 11:28:16: 5000000 INFO @ Mon, 03 Jun 2019 11:28:19: 6000000 INFO @ Mon, 03 Jun 2019 11:28:21: 5000000 INFO @ Mon, 03 Jun 2019 11:28:24: 6000000 INFO @ Mon, 03 Jun 2019 11:28:27: 7000000 INFO @ Mon, 03 Jun 2019 11:28:30: 6000000 INFO @ Mon, 03 Jun 2019 11:28:32: 7000000 INFO @ Mon, 03 Jun 2019 11:28:34: 8000000 INFO @ Mon, 03 Jun 2019 11:28:39: 7000000 INFO @ Mon, 03 Jun 2019 11:28:40: 8000000 INFO @ Mon, 03 Jun 2019 11:28:42: 9000000 INFO @ Mon, 03 Jun 2019 11:28:48: 9000000 INFO @ Mon, 03 Jun 2019 11:28:49: 8000000 INFO @ Mon, 03 Jun 2019 11:28:50: 10000000 INFO @ Mon, 03 Jun 2019 11:28:56: 10000000 INFO @ Mon, 03 Jun 2019 11:28:57: 11000000 INFO @ Mon, 03 Jun 2019 11:28:58: 9000000 INFO @ Mon, 03 Jun 2019 11:29:04: 11000000 INFO @ Mon, 03 Jun 2019 11:29:05: 12000000 INFO @ Mon, 03 Jun 2019 11:29:07: 10000000 INFO @ Mon, 03 Jun 2019 11:29:12: 13000000 INFO @ Mon, 03 Jun 2019 11:29:12: 12000000 INFO @ Mon, 03 Jun 2019 11:29:17: 11000000 INFO @ Mon, 03 Jun 2019 11:29:19: 14000000 INFO @ Mon, 03 Jun 2019 11:29:20: 13000000 INFO @ Mon, 03 Jun 2019 11:29:26: 12000000 INFO @ Mon, 03 Jun 2019 11:29:27: 15000000 INFO @ Mon, 03 Jun 2019 11:29:28: 14000000 INFO @ Mon, 03 Jun 2019 11:29:34: 16000000 INFO @ Mon, 03 Jun 2019 11:29:36: 13000000 INFO @ Mon, 03 Jun 2019 11:29:36: 15000000 INFO @ Mon, 03 Jun 2019 11:29:42: 17000000 INFO @ Mon, 03 Jun 2019 11:29:44: 16000000 INFO @ Mon, 03 Jun 2019 11:29:45: 14000000 INFO @ Mon, 03 Jun 2019 11:29:49: 18000000 INFO @ Mon, 03 Jun 2019 11:29:52: 17000000 INFO @ Mon, 03 Jun 2019 11:29:55: 15000000 INFO @ Mon, 03 Jun 2019 11:29:56: 19000000 INFO @ Mon, 03 Jun 2019 11:29:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:29:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:29:57: #1 total tags in treatment: 19084536 INFO @ Mon, 03 Jun 2019 11:29:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:29:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:29:57: #1 tags after filtering in treatment: 19084536 INFO @ Mon, 03 Jun 2019 11:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:29:57: #1 finished! INFO @ Mon, 03 Jun 2019 11:29:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:29:59: #2 number of paired peaks: 412 WARNING @ Mon, 03 Jun 2019 11:29:59: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Mon, 03 Jun 2019 11:29:59: start model_add_line... INFO @ Mon, 03 Jun 2019 11:29:59: start X-correlation... INFO @ Mon, 03 Jun 2019 11:29:59: end of X-cor INFO @ Mon, 03 Jun 2019 11:29:59: #2 finished! INFO @ Mon, 03 Jun 2019 11:29:59: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 11:29:59: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 11:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.20_model.r INFO @ Mon, 03 Jun 2019 11:29:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:30:00: 18000000 INFO @ Mon, 03 Jun 2019 11:30:04: 16000000 INFO @ Mon, 03 Jun 2019 11:30:08: 19000000 INFO @ Mon, 03 Jun 2019 11:30:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:30:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:30:09: #1 total tags in treatment: 19084536 INFO @ Mon, 03 Jun 2019 11:30:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:30:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:30:09: #1 tags after filtering in treatment: 19084536 INFO @ Mon, 03 Jun 2019 11:30:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:30:09: #1 finished! INFO @ Mon, 03 Jun 2019 11:30:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:30:11: #2 number of paired peaks: 412 WARNING @ Mon, 03 Jun 2019 11:30:11: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Mon, 03 Jun 2019 11:30:11: start model_add_line... INFO @ Mon, 03 Jun 2019 11:30:11: start X-correlation... INFO @ Mon, 03 Jun 2019 11:30:11: end of X-cor INFO @ Mon, 03 Jun 2019 11:30:11: #2 finished! INFO @ Mon, 03 Jun 2019 11:30:11: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 11:30:11: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 11:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.05_model.r INFO @ Mon, 03 Jun 2019 11:30:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:30:13: 17000000 INFO @ Mon, 03 Jun 2019 11:30:23: 18000000 INFO @ Mon, 03 Jun 2019 11:30:32: 19000000 INFO @ Mon, 03 Jun 2019 11:30:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:30:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:30:33: #1 total tags in treatment: 19084536 INFO @ Mon, 03 Jun 2019 11:30:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:30:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:30:33: #1 tags after filtering in treatment: 19084536 INFO @ Mon, 03 Jun 2019 11:30:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:30:33: #1 finished! INFO @ Mon, 03 Jun 2019 11:30:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:30:35: #2 number of paired peaks: 412 WARNING @ Mon, 03 Jun 2019 11:30:35: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Mon, 03 Jun 2019 11:30:35: start model_add_line... INFO @ Mon, 03 Jun 2019 11:30:35: start X-correlation... INFO @ Mon, 03 Jun 2019 11:30:35: end of X-cor INFO @ Mon, 03 Jun 2019 11:30:35: #2 finished! INFO @ Mon, 03 Jun 2019 11:30:35: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 11:30:35: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 11:30:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.10_model.r INFO @ Mon, 03 Jun 2019 11:30:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:30:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:31:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.20_summits.bed INFO @ Mon, 03 Jun 2019 11:31:16: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3419 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:31:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.05_summits.bed INFO @ Mon, 03 Jun 2019 11:31:29: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7621 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:31:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:31:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:31:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288034/SRX288034.10_summits.bed INFO @ Mon, 03 Jun 2019 11:31:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5594 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。