Job ID = 1294280 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,962,425 reads read : 32,962,425 reads written : 32,962,425 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:05 32962425 reads; of these: 32962425 (100.00%) were unpaired; of these: 2527112 (7.67%) aligned 0 times 19699160 (59.76%) aligned exactly 1 time 10736153 (32.57%) aligned >1 times 92.33% overall alignment rate Time searching: 00:10:06 Overall time: 00:10:06 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 8 files... [bam_rmdupse_core] 7587068 / 30435313 = 0.2493 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 06:44:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.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 06:44:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:44:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:44:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.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 06:44:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:44:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:44:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.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 06:44:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:44:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:44:58: 1000000 INFO @ Mon, 03 Jun 2019 06:44:58: 1000000 INFO @ Mon, 03 Jun 2019 06:44:59: 1000000 INFO @ Mon, 03 Jun 2019 06:45:06: 2000000 INFO @ Mon, 03 Jun 2019 06:45:06: 2000000 INFO @ Mon, 03 Jun 2019 06:45:08: 2000000 INFO @ Mon, 03 Jun 2019 06:45:14: 3000000 INFO @ Mon, 03 Jun 2019 06:45:14: 3000000 INFO @ Mon, 03 Jun 2019 06:45:17: 3000000 INFO @ Mon, 03 Jun 2019 06:45:22: 4000000 INFO @ Mon, 03 Jun 2019 06:45:22: 4000000 INFO @ Mon, 03 Jun 2019 06:45:26: 4000000 INFO @ Mon, 03 Jun 2019 06:45:29: 5000000 INFO @ Mon, 03 Jun 2019 06:45:29: 5000000 INFO @ Mon, 03 Jun 2019 06:45:34: 5000000 INFO @ Mon, 03 Jun 2019 06:45:37: 6000000 INFO @ Mon, 03 Jun 2019 06:45:37: 6000000 INFO @ Mon, 03 Jun 2019 06:45:43: 6000000 INFO @ Mon, 03 Jun 2019 06:45:44: 7000000 INFO @ Mon, 03 Jun 2019 06:45:44: 7000000 INFO @ Mon, 03 Jun 2019 06:45:51: 7000000 INFO @ Mon, 03 Jun 2019 06:45:52: 8000000 INFO @ Mon, 03 Jun 2019 06:45:52: 8000000 INFO @ Mon, 03 Jun 2019 06:46:00: 8000000 INFO @ Mon, 03 Jun 2019 06:46:00: 9000000 INFO @ Mon, 03 Jun 2019 06:46:00: 9000000 INFO @ Mon, 03 Jun 2019 06:46:08: 10000000 INFO @ Mon, 03 Jun 2019 06:46:08: 10000000 INFO @ Mon, 03 Jun 2019 06:46:08: 9000000 INFO @ Mon, 03 Jun 2019 06:46:15: 11000000 INFO @ Mon, 03 Jun 2019 06:46:16: 11000000 INFO @ Mon, 03 Jun 2019 06:46:17: 10000000 INFO @ Mon, 03 Jun 2019 06:46:23: 12000000 INFO @ Mon, 03 Jun 2019 06:46:23: 12000000 INFO @ Mon, 03 Jun 2019 06:46:25: 11000000 INFO @ Mon, 03 Jun 2019 06:46:31: 13000000 INFO @ Mon, 03 Jun 2019 06:46:31: 13000000 INFO @ Mon, 03 Jun 2019 06:46:34: 12000000 INFO @ Mon, 03 Jun 2019 06:46:39: 14000000 INFO @ Mon, 03 Jun 2019 06:46:39: 14000000 INFO @ Mon, 03 Jun 2019 06:46:42: 13000000 INFO @ Mon, 03 Jun 2019 06:46:46: 15000000 INFO @ Mon, 03 Jun 2019 06:46:46: 15000000 INFO @ Mon, 03 Jun 2019 06:46:50: 14000000 INFO @ Mon, 03 Jun 2019 06:46:54: 16000000 INFO @ Mon, 03 Jun 2019 06:46:54: 16000000 INFO @ Mon, 03 Jun 2019 06:46:59: 15000000 INFO @ Mon, 03 Jun 2019 06:47:02: 17000000 INFO @ Mon, 03 Jun 2019 06:47:02: 17000000 INFO @ Mon, 03 Jun 2019 06:47:07: 16000000 INFO @ Mon, 03 Jun 2019 06:47:10: 18000000 INFO @ Mon, 03 Jun 2019 06:47:10: 18000000 INFO @ Mon, 03 Jun 2019 06:47:15: 17000000 INFO @ Mon, 03 Jun 2019 06:47:17: 19000000 INFO @ Mon, 03 Jun 2019 06:47:17: 19000000 INFO @ Mon, 03 Jun 2019 06:47:23: 18000000 INFO @ Mon, 03 Jun 2019 06:47:25: 20000000 INFO @ Mon, 03 Jun 2019 06:47:25: 20000000 INFO @ Mon, 03 Jun 2019 06:47:32: 19000000 INFO @ Mon, 03 Jun 2019 06:47:32: 21000000 INFO @ Mon, 03 Jun 2019 06:47:33: 21000000 INFO @ Mon, 03 Jun 2019 06:47:40: 20000000 INFO @ Mon, 03 Jun 2019 06:47:40: 22000000 INFO @ Mon, 03 Jun 2019 06:47:40: 22000000 INFO @ Mon, 03 Jun 2019 06:47:46: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:47:46: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:47:46: #1 total tags in treatment: 22848245 INFO @ Mon, 03 Jun 2019 06:47:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:47:46: #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 06:47:46: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:47:46: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:47:46: #1 total tags in treatment: 22848245 INFO @ Mon, 03 Jun 2019 06:47:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:47:46: #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 06:47:47: #1 tags after filtering in treatment: 22848245 INFO @ Mon, 03 Jun 2019 06:47:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:47:47: #1 finished! INFO @ Mon, 03 Jun 2019 06:47:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:47:47: #1 tags after filtering in treatment: 22848245 INFO @ Mon, 03 Jun 2019 06:47:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:47:47: #1 finished! INFO @ Mon, 03 Jun 2019 06:47:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:47:48: 21000000 INFO @ Mon, 03 Jun 2019 06:47:49: #2 number of paired peaks: 300 WARNING @ Mon, 03 Jun 2019 06:47:49: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Mon, 03 Jun 2019 06:47:49: start model_add_line... INFO @ Mon, 03 Jun 2019 06:47:49: #2 number of paired peaks: 300 WARNING @ Mon, 03 Jun 2019 06:47:49: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Mon, 03 Jun 2019 06:47:49: start model_add_line... INFO @ Mon, 03 Jun 2019 06:47:49: start X-correlation... INFO @ Mon, 03 Jun 2019 06:47:49: end of X-cor INFO @ Mon, 03 Jun 2019 06:47:49: #2 finished! INFO @ Mon, 03 Jun 2019 06:47:49: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 06:47:49: #2 alternative fragment length(s) may be 3,63,598 bps INFO @ Mon, 03 Jun 2019 06:47:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.10_model.r WARNING @ Mon, 03 Jun 2019 06:47:49: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:47:49: #2 You may need to consider one of the other alternative d(s): 3,63,598 WARNING @ Mon, 03 Jun 2019 06:47:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:47:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:47:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:47:49: start X-correlation... INFO @ Mon, 03 Jun 2019 06:47:49: end of X-cor INFO @ Mon, 03 Jun 2019 06:47:49: #2 finished! INFO @ Mon, 03 Jun 2019 06:47:49: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 06:47:49: #2 alternative fragment length(s) may be 3,63,598 bps INFO @ Mon, 03 Jun 2019 06:47:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.05_model.r WARNING @ Mon, 03 Jun 2019 06:47:49: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:47:49: #2 You may need to consider one of the other alternative d(s): 3,63,598 WARNING @ Mon, 03 Jun 2019 06:47:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:47:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:47:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:47:56: 22000000 INFO @ Mon, 03 Jun 2019 06:48:03: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:48:03: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:48:03: #1 total tags in treatment: 22848245 INFO @ Mon, 03 Jun 2019 06:48:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:48:03: #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 06:48:04: #1 tags after filtering in treatment: 22848245 INFO @ Mon, 03 Jun 2019 06:48:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:48:04: #1 finished! INFO @ Mon, 03 Jun 2019 06:48:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:48:06: #2 number of paired peaks: 300 WARNING @ Mon, 03 Jun 2019 06:48:06: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Mon, 03 Jun 2019 06:48:06: start model_add_line... INFO @ Mon, 03 Jun 2019 06:48:06: start X-correlation... INFO @ Mon, 03 Jun 2019 06:48:06: end of X-cor INFO @ Mon, 03 Jun 2019 06:48:06: #2 finished! INFO @ Mon, 03 Jun 2019 06:48:06: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 06:48:06: #2 alternative fragment length(s) may be 3,63,598 bps INFO @ Mon, 03 Jun 2019 06:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.20_model.r WARNING @ Mon, 03 Jun 2019 06:48:06: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:48:06: #2 You may need to consider one of the other alternative d(s): 3,63,598 WARNING @ Mon, 03 Jun 2019 06:48:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:48:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:48:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:48:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:49:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.10_summits.bed INFO @ Mon, 03 Jun 2019 06:49:16: Done! INFO @ Mon, 03 Jun 2019 06:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.05_peaks.xls pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3438 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.05_summits.bed INFO @ Mon, 03 Jun 2019 06:49:16: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (10321 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220306/SRX220306.20_summits.bed INFO @ Mon, 03 Jun 2019 06:49:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。