Job ID = 1294298 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,068,527 reads read : 33,068,527 reads written : 33,068,527 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: 00:16:01 33068527 reads; of these: 33068527 (100.00%) were unpaired; of these: 863279 (2.61%) aligned 0 times 22207526 (67.16%) aligned exactly 1 time 9997722 (30.23%) aligned >1 times 97.39% overall alignment rate Time searching: 00:16:01 Overall time: 00:16:01 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] 4211807 / 32205248 = 0.1308 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 06:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.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 06:51:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:51:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.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 06:51:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:51:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.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 06:51:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:51:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:52:02: 1000000 INFO @ Mon, 03 Jun 2019 06:52:04: 1000000 INFO @ Mon, 03 Jun 2019 06:52:05: 1000000 INFO @ Mon, 03 Jun 2019 06:52:10: 2000000 INFO @ Mon, 03 Jun 2019 06:52:13: 2000000 INFO @ Mon, 03 Jun 2019 06:52:14: 2000000 INFO @ Mon, 03 Jun 2019 06:52:17: 3000000 INFO @ Mon, 03 Jun 2019 06:52:22: 3000000 INFO @ Mon, 03 Jun 2019 06:52:24: 3000000 INFO @ Mon, 03 Jun 2019 06:52:24: 4000000 INFO @ Mon, 03 Jun 2019 06:52:30: 4000000 INFO @ Mon, 03 Jun 2019 06:52:31: 5000000 INFO @ Mon, 03 Jun 2019 06:52:33: 4000000 INFO @ Mon, 03 Jun 2019 06:52:38: 6000000 INFO @ Mon, 03 Jun 2019 06:52:38: 5000000 INFO @ Mon, 03 Jun 2019 06:52:42: 5000000 INFO @ Mon, 03 Jun 2019 06:52:45: 7000000 INFO @ Mon, 03 Jun 2019 06:52:47: 6000000 INFO @ Mon, 03 Jun 2019 06:52:52: 6000000 INFO @ Mon, 03 Jun 2019 06:52:52: 8000000 INFO @ Mon, 03 Jun 2019 06:52:55: 7000000 INFO @ Mon, 03 Jun 2019 06:52:59: 9000000 INFO @ Mon, 03 Jun 2019 06:53:01: 7000000 INFO @ Mon, 03 Jun 2019 06:53:04: 8000000 INFO @ Mon, 03 Jun 2019 06:53:06: 10000000 INFO @ Mon, 03 Jun 2019 06:53:11: 8000000 INFO @ Mon, 03 Jun 2019 06:53:12: 9000000 INFO @ Mon, 03 Jun 2019 06:53:13: 11000000 INFO @ Mon, 03 Jun 2019 06:53:20: 9000000 INFO @ Mon, 03 Jun 2019 06:53:20: 12000000 INFO @ Mon, 03 Jun 2019 06:53:20: 10000000 INFO @ Mon, 03 Jun 2019 06:53:27: 13000000 INFO @ Mon, 03 Jun 2019 06:53:29: 11000000 INFO @ Mon, 03 Jun 2019 06:53:29: 10000000 INFO @ Mon, 03 Jun 2019 06:53:34: 14000000 INFO @ Mon, 03 Jun 2019 06:53:37: 12000000 INFO @ Mon, 03 Jun 2019 06:53:38: 11000000 INFO @ Mon, 03 Jun 2019 06:53:41: 15000000 INFO @ Mon, 03 Jun 2019 06:53:46: 13000000 INFO @ Mon, 03 Jun 2019 06:53:47: 12000000 INFO @ Mon, 03 Jun 2019 06:53:48: 16000000 INFO @ Mon, 03 Jun 2019 06:53:54: 14000000 INFO @ Mon, 03 Jun 2019 06:53:55: 17000000 INFO @ Mon, 03 Jun 2019 06:53:56: 13000000 INFO @ Mon, 03 Jun 2019 06:54:02: 18000000 INFO @ Mon, 03 Jun 2019 06:54:02: 15000000 INFO @ Mon, 03 Jun 2019 06:54:05: 14000000 INFO @ Mon, 03 Jun 2019 06:54:09: 19000000 INFO @ Mon, 03 Jun 2019 06:54:11: 16000000 INFO @ Mon, 03 Jun 2019 06:54:14: 15000000 INFO @ Mon, 03 Jun 2019 06:54:16: 20000000 INFO @ Mon, 03 Jun 2019 06:54:19: 17000000 INFO @ Mon, 03 Jun 2019 06:54:23: 21000000 INFO @ Mon, 03 Jun 2019 06:54:23: 16000000 INFO @ Mon, 03 Jun 2019 06:54:29: 18000000 INFO @ Mon, 03 Jun 2019 06:54:29: 22000000 INFO @ Mon, 03 Jun 2019 06:54:32: 17000000 INFO @ Mon, 03 Jun 2019 06:54:36: 23000000 INFO @ Mon, 03 Jun 2019 06:54:37: 19000000 INFO @ Mon, 03 Jun 2019 06:54:41: 18000000 INFO @ Mon, 03 Jun 2019 06:54:43: 24000000 INFO @ Mon, 03 Jun 2019 06:54:46: 20000000 INFO @ Mon, 03 Jun 2019 06:54:50: 25000000 INFO @ Mon, 03 Jun 2019 06:54:51: 19000000 INFO @ Mon, 03 Jun 2019 06:54:54: 21000000 INFO @ Mon, 03 Jun 2019 06:54:57: 26000000 INFO @ Mon, 03 Jun 2019 06:55:00: 20000000 INFO @ Mon, 03 Jun 2019 06:55:02: 22000000 INFO @ Mon, 03 Jun 2019 06:55:04: 27000000 INFO @ Mon, 03 Jun 2019 06:55:08: 21000000 INFO @ Mon, 03 Jun 2019 06:55:10: 23000000 INFO @ Mon, 03 Jun 2019 06:55:11: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:55:11: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:55:11: #1 total tags in treatment: 27993441 INFO @ Mon, 03 Jun 2019 06:55:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:55:11: #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 06:55:12: #1 tags after filtering in treatment: 27993441 INFO @ Mon, 03 Jun 2019 06:55:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:55:12: #1 finished! INFO @ Mon, 03 Jun 2019 06:55:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:55:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:55:14: #2 number of paired peaks: 398 WARNING @ Mon, 03 Jun 2019 06:55:14: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Mon, 03 Jun 2019 06:55:14: start model_add_line... INFO @ Mon, 03 Jun 2019 06:55:14: start X-correlation... INFO @ Mon, 03 Jun 2019 06:55:14: end of X-cor INFO @ Mon, 03 Jun 2019 06:55:14: #2 finished! INFO @ Mon, 03 Jun 2019 06:55:14: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 06:55:14: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 03 Jun 2019 06:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.20_model.r WARNING @ Mon, 03 Jun 2019 06:55:14: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:55:14: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 03 Jun 2019 06:55:14: #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 06:55:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:55:17: 22000000 INFO @ Mon, 03 Jun 2019 06:55:19: 24000000 INFO @ Mon, 03 Jun 2019 06:55:26: 23000000 INFO @ Mon, 03 Jun 2019 06:55:27: 25000000 INFO @ Mon, 03 Jun 2019 06:55:35: 24000000 INFO @ Mon, 03 Jun 2019 06:55:36: 26000000 INFO @ Mon, 03 Jun 2019 06:55:44: 25000000 INFO @ Mon, 03 Jun 2019 06:55:45: 27000000 INFO @ Mon, 03 Jun 2019 06:55:52: 26000000 INFO @ Mon, 03 Jun 2019 06:55:53: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:55:53: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:55:53: #1 total tags in treatment: 27993441 INFO @ Mon, 03 Jun 2019 06:55:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:55:53: #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 06:55:54: #1 tags after filtering in treatment: 27993441 INFO @ Mon, 03 Jun 2019 06:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:55:54: #1 finished! INFO @ Mon, 03 Jun 2019 06:55:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:55:56: #2 number of paired peaks: 398 WARNING @ Mon, 03 Jun 2019 06:55:56: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Mon, 03 Jun 2019 06:55:56: start model_add_line... INFO @ Mon, 03 Jun 2019 06:55:56: start X-correlation... INFO @ Mon, 03 Jun 2019 06:55:56: end of X-cor INFO @ Mon, 03 Jun 2019 06:55:56: #2 finished! INFO @ Mon, 03 Jun 2019 06:55:56: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 06:55:56: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 03 Jun 2019 06:55:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.05_model.r WARNING @ Mon, 03 Jun 2019 06:55:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:55:56: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 03 Jun 2019 06:55:56: #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 06:55:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:56:01: 27000000 INFO @ Mon, 03 Jun 2019 06:56:10: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:56:10: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:56:10: #1 total tags in treatment: 27993441 INFO @ Mon, 03 Jun 2019 06:56:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:56:10: #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 06:56:10: #1 tags after filtering in treatment: 27993441 INFO @ Mon, 03 Jun 2019 06:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:56:10: #1 finished! INFO @ Mon, 03 Jun 2019 06:56:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:56:13: #2 number of paired peaks: 398 WARNING @ Mon, 03 Jun 2019 06:56:13: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Mon, 03 Jun 2019 06:56:13: start model_add_line... INFO @ Mon, 03 Jun 2019 06:56:13: start X-correlation... INFO @ Mon, 03 Jun 2019 06:56:13: end of X-cor INFO @ Mon, 03 Jun 2019 06:56:13: #2 finished! INFO @ Mon, 03 Jun 2019 06:56:13: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 06:56:13: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 03 Jun 2019 06:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.10_model.r WARNING @ Mon, 03 Jun 2019 06:56:13: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:56:13: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 03 Jun 2019 06:56:13: #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 06:56:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:56:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:56:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.20_summits.bed INFO @ Mon, 03 Jun 2019 06:56:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (931 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:57:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:57:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.05_summits.bed INFO @ Mon, 03 Jun 2019 06:57:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3869 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:57:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:57:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:57:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422628/SRX2422628.10_summits.bed INFO @ Mon, 03 Jun 2019 06:57:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2108 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。