Job ID = 1295014 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,066,666 reads read : 34,066,666 reads written : 34,066,666 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: 00:12:25 34066666 reads; of these: 34066666 (100.00%) were unpaired; of these: 2279668 (6.69%) aligned 0 times 23330975 (68.49%) aligned exactly 1 time 8456023 (24.82%) aligned >1 times 93.31% overall alignment rate Time searching: 00:12:25 Overall time: 00:12:25 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] 3791395 / 31786998 = 0.1193 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 11:52:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.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 11:52:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:52:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:52:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.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 11:52:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:52:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.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 11:52:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:52:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:52:42: 1000000 INFO @ Mon, 03 Jun 2019 11:52:43: 1000000 INFO @ Mon, 03 Jun 2019 11:52:46: 1000000 INFO @ Mon, 03 Jun 2019 11:52:50: 2000000 INFO @ Mon, 03 Jun 2019 11:52:52: 2000000 INFO @ Mon, 03 Jun 2019 11:52:58: 2000000 INFO @ Mon, 03 Jun 2019 11:52:58: 3000000 INFO @ Mon, 03 Jun 2019 11:53:01: 3000000 INFO @ Mon, 03 Jun 2019 11:53:06: 4000000 INFO @ Mon, 03 Jun 2019 11:53:09: 3000000 INFO @ Mon, 03 Jun 2019 11:53:10: 4000000 INFO @ Mon, 03 Jun 2019 11:53:14: 5000000 INFO @ Mon, 03 Jun 2019 11:53:18: 5000000 INFO @ Mon, 03 Jun 2019 11:53:20: 4000000 INFO @ Mon, 03 Jun 2019 11:53:22: 6000000 INFO @ Mon, 03 Jun 2019 11:53:27: 6000000 INFO @ Mon, 03 Jun 2019 11:53:30: 7000000 INFO @ Mon, 03 Jun 2019 11:53:32: 5000000 INFO @ Mon, 03 Jun 2019 11:53:36: 7000000 INFO @ Mon, 03 Jun 2019 11:53:37: 8000000 INFO @ Mon, 03 Jun 2019 11:53:43: 6000000 INFO @ Mon, 03 Jun 2019 11:53:45: 8000000 INFO @ Mon, 03 Jun 2019 11:53:45: 9000000 INFO @ Mon, 03 Jun 2019 11:53:54: 10000000 INFO @ Mon, 03 Jun 2019 11:53:54: 9000000 INFO @ Mon, 03 Jun 2019 11:53:55: 7000000 INFO @ Mon, 03 Jun 2019 11:54:02: 11000000 INFO @ Mon, 03 Jun 2019 11:54:03: 10000000 INFO @ Mon, 03 Jun 2019 11:54:06: 8000000 INFO @ Mon, 03 Jun 2019 11:54:09: 12000000 INFO @ Mon, 03 Jun 2019 11:54:11: 11000000 INFO @ Mon, 03 Jun 2019 11:54:17: 9000000 INFO @ Mon, 03 Jun 2019 11:54:17: 13000000 INFO @ Mon, 03 Jun 2019 11:54:20: 12000000 INFO @ Mon, 03 Jun 2019 11:54:25: 14000000 INFO @ Mon, 03 Jun 2019 11:54:28: 10000000 INFO @ Mon, 03 Jun 2019 11:54:29: 13000000 INFO @ Mon, 03 Jun 2019 11:54:33: 15000000 INFO @ Mon, 03 Jun 2019 11:54:37: 14000000 INFO @ Mon, 03 Jun 2019 11:54:39: 11000000 INFO @ Mon, 03 Jun 2019 11:54:41: 16000000 INFO @ Mon, 03 Jun 2019 11:54:46: 15000000 INFO @ Mon, 03 Jun 2019 11:54:49: 17000000 INFO @ Mon, 03 Jun 2019 11:54:50: 12000000 INFO @ Mon, 03 Jun 2019 11:54:54: 16000000 INFO @ Mon, 03 Jun 2019 11:54:57: 18000000 INFO @ Mon, 03 Jun 2019 11:55:01: 13000000 INFO @ Mon, 03 Jun 2019 11:55:03: 17000000 INFO @ Mon, 03 Jun 2019 11:55:04: 19000000 INFO @ Mon, 03 Jun 2019 11:55:12: 18000000 INFO @ Mon, 03 Jun 2019 11:55:13: 20000000 INFO @ Mon, 03 Jun 2019 11:55:13: 14000000 INFO @ Mon, 03 Jun 2019 11:55:21: 21000000 INFO @ Mon, 03 Jun 2019 11:55:21: 19000000 INFO @ Mon, 03 Jun 2019 11:55:24: 15000000 INFO @ Mon, 03 Jun 2019 11:55:28: 22000000 INFO @ Mon, 03 Jun 2019 11:55:29: 20000000 INFO @ Mon, 03 Jun 2019 11:55:35: 16000000 INFO @ Mon, 03 Jun 2019 11:55:36: 23000000 INFO @ Mon, 03 Jun 2019 11:55:38: 21000000 INFO @ Mon, 03 Jun 2019 11:55:44: 24000000 INFO @ Mon, 03 Jun 2019 11:55:46: 17000000 INFO @ Mon, 03 Jun 2019 11:55:47: 22000000 INFO @ Mon, 03 Jun 2019 11:55:53: 25000000 INFO @ Mon, 03 Jun 2019 11:55:56: 23000000 INFO @ Mon, 03 Jun 2019 11:55:58: 18000000 INFO @ Mon, 03 Jun 2019 11:56:04: 26000000 INFO @ Mon, 03 Jun 2019 11:56:04: 24000000 INFO @ Mon, 03 Jun 2019 11:56:09: 19000000 INFO @ Mon, 03 Jun 2019 11:56:12: 27000000 INFO @ Mon, 03 Jun 2019 11:56:13: 25000000 INFO @ Mon, 03 Jun 2019 11:56:20: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:56:20: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:56:20: #1 total tags in treatment: 27995603 INFO @ Mon, 03 Jun 2019 11:56:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:56:20: #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 11:56:20: 20000000 INFO @ Mon, 03 Jun 2019 11:56:21: #1 tags after filtering in treatment: 27995603 INFO @ Mon, 03 Jun 2019 11:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:56:21: #1 finished! INFO @ Mon, 03 Jun 2019 11:56:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:56:22: 26000000 INFO @ Mon, 03 Jun 2019 11:56:23: #2 number of paired peaks: 176 WARNING @ Mon, 03 Jun 2019 11:56:23: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 03 Jun 2019 11:56:23: start model_add_line... INFO @ Mon, 03 Jun 2019 11:56:23: start X-correlation... INFO @ Mon, 03 Jun 2019 11:56:23: end of X-cor INFO @ Mon, 03 Jun 2019 11:56:23: #2 finished! INFO @ Mon, 03 Jun 2019 11:56:23: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 11:56:23: #2 alternative fragment length(s) may be 3,53,566 bps INFO @ Mon, 03 Jun 2019 11:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.05_model.r WARNING @ Mon, 03 Jun 2019 11:56:23: #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 11:56:23: #2 You may need to consider one of the other alternative d(s): 3,53,566 WARNING @ Mon, 03 Jun 2019 11:56:23: #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 11:56:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:56:30: 27000000 INFO @ Mon, 03 Jun 2019 11:56:31: 21000000 INFO @ Mon, 03 Jun 2019 11:56:40: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:56:40: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:56:40: #1 total tags in treatment: 27995603 INFO @ Mon, 03 Jun 2019 11:56:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:56:40: #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 11:56:40: #1 tags after filtering in treatment: 27995603 INFO @ Mon, 03 Jun 2019 11:56:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:56:40: #1 finished! INFO @ Mon, 03 Jun 2019 11:56:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:56:41: 22000000 INFO @ Mon, 03 Jun 2019 11:56:42: #2 number of paired peaks: 176 WARNING @ Mon, 03 Jun 2019 11:56:42: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 03 Jun 2019 11:56:42: start model_add_line... INFO @ Mon, 03 Jun 2019 11:56:43: start X-correlation... INFO @ Mon, 03 Jun 2019 11:56:43: end of X-cor INFO @ Mon, 03 Jun 2019 11:56:43: #2 finished! INFO @ Mon, 03 Jun 2019 11:56:43: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 11:56:43: #2 alternative fragment length(s) may be 3,53,566 bps INFO @ Mon, 03 Jun 2019 11:56:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.10_model.r WARNING @ Mon, 03 Jun 2019 11:56:43: #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 11:56:43: #2 You may need to consider one of the other alternative d(s): 3,53,566 WARNING @ Mon, 03 Jun 2019 11:56:43: #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 11:56:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:56:51: 23000000 INFO @ Mon, 03 Jun 2019 11:57:02: 24000000 INFO @ Mon, 03 Jun 2019 11:57:12: 25000000 INFO @ Mon, 03 Jun 2019 11:57:23: 26000000 INFO @ Mon, 03 Jun 2019 11:57:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:57:34: 27000000 INFO @ Mon, 03 Jun 2019 11:57:45: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:57:45: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:57:45: #1 total tags in treatment: 27995603 INFO @ Mon, 03 Jun 2019 11:57:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:57:45: #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 11:57:45: #1 tags after filtering in treatment: 27995603 INFO @ Mon, 03 Jun 2019 11:57:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:57:45: #1 finished! INFO @ Mon, 03 Jun 2019 11:57:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:57:48: #2 number of paired peaks: 176 WARNING @ Mon, 03 Jun 2019 11:57:48: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 03 Jun 2019 11:57:48: start model_add_line... INFO @ Mon, 03 Jun 2019 11:57:48: start X-correlation... INFO @ Mon, 03 Jun 2019 11:57:48: end of X-cor INFO @ Mon, 03 Jun 2019 11:57:48: #2 finished! INFO @ Mon, 03 Jun 2019 11:57:48: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 11:57:48: #2 alternative fragment length(s) may be 3,53,566 bps INFO @ Mon, 03 Jun 2019 11:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.20_model.r WARNING @ Mon, 03 Jun 2019 11:57:48: #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 11:57:48: #2 You may need to consider one of the other alternative d(s): 3,53,566 WARNING @ Mon, 03 Jun 2019 11:57:48: #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 11:57:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:57:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.05_summits.bed INFO @ Mon, 03 Jun 2019 11:58:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5060 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.10_summits.bed INFO @ Mon, 03 Jun 2019 11:58:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2893 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:58:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:59:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306190/SRX306190.20_summits.bed INFO @ Mon, 03 Jun 2019 11:59:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1336 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。