Job ID = 1295752 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,691,262 reads read : 38,691,262 reads written : 38,691,262 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: 00:08:36 38691262 reads; of these: 38691262 (100.00%) were unpaired; of these: 8387903 (21.68%) aligned 0 times 24117732 (62.33%) aligned exactly 1 time 6185627 (15.99%) aligned >1 times 78.32% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 7732911 / 30303359 = 0.2552 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 15:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.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 15:37:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:37:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.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 15:37:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:37:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.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 15:37:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:37:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:37:09: 1000000 INFO @ Mon, 03 Jun 2019 15:37:10: 1000000 INFO @ Mon, 03 Jun 2019 15:37:10: 1000000 INFO @ Mon, 03 Jun 2019 15:37:16: 2000000 INFO @ Mon, 03 Jun 2019 15:37:18: 2000000 INFO @ Mon, 03 Jun 2019 15:37:18: 2000000 INFO @ Mon, 03 Jun 2019 15:37:23: 3000000 INFO @ Mon, 03 Jun 2019 15:37:25: 3000000 INFO @ Mon, 03 Jun 2019 15:37:25: 3000000 INFO @ Mon, 03 Jun 2019 15:37:30: 4000000 INFO @ Mon, 03 Jun 2019 15:37:32: 4000000 INFO @ Mon, 03 Jun 2019 15:37:32: 4000000 INFO @ Mon, 03 Jun 2019 15:37:37: 5000000 INFO @ Mon, 03 Jun 2019 15:37:39: 5000000 INFO @ Mon, 03 Jun 2019 15:37:39: 5000000 INFO @ Mon, 03 Jun 2019 15:37:43: 6000000 INFO @ Mon, 03 Jun 2019 15:37:46: 6000000 INFO @ Mon, 03 Jun 2019 15:37:46: 6000000 INFO @ Mon, 03 Jun 2019 15:37:50: 7000000 INFO @ Mon, 03 Jun 2019 15:37:53: 7000000 INFO @ Mon, 03 Jun 2019 15:37:53: 7000000 INFO @ Mon, 03 Jun 2019 15:37:57: 8000000 INFO @ Mon, 03 Jun 2019 15:38:00: 8000000 INFO @ Mon, 03 Jun 2019 15:38:00: 8000000 INFO @ Mon, 03 Jun 2019 15:38:04: 9000000 INFO @ Mon, 03 Jun 2019 15:38:07: 9000000 INFO @ Mon, 03 Jun 2019 15:38:08: 9000000 INFO @ Mon, 03 Jun 2019 15:38:10: 10000000 INFO @ Mon, 03 Jun 2019 15:38:14: 10000000 INFO @ Mon, 03 Jun 2019 15:38:15: 10000000 INFO @ Mon, 03 Jun 2019 15:38:17: 11000000 INFO @ Mon, 03 Jun 2019 15:38:21: 11000000 INFO @ Mon, 03 Jun 2019 15:38:21: 11000000 INFO @ Mon, 03 Jun 2019 15:38:23: 12000000 INFO @ Mon, 03 Jun 2019 15:38:28: 12000000 INFO @ Mon, 03 Jun 2019 15:38:29: 12000000 INFO @ Mon, 03 Jun 2019 15:38:30: 13000000 INFO @ Mon, 03 Jun 2019 15:38:36: 13000000 INFO @ Mon, 03 Jun 2019 15:38:36: 13000000 INFO @ Mon, 03 Jun 2019 15:38:37: 14000000 INFO @ Mon, 03 Jun 2019 15:38:43: 14000000 INFO @ Mon, 03 Jun 2019 15:38:43: 14000000 INFO @ Mon, 03 Jun 2019 15:38:43: 15000000 INFO @ Mon, 03 Jun 2019 15:38:49: 15000000 INFO @ Mon, 03 Jun 2019 15:38:49: 15000000 INFO @ Mon, 03 Jun 2019 15:38:50: 16000000 INFO @ Mon, 03 Jun 2019 15:38:56: 16000000 INFO @ Mon, 03 Jun 2019 15:38:56: 16000000 INFO @ Mon, 03 Jun 2019 15:38:56: 17000000 INFO @ Mon, 03 Jun 2019 15:39:03: 17000000 INFO @ Mon, 03 Jun 2019 15:39:03: 18000000 INFO @ Mon, 03 Jun 2019 15:39:03: 17000000 INFO @ Mon, 03 Jun 2019 15:39:09: 19000000 INFO @ Mon, 03 Jun 2019 15:39:09: 18000000 INFO @ Mon, 03 Jun 2019 15:39:10: 18000000 INFO @ Mon, 03 Jun 2019 15:39:16: 19000000 INFO @ Mon, 03 Jun 2019 15:39:16: 20000000 INFO @ Mon, 03 Jun 2019 15:39:17: 19000000 INFO @ Mon, 03 Jun 2019 15:39:23: 21000000 INFO @ Mon, 03 Jun 2019 15:39:24: 20000000 INFO @ Mon, 03 Jun 2019 15:39:24: 20000000 INFO @ Mon, 03 Jun 2019 15:39:30: 22000000 INFO @ Mon, 03 Jun 2019 15:39:31: 21000000 INFO @ Mon, 03 Jun 2019 15:39:31: 21000000 INFO @ Mon, 03 Jun 2019 15:39:34: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:39:34: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:39:34: #1 total tags in treatment: 22570448 INFO @ Mon, 03 Jun 2019 15:39:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:39:34: #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 15:39:34: #1 tags after filtering in treatment: 22570448 INFO @ Mon, 03 Jun 2019 15:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:39:34: #1 finished! INFO @ Mon, 03 Jun 2019 15:39:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:39:36: #2 number of paired peaks: 345 WARNING @ Mon, 03 Jun 2019 15:39:36: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Mon, 03 Jun 2019 15:39:36: start model_add_line... INFO @ Mon, 03 Jun 2019 15:39:36: start X-correlation... INFO @ Mon, 03 Jun 2019 15:39:36: end of X-cor INFO @ Mon, 03 Jun 2019 15:39:36: #2 finished! INFO @ Mon, 03 Jun 2019 15:39:36: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 15:39:36: #2 alternative fragment length(s) may be 4,41 bps INFO @ Mon, 03 Jun 2019 15:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.05_model.r WARNING @ Mon, 03 Jun 2019 15:39:36: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:39:36: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Mon, 03 Jun 2019 15:39:36: #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 15:39:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:39:37: 22000000 INFO @ Mon, 03 Jun 2019 15:39:38: 22000000 INFO @ Mon, 03 Jun 2019 15:39:41: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:39:41: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:39:41: #1 total tags in treatment: 22570448 INFO @ Mon, 03 Jun 2019 15:39:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:39:41: #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 15:39:42: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:39:42: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:39:42: #1 total tags in treatment: 22570448 INFO @ Mon, 03 Jun 2019 15:39:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:39:42: #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 15:39:42: #1 tags after filtering in treatment: 22570448 INFO @ Mon, 03 Jun 2019 15:39:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:39:42: #1 finished! INFO @ Mon, 03 Jun 2019 15:39:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:39:42: #1 tags after filtering in treatment: 22570448 INFO @ Mon, 03 Jun 2019 15:39:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:39:42: #1 finished! INFO @ Mon, 03 Jun 2019 15:39:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:39:44: #2 number of paired peaks: 345 WARNING @ Mon, 03 Jun 2019 15:39:44: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Mon, 03 Jun 2019 15:39:44: start model_add_line... INFO @ Mon, 03 Jun 2019 15:39:44: #2 number of paired peaks: 345 WARNING @ Mon, 03 Jun 2019 15:39:44: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Mon, 03 Jun 2019 15:39:44: start model_add_line... INFO @ Mon, 03 Jun 2019 15:39:44: start X-correlation... INFO @ Mon, 03 Jun 2019 15:39:44: end of X-cor INFO @ Mon, 03 Jun 2019 15:39:44: #2 finished! INFO @ Mon, 03 Jun 2019 15:39:44: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 15:39:44: #2 alternative fragment length(s) may be 4,41 bps INFO @ Mon, 03 Jun 2019 15:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.20_model.r WARNING @ Mon, 03 Jun 2019 15:39:44: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:39:44: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Mon, 03 Jun 2019 15:39:44: #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 15:39:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:39:44: start X-correlation... INFO @ Mon, 03 Jun 2019 15:39:44: end of X-cor INFO @ Mon, 03 Jun 2019 15:39:44: #2 finished! INFO @ Mon, 03 Jun 2019 15:39:44: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 15:39:44: #2 alternative fragment length(s) may be 4,41 bps INFO @ Mon, 03 Jun 2019 15:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.10_model.r WARNING @ Mon, 03 Jun 2019 15:39:44: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:39:44: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Mon, 03 Jun 2019 15:39:44: #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 15:39:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:40:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:40:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:40:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.05_summits.bed INFO @ Mon, 03 Jun 2019 15:40:56: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7935 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:41:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:41:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:41:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.20_summits.bed INFO @ Mon, 03 Jun 2019 15:41:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1525 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:41:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:41:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:41:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447393/SRX447393.10_summits.bed INFO @ Mon, 03 Jun 2019 15:41:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3409 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。