Job ID = 1305962 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 45,299,559 reads read : 45,299,559 reads written : 45,299,559 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: 00:25:22 45299559 reads; of these: 45299559 (100.00%) were unpaired; of these: 1510710 (3.33%) aligned 0 times 28753311 (63.47%) aligned exactly 1 time 15035538 (33.19%) aligned >1 times 96.67% overall alignment rate Time searching: 00:25:22 Overall time: 00:25:22 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 20 files... [bam_rmdupse_core] 21975667 / 43788849 = 0.5019 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 22:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.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 22:24:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.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 22:24:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.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 22:24:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:21: 1000000 INFO @ Mon, 03 Jun 2019 22:24:22: 1000000 INFO @ Mon, 03 Jun 2019 22:24:24: 1000000 INFO @ Mon, 03 Jun 2019 22:24:28: 2000000 INFO @ Mon, 03 Jun 2019 22:24:30: 2000000 INFO @ Mon, 03 Jun 2019 22:24:32: 2000000 INFO @ Mon, 03 Jun 2019 22:24:35: 3000000 INFO @ Mon, 03 Jun 2019 22:24:38: 3000000 INFO @ Mon, 03 Jun 2019 22:24:41: 3000000 INFO @ Mon, 03 Jun 2019 22:24:42: 4000000 INFO @ Mon, 03 Jun 2019 22:24:46: 4000000 INFO @ Mon, 03 Jun 2019 22:24:48: 5000000 INFO @ Mon, 03 Jun 2019 22:24:50: 4000000 INFO @ Mon, 03 Jun 2019 22:24:53: 5000000 INFO @ Mon, 03 Jun 2019 22:24:55: 6000000 INFO @ Mon, 03 Jun 2019 22:24:58: 5000000 INFO @ Mon, 03 Jun 2019 22:25:01: 6000000 INFO @ Mon, 03 Jun 2019 22:25:02: 7000000 INFO @ Mon, 03 Jun 2019 22:25:07: 6000000 INFO @ Mon, 03 Jun 2019 22:25:08: 8000000 INFO @ Mon, 03 Jun 2019 22:25:09: 7000000 INFO @ Mon, 03 Jun 2019 22:25:15: 9000000 INFO @ Mon, 03 Jun 2019 22:25:15: 7000000 INFO @ Mon, 03 Jun 2019 22:25:16: 8000000 INFO @ Mon, 03 Jun 2019 22:25:21: 10000000 INFO @ Mon, 03 Jun 2019 22:25:24: 9000000 INFO @ Mon, 03 Jun 2019 22:25:24: 8000000 INFO @ Mon, 03 Jun 2019 22:25:28: 11000000 INFO @ Mon, 03 Jun 2019 22:25:31: 10000000 INFO @ Mon, 03 Jun 2019 22:25:33: 9000000 INFO @ Mon, 03 Jun 2019 22:25:35: 12000000 INFO @ Mon, 03 Jun 2019 22:25:39: 11000000 INFO @ Mon, 03 Jun 2019 22:25:41: 10000000 INFO @ Mon, 03 Jun 2019 22:25:42: 13000000 INFO @ Mon, 03 Jun 2019 22:25:46: 12000000 INFO @ Mon, 03 Jun 2019 22:25:48: 14000000 INFO @ Mon, 03 Jun 2019 22:25:50: 11000000 INFO @ Mon, 03 Jun 2019 22:25:54: 13000000 INFO @ Mon, 03 Jun 2019 22:25:55: 15000000 INFO @ Mon, 03 Jun 2019 22:26:00: 12000000 INFO @ Mon, 03 Jun 2019 22:26:02: 16000000 INFO @ Mon, 03 Jun 2019 22:26:02: 14000000 INFO @ Mon, 03 Jun 2019 22:26:08: 17000000 INFO @ Mon, 03 Jun 2019 22:26:08: 13000000 INFO @ Mon, 03 Jun 2019 22:26:09: 15000000 INFO @ Mon, 03 Jun 2019 22:26:15: 18000000 INFO @ Mon, 03 Jun 2019 22:26:17: 16000000 INFO @ Mon, 03 Jun 2019 22:26:17: 14000000 INFO @ Mon, 03 Jun 2019 22:26:21: 19000000 INFO @ Mon, 03 Jun 2019 22:26:24: 17000000 INFO @ Mon, 03 Jun 2019 22:26:26: 15000000 INFO @ Mon, 03 Jun 2019 22:26:28: 20000000 INFO @ Mon, 03 Jun 2019 22:26:32: 18000000 INFO @ Mon, 03 Jun 2019 22:26:34: 16000000 INFO @ Mon, 03 Jun 2019 22:26:35: 21000000 INFO @ Mon, 03 Jun 2019 22:26:39: 19000000 INFO @ Mon, 03 Jun 2019 22:26:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:26:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:26:41: #1 total tags in treatment: 21813182 INFO @ Mon, 03 Jun 2019 22:26:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:26:41: #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 22:26:41: #1 tags after filtering in treatment: 21813182 INFO @ Mon, 03 Jun 2019 22:26:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:26:41: #1 finished! INFO @ Mon, 03 Jun 2019 22:26:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:26:43: 17000000 INFO @ Mon, 03 Jun 2019 22:26:43: #2 number of paired peaks: 515 WARNING @ Mon, 03 Jun 2019 22:26:43: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Mon, 03 Jun 2019 22:26:43: start model_add_line... INFO @ Mon, 03 Jun 2019 22:26:43: start X-correlation... INFO @ Mon, 03 Jun 2019 22:26:43: end of X-cor INFO @ Mon, 03 Jun 2019 22:26:43: #2 finished! INFO @ Mon, 03 Jun 2019 22:26:43: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 22:26:43: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 22:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.20_model.r WARNING @ Mon, 03 Jun 2019 22:26:43: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:26:43: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 22:26:43: #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 22:26:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:26:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:26:47: 20000000 INFO @ Mon, 03 Jun 2019 22:26:51: 18000000 INFO @ Mon, 03 Jun 2019 22:26:54: 21000000 INFO @ Mon, 03 Jun 2019 22:27:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:27:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:27:01: #1 total tags in treatment: 21813182 INFO @ Mon, 03 Jun 2019 22:27:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:27:01: #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 22:27:01: 19000000 INFO @ Mon, 03 Jun 2019 22:27:01: #1 tags after filtering in treatment: 21813182 INFO @ Mon, 03 Jun 2019 22:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:27:01: #1 finished! INFO @ Mon, 03 Jun 2019 22:27:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:27:03: #2 number of paired peaks: 515 WARNING @ Mon, 03 Jun 2019 22:27:03: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Mon, 03 Jun 2019 22:27:03: start model_add_line... INFO @ Mon, 03 Jun 2019 22:27:03: start X-correlation... INFO @ Mon, 03 Jun 2019 22:27:03: end of X-cor INFO @ Mon, 03 Jun 2019 22:27:03: #2 finished! INFO @ Mon, 03 Jun 2019 22:27:03: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 22:27:03: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 22:27:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.10_model.r WARNING @ Mon, 03 Jun 2019 22:27:03: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:27:03: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 22:27:03: #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 22:27:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:27:09: 20000000 INFO @ Mon, 03 Jun 2019 22:27:18: 21000000 INFO @ Mon, 03 Jun 2019 22:27:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:27:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:27:25: #1 total tags in treatment: 21813182 INFO @ Mon, 03 Jun 2019 22:27:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:27:25: #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 22:27:25: #1 tags after filtering in treatment: 21813182 INFO @ Mon, 03 Jun 2019 22:27:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:27:25: #1 finished! INFO @ Mon, 03 Jun 2019 22:27:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:27:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:27:27: #2 number of paired peaks: 515 WARNING @ Mon, 03 Jun 2019 22:27:27: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Mon, 03 Jun 2019 22:27:27: start model_add_line... INFO @ Mon, 03 Jun 2019 22:27:27: start X-correlation... INFO @ Mon, 03 Jun 2019 22:27:28: end of X-cor INFO @ Mon, 03 Jun 2019 22:27:28: #2 finished! INFO @ Mon, 03 Jun 2019 22:27:28: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 22:27:28: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 22:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.05_model.r WARNING @ Mon, 03 Jun 2019 22:27:28: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:27:28: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 22:27:28: #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 22:27:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:27:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:27:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:28:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:28:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.20_summits.bed INFO @ Mon, 03 Jun 2019 22:28:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1642 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:28:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:28:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:28:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.10_summits.bed INFO @ Mon, 03 Jun 2019 22:28:25: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4940 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495313/SRX495313.05_summits.bed INFO @ Mon, 03 Jun 2019 22:28:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7476 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。