Job ID = 1308658 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,775,092 reads read : 57,550,184 reads written : 28,775,092 reads 0-length : 28,775,092 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: 00:16:15 28775092 reads; of these: 28775092 (100.00%) were unpaired; of these: 1384237 (4.81%) aligned 0 times 18666762 (64.87%) aligned exactly 1 time 8724093 (30.32%) aligned >1 times 95.19% overall alignment rate Time searching: 00:16:15 Overall time: 00:16:15 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 12 files... [bam_rmdupse_core] 3626032 / 27390855 = 0.1324 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 23:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.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 23:30:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:30:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.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 23:30:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:30:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.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 23:30:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:30:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:30:38: 1000000 INFO @ Mon, 03 Jun 2019 23:30:40: 1000000 INFO @ Mon, 03 Jun 2019 23:30:41: 1000000 INFO @ Mon, 03 Jun 2019 23:30:47: 2000000 INFO @ Mon, 03 Jun 2019 23:30:52: 2000000 INFO @ Mon, 03 Jun 2019 23:30:53: 2000000 INFO @ Mon, 03 Jun 2019 23:30:56: 3000000 INFO @ Mon, 03 Jun 2019 23:31:05: 3000000 INFO @ Mon, 03 Jun 2019 23:31:06: 3000000 INFO @ Mon, 03 Jun 2019 23:31:06: 4000000 INFO @ Mon, 03 Jun 2019 23:31:15: 5000000 INFO @ Mon, 03 Jun 2019 23:31:17: 4000000 INFO @ Mon, 03 Jun 2019 23:31:18: 4000000 INFO @ Mon, 03 Jun 2019 23:31:25: 6000000 INFO @ Mon, 03 Jun 2019 23:31:30: 5000000 INFO @ Mon, 03 Jun 2019 23:31:31: 5000000 INFO @ Mon, 03 Jun 2019 23:31:34: 7000000 INFO @ Mon, 03 Jun 2019 23:31:43: 6000000 INFO @ Mon, 03 Jun 2019 23:31:43: 8000000 INFO @ Mon, 03 Jun 2019 23:31:44: 6000000 INFO @ Mon, 03 Jun 2019 23:31:52: 9000000 INFO @ Mon, 03 Jun 2019 23:31:55: 7000000 INFO @ Mon, 03 Jun 2019 23:31:56: 7000000 INFO @ Mon, 03 Jun 2019 23:32:02: 10000000 INFO @ Mon, 03 Jun 2019 23:32:08: 8000000 INFO @ Mon, 03 Jun 2019 23:32:08: 8000000 INFO @ Mon, 03 Jun 2019 23:32:11: 11000000 INFO @ Mon, 03 Jun 2019 23:32:19: 9000000 INFO @ Mon, 03 Jun 2019 23:32:20: 9000000 INFO @ Mon, 03 Jun 2019 23:32:21: 12000000 INFO @ Mon, 03 Jun 2019 23:32:31: 13000000 INFO @ Mon, 03 Jun 2019 23:32:32: 10000000 INFO @ Mon, 03 Jun 2019 23:32:33: 10000000 INFO @ Mon, 03 Jun 2019 23:32:40: 14000000 INFO @ Mon, 03 Jun 2019 23:32:44: 11000000 INFO @ Mon, 03 Jun 2019 23:32:45: 11000000 INFO @ Mon, 03 Jun 2019 23:32:49: 15000000 INFO @ Mon, 03 Jun 2019 23:32:57: 12000000 INFO @ Mon, 03 Jun 2019 23:32:58: 12000000 INFO @ Mon, 03 Jun 2019 23:32:59: 16000000 INFO @ Mon, 03 Jun 2019 23:33:08: 17000000 INFO @ Mon, 03 Jun 2019 23:33:09: 13000000 INFO @ Mon, 03 Jun 2019 23:33:10: 13000000 INFO @ Mon, 03 Jun 2019 23:33:18: 18000000 INFO @ Mon, 03 Jun 2019 23:33:22: 14000000 INFO @ Mon, 03 Jun 2019 23:33:22: 14000000 INFO @ Mon, 03 Jun 2019 23:33:29: 19000000 INFO @ Mon, 03 Jun 2019 23:33:34: 15000000 INFO @ Mon, 03 Jun 2019 23:33:36: 15000000 INFO @ Mon, 03 Jun 2019 23:33:38: 20000000 INFO @ Mon, 03 Jun 2019 23:33:47: 16000000 INFO @ Mon, 03 Jun 2019 23:33:47: 21000000 INFO @ Mon, 03 Jun 2019 23:33:48: 16000000 INFO @ Mon, 03 Jun 2019 23:33:57: 22000000 INFO @ Mon, 03 Jun 2019 23:33:59: 17000000 INFO @ Mon, 03 Jun 2019 23:34:00: 17000000 INFO @ Mon, 03 Jun 2019 23:34:07: 23000000 INFO @ Mon, 03 Jun 2019 23:34:12: 18000000 INFO @ Mon, 03 Jun 2019 23:34:12: 18000000 INFO @ Mon, 03 Jun 2019 23:34:14: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:34:14: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:34:14: #1 total tags in treatment: 23764823 INFO @ Mon, 03 Jun 2019 23:34:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:34:14: #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 23:34:15: #1 tags after filtering in treatment: 23764823 INFO @ Mon, 03 Jun 2019 23:34:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:34:15: #1 finished! INFO @ Mon, 03 Jun 2019 23:34:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:34:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:34:17: #2 number of paired peaks: 105 WARNING @ Mon, 03 Jun 2019 23:34:17: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Mon, 03 Jun 2019 23:34:17: start model_add_line... INFO @ Mon, 03 Jun 2019 23:34:17: start X-correlation... INFO @ Mon, 03 Jun 2019 23:34:17: end of X-cor INFO @ Mon, 03 Jun 2019 23:34:17: #2 finished! INFO @ Mon, 03 Jun 2019 23:34:17: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 23:34:17: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 23:34:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.05_model.r WARNING @ Mon, 03 Jun 2019 23:34:17: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:34:17: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 23:34:17: #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 23:34:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:34:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:34:24: 19000000 INFO @ Mon, 03 Jun 2019 23:34:25: 19000000 INFO @ Mon, 03 Jun 2019 23:34:36: 20000000 INFO @ Mon, 03 Jun 2019 23:34:37: 20000000 INFO @ Mon, 03 Jun 2019 23:34:49: 21000000 INFO @ Mon, 03 Jun 2019 23:34:50: 21000000 INFO @ Mon, 03 Jun 2019 23:35:01: 22000000 INFO @ Mon, 03 Jun 2019 23:35:02: 22000000 INFO @ Mon, 03 Jun 2019 23:35:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:35:14: 23000000 INFO @ Mon, 03 Jun 2019 23:35:14: 23000000 INFO @ Mon, 03 Jun 2019 23:35:23: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:35:23: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:35:23: #1 total tags in treatment: 23764823 INFO @ Mon, 03 Jun 2019 23:35:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:35:23: #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 23:35:24: #1 tags after filtering in treatment: 23764823 INFO @ Mon, 03 Jun 2019 23:35:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:35:24: #1 finished! INFO @ Mon, 03 Jun 2019 23:35:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:35:25: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:35:25: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:35:25: #1 total tags in treatment: 23764823 INFO @ Mon, 03 Jun 2019 23:35:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:35:25: #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 23:35:25: #1 tags after filtering in treatment: 23764823 INFO @ Mon, 03 Jun 2019 23:35:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:35:25: #1 finished! INFO @ Mon, 03 Jun 2019 23:35:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:35:26: #2 number of paired peaks: 105 WARNING @ Mon, 03 Jun 2019 23:35:26: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Mon, 03 Jun 2019 23:35:26: start model_add_line... INFO @ Mon, 03 Jun 2019 23:35:26: start X-correlation... INFO @ Mon, 03 Jun 2019 23:35:26: end of X-cor INFO @ Mon, 03 Jun 2019 23:35:26: #2 finished! INFO @ Mon, 03 Jun 2019 23:35:26: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 23:35:26: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 23:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.10_model.r WARNING @ Mon, 03 Jun 2019 23:35:26: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:35:26: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 23:35:26: #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 23:35:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:35:27: #2 number of paired peaks: 105 WARNING @ Mon, 03 Jun 2019 23:35:27: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Mon, 03 Jun 2019 23:35:27: start model_add_line... INFO @ Mon, 03 Jun 2019 23:35:27: start X-correlation... INFO @ Mon, 03 Jun 2019 23:35:27: end of X-cor INFO @ Mon, 03 Jun 2019 23:35:27: #2 finished! INFO @ Mon, 03 Jun 2019 23:35:27: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 23:35:27: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 23:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.20_model.r WARNING @ Mon, 03 Jun 2019 23:35:27: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:35:27: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 23:35:27: #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 23:35:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:35:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:35:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:35:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:35:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.05_summits.bed INFO @ Mon, 03 Jun 2019 23:35:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1917 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:36:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:36:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.10_summits.bed INFO @ Mon, 03 Jun 2019 23:36:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1435 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:36:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:36:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:36:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343158/SRX5343158.20_summits.bed INFO @ Mon, 03 Jun 2019 23:36:51: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1083 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。