Job ID = 2590683 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 41,935,371 reads read : 83,870,742 reads written : 41,935,371 reads 0-length : 41,935,371 rm: cannot remove ‘[DSE]RR*’: 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: 00:18:51 41935371 reads; of these: 41935371 (100.00%) were unpaired; of these: 947944 (2.26%) aligned 0 times 27756566 (66.19%) aligned exactly 1 time 13230861 (31.55%) aligned >1 times 97.74% overall alignment rate Time searching: 00:18:51 Overall time: 00:18:51 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] 18349402 / 40987427 = 0.4477 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, 12 Aug 2019 23:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.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, 12 Aug 2019 23:43:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:43:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:43:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.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, 12 Aug 2019 23:43:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:43:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:44:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.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, 12 Aug 2019 23:44:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:44:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:44:06: 1000000 INFO @ Mon, 12 Aug 2019 23:44:09: 1000000 INFO @ Mon, 12 Aug 2019 23:44:11: 1000000 INFO @ Mon, 12 Aug 2019 23:44:13: 2000000 INFO @ Mon, 12 Aug 2019 23:44:18: 2000000 INFO @ Mon, 12 Aug 2019 23:44:20: 3000000 INFO @ Mon, 12 Aug 2019 23:44:20: 2000000 INFO @ Mon, 12 Aug 2019 23:44:27: 4000000 INFO @ Mon, 12 Aug 2019 23:44:27: 3000000 INFO @ Mon, 12 Aug 2019 23:44:30: 3000000 INFO @ Mon, 12 Aug 2019 23:44:34: 5000000 INFO @ Mon, 12 Aug 2019 23:44:37: 4000000 INFO @ Mon, 12 Aug 2019 23:44:39: 4000000 INFO @ Mon, 12 Aug 2019 23:44:41: 6000000 INFO @ Mon, 12 Aug 2019 23:44:46: 5000000 INFO @ Mon, 12 Aug 2019 23:44:48: 5000000 INFO @ Mon, 12 Aug 2019 23:44:48: 7000000 INFO @ Mon, 12 Aug 2019 23:44:54: 6000000 INFO @ Mon, 12 Aug 2019 23:44:55: 8000000 INFO @ Mon, 12 Aug 2019 23:44:57: 6000000 INFO @ Mon, 12 Aug 2019 23:45:02: 9000000 INFO @ Mon, 12 Aug 2019 23:45:03: 7000000 INFO @ Mon, 12 Aug 2019 23:45:07: 7000000 INFO @ Mon, 12 Aug 2019 23:45:09: 10000000 INFO @ Mon, 12 Aug 2019 23:45:12: 8000000 INFO @ Mon, 12 Aug 2019 23:45:16: 8000000 INFO @ Mon, 12 Aug 2019 23:45:16: 11000000 INFO @ Mon, 12 Aug 2019 23:45:21: 9000000 INFO @ Mon, 12 Aug 2019 23:45:24: 12000000 INFO @ Mon, 12 Aug 2019 23:45:25: 9000000 INFO @ Mon, 12 Aug 2019 23:45:30: 10000000 INFO @ Mon, 12 Aug 2019 23:45:31: 13000000 INFO @ Mon, 12 Aug 2019 23:45:34: 10000000 INFO @ Mon, 12 Aug 2019 23:45:38: 14000000 INFO @ Mon, 12 Aug 2019 23:45:39: 11000000 INFO @ Mon, 12 Aug 2019 23:45:43: 11000000 INFO @ Mon, 12 Aug 2019 23:45:45: 15000000 INFO @ Mon, 12 Aug 2019 23:45:48: 12000000 INFO @ Mon, 12 Aug 2019 23:45:52: 16000000 INFO @ Mon, 12 Aug 2019 23:45:53: 12000000 INFO @ Mon, 12 Aug 2019 23:45:57: 13000000 INFO @ Mon, 12 Aug 2019 23:45:59: 17000000 INFO @ Mon, 12 Aug 2019 23:46:02: 13000000 INFO @ Mon, 12 Aug 2019 23:46:06: 14000000 INFO @ Mon, 12 Aug 2019 23:46:06: 18000000 INFO @ Mon, 12 Aug 2019 23:46:11: 14000000 INFO @ Mon, 12 Aug 2019 23:46:13: 19000000 INFO @ Mon, 12 Aug 2019 23:46:15: 15000000 INFO @ Mon, 12 Aug 2019 23:46:20: 20000000 INFO @ Mon, 12 Aug 2019 23:46:20: 15000000 INFO @ Mon, 12 Aug 2019 23:46:24: 16000000 INFO @ Mon, 12 Aug 2019 23:46:27: 21000000 INFO @ Mon, 12 Aug 2019 23:46:29: 16000000 INFO @ Mon, 12 Aug 2019 23:46:32: 17000000 INFO @ Mon, 12 Aug 2019 23:46:34: 22000000 INFO @ Mon, 12 Aug 2019 23:46:38: 17000000 INFO @ Mon, 12 Aug 2019 23:46:39: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:46:39: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:46:39: #1 total tags in treatment: 22638025 INFO @ Mon, 12 Aug 2019 23:46:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:46:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:46:39: #1 tags after filtering in treatment: 22638025 INFO @ Mon, 12 Aug 2019 23:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:46:39: #1 finished! INFO @ Mon, 12 Aug 2019 23:46:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:46:41: #2 number of paired peaks: 469 WARNING @ Mon, 12 Aug 2019 23:46:41: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 12 Aug 2019 23:46:41: start model_add_line... INFO @ Mon, 12 Aug 2019 23:46:41: 18000000 INFO @ Mon, 12 Aug 2019 23:46:41: start X-correlation... INFO @ Mon, 12 Aug 2019 23:46:41: end of X-cor INFO @ Mon, 12 Aug 2019 23:46:41: #2 finished! INFO @ Mon, 12 Aug 2019 23:46:41: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:46:41: #2 alternative fragment length(s) may be 2,49,592 bps INFO @ Mon, 12 Aug 2019 23:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.05_model.r WARNING @ Mon, 12 Aug 2019 23:46:41: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:46:41: #2 You may need to consider one of the other alternative d(s): 2,49,592 WARNING @ Mon, 12 Aug 2019 23:46:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:46:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:46:48: 18000000 INFO @ Mon, 12 Aug 2019 23:46:50: 19000000 INFO @ Mon, 12 Aug 2019 23:46:57: 19000000 INFO @ Mon, 12 Aug 2019 23:46:59: 20000000 INFO @ Mon, 12 Aug 2019 23:47:06: 20000000 INFO @ Mon, 12 Aug 2019 23:47:08: 21000000 INFO @ Mon, 12 Aug 2019 23:47:15: 21000000 INFO @ Mon, 12 Aug 2019 23:47:16: 22000000 INFO @ Mon, 12 Aug 2019 23:47:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:47:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:47:22: #1 total tags in treatment: 22638025 INFO @ Mon, 12 Aug 2019 23:47:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:47:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:47:22: #1 tags after filtering in treatment: 22638025 INFO @ Mon, 12 Aug 2019 23:47:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:47:22: #1 finished! INFO @ Mon, 12 Aug 2019 23:47:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:47:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:47:24: 22000000 INFO @ Mon, 12 Aug 2019 23:47:24: #2 number of paired peaks: 469 WARNING @ Mon, 12 Aug 2019 23:47:24: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 12 Aug 2019 23:47:24: start model_add_line... INFO @ Mon, 12 Aug 2019 23:47:25: start X-correlation... INFO @ Mon, 12 Aug 2019 23:47:25: end of X-cor INFO @ Mon, 12 Aug 2019 23:47:25: #2 finished! INFO @ Mon, 12 Aug 2019 23:47:25: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:47:25: #2 alternative fragment length(s) may be 2,49,592 bps INFO @ Mon, 12 Aug 2019 23:47:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.10_model.r WARNING @ Mon, 12 Aug 2019 23:47:25: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:47:25: #2 You may need to consider one of the other alternative d(s): 2,49,592 WARNING @ Mon, 12 Aug 2019 23:47:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:47:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:47:29: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:47:29: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:47:29: #1 total tags in treatment: 22638025 INFO @ Mon, 12 Aug 2019 23:47:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:47:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:47:30: #1 tags after filtering in treatment: 22638025 INFO @ Mon, 12 Aug 2019 23:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:47:30: #1 finished! INFO @ Mon, 12 Aug 2019 23:47:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:47:32: #2 number of paired peaks: 469 WARNING @ Mon, 12 Aug 2019 23:47:32: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 12 Aug 2019 23:47:32: start model_add_line... INFO @ Mon, 12 Aug 2019 23:47:32: start X-correlation... INFO @ Mon, 12 Aug 2019 23:47:32: end of X-cor INFO @ Mon, 12 Aug 2019 23:47:32: #2 finished! INFO @ Mon, 12 Aug 2019 23:47:32: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:47:32: #2 alternative fragment length(s) may be 2,49,592 bps INFO @ Mon, 12 Aug 2019 23:47:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.20_model.r WARNING @ Mon, 12 Aug 2019 23:47:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:47:32: #2 You may need to consider one of the other alternative d(s): 2,49,592 WARNING @ Mon, 12 Aug 2019 23:47:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:47:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:47:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.05_summits.bed INFO @ Mon, 12 Aug 2019 23:48:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4038 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:48:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:48:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.10_summits.bed INFO @ Mon, 12 Aug 2019 23:48:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2311 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:48:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:48:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011029/SRX5011029.20_summits.bed INFO @ Mon, 12 Aug 2019 23:48:56: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。