Job ID = 2590823 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 54,438,852 reads read : 108,877,704 reads written : 54,438,852 reads 0-length : 54,438,852 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: 00:21:53 54438852 reads; of these: 54438852 (100.00%) were unpaired; of these: 4301662 (7.90%) aligned 0 times 37726875 (69.30%) aligned exactly 1 time 12410315 (22.80%) aligned >1 times 92.10% overall alignment rate Time searching: 00:21:53 Overall time: 00:21:53 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 24 files... [bam_rmdupse_core] 23455605 / 50137190 = 0.4678 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 @ Tue, 13 Aug 2019 00:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.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 @ Tue, 13 Aug 2019 00:06:44: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:06:44: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.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 @ Tue, 13 Aug 2019 00:06:45: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:06:45: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.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 @ Tue, 13 Aug 2019 00:06:46: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:06:46: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:06:53: 1000000 INFO @ Tue, 13 Aug 2019 00:06:54: 1000000 INFO @ Tue, 13 Aug 2019 00:06:56: 1000000 INFO @ Tue, 13 Aug 2019 00:07:02: 2000000 INFO @ Tue, 13 Aug 2019 00:07:04: 2000000 INFO @ Tue, 13 Aug 2019 00:07:06: 2000000 INFO @ Tue, 13 Aug 2019 00:07:12: 3000000 INFO @ Tue, 13 Aug 2019 00:07:13: 3000000 INFO @ Tue, 13 Aug 2019 00:07:16: 3000000 INFO @ Tue, 13 Aug 2019 00:07:21: 4000000 INFO @ Tue, 13 Aug 2019 00:07:22: 4000000 INFO @ Tue, 13 Aug 2019 00:07:26: 4000000 INFO @ Tue, 13 Aug 2019 00:07:30: 5000000 INFO @ Tue, 13 Aug 2019 00:07:31: 5000000 INFO @ Tue, 13 Aug 2019 00:07:36: 5000000 INFO @ Tue, 13 Aug 2019 00:07:39: 6000000 INFO @ Tue, 13 Aug 2019 00:07:40: 6000000 INFO @ Tue, 13 Aug 2019 00:07:45: 6000000 INFO @ Tue, 13 Aug 2019 00:07:48: 7000000 INFO @ Tue, 13 Aug 2019 00:07:49: 7000000 INFO @ Tue, 13 Aug 2019 00:07:55: 7000000 INFO @ Tue, 13 Aug 2019 00:07:57: 8000000 INFO @ Tue, 13 Aug 2019 00:07:58: 8000000 INFO @ Tue, 13 Aug 2019 00:08:05: 8000000 INFO @ Tue, 13 Aug 2019 00:08:06: 9000000 INFO @ Tue, 13 Aug 2019 00:08:07: 9000000 INFO @ Tue, 13 Aug 2019 00:08:15: 9000000 INFO @ Tue, 13 Aug 2019 00:08:15: 10000000 INFO @ Tue, 13 Aug 2019 00:08:16: 10000000 INFO @ Tue, 13 Aug 2019 00:08:24: 11000000 INFO @ Tue, 13 Aug 2019 00:08:24: 10000000 INFO @ Tue, 13 Aug 2019 00:08:25: 11000000 INFO @ Tue, 13 Aug 2019 00:08:33: 12000000 INFO @ Tue, 13 Aug 2019 00:08:34: 12000000 INFO @ Tue, 13 Aug 2019 00:08:34: 11000000 INFO @ Tue, 13 Aug 2019 00:08:42: 13000000 INFO @ Tue, 13 Aug 2019 00:08:43: 13000000 INFO @ Tue, 13 Aug 2019 00:08:44: 12000000 INFO @ Tue, 13 Aug 2019 00:08:50: 14000000 INFO @ Tue, 13 Aug 2019 00:08:52: 14000000 INFO @ Tue, 13 Aug 2019 00:08:54: 13000000 INFO @ Tue, 13 Aug 2019 00:08:59: 15000000 INFO @ Tue, 13 Aug 2019 00:09:00: 15000000 INFO @ Tue, 13 Aug 2019 00:09:03: 14000000 INFO @ Tue, 13 Aug 2019 00:09:08: 16000000 INFO @ Tue, 13 Aug 2019 00:09:09: 16000000 INFO @ Tue, 13 Aug 2019 00:09:13: 15000000 INFO @ Tue, 13 Aug 2019 00:09:17: 17000000 INFO @ Tue, 13 Aug 2019 00:09:18: 17000000 INFO @ Tue, 13 Aug 2019 00:09:23: 16000000 INFO @ Tue, 13 Aug 2019 00:09:26: 18000000 INFO @ Tue, 13 Aug 2019 00:09:27: 18000000 INFO @ Tue, 13 Aug 2019 00:09:32: 17000000 INFO @ Tue, 13 Aug 2019 00:09:35: 19000000 INFO @ Tue, 13 Aug 2019 00:09:36: 19000000 INFO @ Tue, 13 Aug 2019 00:09:42: 18000000 INFO @ Tue, 13 Aug 2019 00:09:44: 20000000 INFO @ Tue, 13 Aug 2019 00:09:45: 20000000 INFO @ Tue, 13 Aug 2019 00:09:52: 19000000 INFO @ Tue, 13 Aug 2019 00:09:52: 21000000 INFO @ Tue, 13 Aug 2019 00:09:54: 21000000 INFO @ Tue, 13 Aug 2019 00:10:01: 22000000 INFO @ Tue, 13 Aug 2019 00:10:02: 20000000 INFO @ Tue, 13 Aug 2019 00:10:03: 22000000 INFO @ Tue, 13 Aug 2019 00:10:10: 23000000 INFO @ Tue, 13 Aug 2019 00:10:11: 21000000 INFO @ Tue, 13 Aug 2019 00:10:11: 23000000 INFO @ Tue, 13 Aug 2019 00:10:19: 24000000 INFO @ Tue, 13 Aug 2019 00:10:20: 24000000 INFO @ Tue, 13 Aug 2019 00:10:21: 22000000 INFO @ Tue, 13 Aug 2019 00:10:28: 25000000 INFO @ Tue, 13 Aug 2019 00:10:29: 25000000 INFO @ Tue, 13 Aug 2019 00:10:31: 23000000 INFO @ Tue, 13 Aug 2019 00:10:37: 26000000 INFO @ Tue, 13 Aug 2019 00:10:38: 26000000 INFO @ Tue, 13 Aug 2019 00:10:40: 24000000 INFO @ Tue, 13 Aug 2019 00:10:43: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:10:43: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:10:43: #1 total tags in treatment: 26681585 INFO @ Tue, 13 Aug 2019 00:10:43: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:10:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:10:43: #1 tags after filtering in treatment: 26681585 INFO @ Tue, 13 Aug 2019 00:10:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:10:43: #1 finished! INFO @ Tue, 13 Aug 2019 00:10:43: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:10:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:10:44: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:10:44: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:10:44: #1 total tags in treatment: 26681585 INFO @ Tue, 13 Aug 2019 00:10:44: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:10:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:10:44: #1 tags after filtering in treatment: 26681585 INFO @ Tue, 13 Aug 2019 00:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:10:44: #1 finished! INFO @ Tue, 13 Aug 2019 00:10:44: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:10:46: #2 number of paired peaks: 257 WARNING @ Tue, 13 Aug 2019 00:10:46: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Tue, 13 Aug 2019 00:10:46: start model_add_line... INFO @ Tue, 13 Aug 2019 00:10:46: start X-correlation... INFO @ Tue, 13 Aug 2019 00:10:46: end of X-cor INFO @ Tue, 13 Aug 2019 00:10:46: #2 finished! INFO @ Tue, 13 Aug 2019 00:10:46: #2 predicted fragment length is 45 bps INFO @ Tue, 13 Aug 2019 00:10:46: #2 alternative fragment length(s) may be 45 bps INFO @ Tue, 13 Aug 2019 00:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.05_model.r WARNING @ Tue, 13 Aug 2019 00:10:46: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:10:46: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Tue, 13 Aug 2019 00:10:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:10:46: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:10:47: #2 number of paired peaks: 257 WARNING @ Tue, 13 Aug 2019 00:10:47: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Tue, 13 Aug 2019 00:10:47: start model_add_line... INFO @ Tue, 13 Aug 2019 00:10:47: start X-correlation... INFO @ Tue, 13 Aug 2019 00:10:47: end of X-cor INFO @ Tue, 13 Aug 2019 00:10:47: #2 finished! INFO @ Tue, 13 Aug 2019 00:10:47: #2 predicted fragment length is 45 bps INFO @ Tue, 13 Aug 2019 00:10:47: #2 alternative fragment length(s) may be 45 bps INFO @ Tue, 13 Aug 2019 00:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.10_model.r WARNING @ Tue, 13 Aug 2019 00:10:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:10:47: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Tue, 13 Aug 2019 00:10:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:10:47: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:10:50: 25000000 INFO @ Tue, 13 Aug 2019 00:10:59: 26000000 INFO @ Tue, 13 Aug 2019 00:11:05: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:11:05: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:11:05: #1 total tags in treatment: 26681585 INFO @ Tue, 13 Aug 2019 00:11:05: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:11:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:11:05: #1 tags after filtering in treatment: 26681585 INFO @ Tue, 13 Aug 2019 00:11:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:11:05: #1 finished! INFO @ Tue, 13 Aug 2019 00:11:05: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:11:08: #2 number of paired peaks: 257 WARNING @ Tue, 13 Aug 2019 00:11:08: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Tue, 13 Aug 2019 00:11:08: start model_add_line... INFO @ Tue, 13 Aug 2019 00:11:08: start X-correlation... INFO @ Tue, 13 Aug 2019 00:11:08: end of X-cor INFO @ Tue, 13 Aug 2019 00:11:08: #2 finished! INFO @ Tue, 13 Aug 2019 00:11:08: #2 predicted fragment length is 45 bps INFO @ Tue, 13 Aug 2019 00:11:08: #2 alternative fragment length(s) may be 45 bps INFO @ Tue, 13 Aug 2019 00:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.20_model.r WARNING @ Tue, 13 Aug 2019 00:11:08: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:11:08: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Tue, 13 Aug 2019 00:11:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:11:08: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:11:49: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:11:50: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:12:10: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.05_summits.bed INFO @ Tue, 13 Aug 2019 00:12:18: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6761 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:12:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:12:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:12:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.10_summits.bed INFO @ Tue, 13 Aug 2019 00:12:19: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4038 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011062/SRX5011062.20_summits.bed INFO @ Tue, 13 Aug 2019 00:12:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2333 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。