Job ID = 2590625 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,162,813 reads read : 25,162,813 reads written : 25,162,813 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198773.sra.cache’: 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: 00:10:07 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1368963 (5.44%) aligned 0 times 16619140 (66.05%) aligned exactly 1 time 7174710 (28.51%) aligned >1 times 94.56% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 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] 5652350 / 23793850 = 0.2376 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 23:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.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 23:03:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:03:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.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 23:03:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:03:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.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 23:03:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:03:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:03:32: 1000000 INFO @ Mon, 12 Aug 2019 23:03:33: 1000000 INFO @ Mon, 12 Aug 2019 23:03:34: 1000000 INFO @ Mon, 12 Aug 2019 23:03:38: 2000000 INFO @ Mon, 12 Aug 2019 23:03:40: 2000000 INFO @ Mon, 12 Aug 2019 23:03:41: 2000000 INFO @ Mon, 12 Aug 2019 23:03:44: 3000000 INFO @ Mon, 12 Aug 2019 23:03:47: 3000000 INFO @ Mon, 12 Aug 2019 23:03:48: 3000000 INFO @ Mon, 12 Aug 2019 23:03:51: 4000000 INFO @ Mon, 12 Aug 2019 23:03:54: 4000000 INFO @ Mon, 12 Aug 2019 23:03:55: 4000000 INFO @ Mon, 12 Aug 2019 23:03:57: 5000000 INFO @ Mon, 12 Aug 2019 23:04:01: 5000000 INFO @ Mon, 12 Aug 2019 23:04:02: 5000000 INFO @ Mon, 12 Aug 2019 23:04:04: 6000000 INFO @ Mon, 12 Aug 2019 23:04:08: 6000000 INFO @ Mon, 12 Aug 2019 23:04:09: 6000000 INFO @ Mon, 12 Aug 2019 23:04:10: 7000000 INFO @ Mon, 12 Aug 2019 23:04:15: 7000000 INFO @ Mon, 12 Aug 2019 23:04:16: 7000000 INFO @ Mon, 12 Aug 2019 23:04:17: 8000000 INFO @ Mon, 12 Aug 2019 23:04:22: 8000000 INFO @ Mon, 12 Aug 2019 23:04:23: 9000000 INFO @ Mon, 12 Aug 2019 23:04:23: 8000000 INFO @ Mon, 12 Aug 2019 23:04:29: 9000000 INFO @ Mon, 12 Aug 2019 23:04:29: 10000000 INFO @ Mon, 12 Aug 2019 23:04:30: 9000000 INFO @ Mon, 12 Aug 2019 23:04:36: 11000000 INFO @ Mon, 12 Aug 2019 23:04:36: 10000000 INFO @ Mon, 12 Aug 2019 23:04:37: 10000000 INFO @ Mon, 12 Aug 2019 23:04:42: 12000000 INFO @ Mon, 12 Aug 2019 23:04:43: 11000000 INFO @ Mon, 12 Aug 2019 23:04:44: 11000000 INFO @ Mon, 12 Aug 2019 23:04:48: 13000000 INFO @ Mon, 12 Aug 2019 23:04:49: 12000000 INFO @ Mon, 12 Aug 2019 23:04:51: 12000000 INFO @ Mon, 12 Aug 2019 23:04:55: 14000000 INFO @ Mon, 12 Aug 2019 23:04:56: 13000000 INFO @ Mon, 12 Aug 2019 23:04:57: 13000000 INFO @ Mon, 12 Aug 2019 23:05:01: 15000000 INFO @ Mon, 12 Aug 2019 23:05:03: 14000000 INFO @ Mon, 12 Aug 2019 23:05:04: 14000000 INFO @ Mon, 12 Aug 2019 23:05:08: 16000000 INFO @ Mon, 12 Aug 2019 23:05:10: 15000000 INFO @ Mon, 12 Aug 2019 23:05:11: 15000000 INFO @ Mon, 12 Aug 2019 23:05:14: 17000000 INFO @ Mon, 12 Aug 2019 23:05:17: 16000000 INFO @ Mon, 12 Aug 2019 23:05:18: 16000000 INFO @ Mon, 12 Aug 2019 23:05:20: 18000000 INFO @ Mon, 12 Aug 2019 23:05:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:05:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:05:21: #1 total tags in treatment: 18141500 INFO @ Mon, 12 Aug 2019 23:05:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:05:21: #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 23:05:22: #1 tags after filtering in treatment: 18141500 INFO @ Mon, 12 Aug 2019 23:05:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:05:22: #1 finished! INFO @ Mon, 12 Aug 2019 23:05:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:05:23: #2 number of paired peaks: 116 WARNING @ Mon, 12 Aug 2019 23:05:23: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 12 Aug 2019 23:05:23: start model_add_line... INFO @ Mon, 12 Aug 2019 23:05:23: start X-correlation... INFO @ Mon, 12 Aug 2019 23:05:23: end of X-cor INFO @ Mon, 12 Aug 2019 23:05:23: #2 finished! INFO @ Mon, 12 Aug 2019 23:05:23: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 23:05:23: #2 alternative fragment length(s) may be 4,10,48,156,193,302,468,505,592 bps INFO @ Mon, 12 Aug 2019 23:05:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.05_model.r WARNING @ Mon, 12 Aug 2019 23:05:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:05:23: #2 You may need to consider one of the other alternative d(s): 4,10,48,156,193,302,468,505,592 WARNING @ Mon, 12 Aug 2019 23:05:23: #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 23:05:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:05:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:05:24: 17000000 INFO @ Mon, 12 Aug 2019 23:05:25: 17000000 INFO @ Mon, 12 Aug 2019 23:05:31: 18000000 INFO @ Mon, 12 Aug 2019 23:05:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:05:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:05:32: #1 total tags in treatment: 18141500 INFO @ Mon, 12 Aug 2019 23:05:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:05:32: #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 23:05:32: 18000000 INFO @ Mon, 12 Aug 2019 23:05:32: #1 tags after filtering in treatment: 18141500 INFO @ Mon, 12 Aug 2019 23:05:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:05:32: #1 finished! INFO @ Mon, 12 Aug 2019 23:05:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:05:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:05:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:05:33: #1 total tags in treatment: 18141500 INFO @ Mon, 12 Aug 2019 23:05:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:05:33: #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 23:05:33: #1 tags after filtering in treatment: 18141500 INFO @ Mon, 12 Aug 2019 23:05:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:05:33: #1 finished! INFO @ Mon, 12 Aug 2019 23:05:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:05:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:05:34: #2 number of paired peaks: 116 WARNING @ Mon, 12 Aug 2019 23:05:34: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 12 Aug 2019 23:05:34: start model_add_line... INFO @ Mon, 12 Aug 2019 23:05:34: start X-correlation... INFO @ Mon, 12 Aug 2019 23:05:34: end of X-cor INFO @ Mon, 12 Aug 2019 23:05:34: #2 finished! INFO @ Mon, 12 Aug 2019 23:05:34: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 23:05:34: #2 alternative fragment length(s) may be 4,10,48,156,193,302,468,505,592 bps INFO @ Mon, 12 Aug 2019 23:05:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.10_model.r WARNING @ Mon, 12 Aug 2019 23:05:34: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:05:34: #2 You may need to consider one of the other alternative d(s): 4,10,48,156,193,302,468,505,592 WARNING @ Mon, 12 Aug 2019 23:05:34: #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 23:05:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:05:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:05:35: #2 number of paired peaks: 116 WARNING @ Mon, 12 Aug 2019 23:05:35: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 12 Aug 2019 23:05:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:05:35: start X-correlation... INFO @ Mon, 12 Aug 2019 23:05:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:05:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:05:35: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 23:05:35: #2 alternative fragment length(s) may be 4,10,48,156,193,302,468,505,592 bps INFO @ Mon, 12 Aug 2019 23:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.20_model.r WARNING @ Mon, 12 Aug 2019 23:05:35: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:05:35: #2 You may need to consider one of the other alternative d(s): 4,10,48,156,193,302,468,505,592 WARNING @ Mon, 12 Aug 2019 23:05:35: #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 23:05:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:06:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:06:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:06:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:06:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:06:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.05_summits.bed INFO @ Mon, 12 Aug 2019 23:06:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2369 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:06:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:06:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:06:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.10_summits.bed INFO @ Mon, 12 Aug 2019 23:06:43: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1099 records, 4 fields): 104 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:06:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495268/SRX495268.20_summits.bed INFO @ Mon, 12 Aug 2019 23:06:44: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。