Job ID = 2590285 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,781,432 reads read : 17,781,432 reads written : 17,781,432 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: 00:09:10 17781432 reads; of these: 17781432 (100.00%) were unpaired; of these: 826960 (4.65%) aligned 0 times 10836373 (60.94%) aligned exactly 1 time 6118099 (34.41%) aligned >1 times 95.35% overall alignment rate Time searching: 00:09:10 Overall time: 00:09:10 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 8 files... [bam_rmdupse_core] 2674245 / 16954472 = 0.1577 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 20:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.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 20:50:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:50:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.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 20:50:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:50:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.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 20:50:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:50:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:50:38: 1000000 INFO @ Mon, 12 Aug 2019 20:50:40: 1000000 INFO @ Mon, 12 Aug 2019 20:50:41: 1000000 INFO @ Mon, 12 Aug 2019 20:50:46: 2000000 INFO @ Mon, 12 Aug 2019 20:50:49: 2000000 INFO @ Mon, 12 Aug 2019 20:50:51: 2000000 INFO @ Mon, 12 Aug 2019 20:50:54: 3000000 INFO @ Mon, 12 Aug 2019 20:50:57: 3000000 INFO @ Mon, 12 Aug 2019 20:51:02: 3000000 INFO @ Mon, 12 Aug 2019 20:51:02: 4000000 INFO @ Mon, 12 Aug 2019 20:51:05: 4000000 INFO @ Mon, 12 Aug 2019 20:51:10: 5000000 INFO @ Mon, 12 Aug 2019 20:51:12: 4000000 INFO @ Mon, 12 Aug 2019 20:51:13: 5000000 INFO @ Mon, 12 Aug 2019 20:51:18: 6000000 INFO @ Mon, 12 Aug 2019 20:51:22: 6000000 INFO @ Mon, 12 Aug 2019 20:51:22: 5000000 INFO @ Mon, 12 Aug 2019 20:51:25: 7000000 INFO @ Mon, 12 Aug 2019 20:51:30: 7000000 INFO @ Mon, 12 Aug 2019 20:51:32: 6000000 INFO @ Mon, 12 Aug 2019 20:51:34: 8000000 INFO @ Mon, 12 Aug 2019 20:51:39: 8000000 INFO @ Mon, 12 Aug 2019 20:51:42: 9000000 INFO @ Mon, 12 Aug 2019 20:51:43: 7000000 INFO @ Mon, 12 Aug 2019 20:51:48: 9000000 INFO @ Mon, 12 Aug 2019 20:51:51: 10000000 INFO @ Mon, 12 Aug 2019 20:51:53: 8000000 INFO @ Mon, 12 Aug 2019 20:51:58: 10000000 INFO @ Mon, 12 Aug 2019 20:51:59: 11000000 INFO @ Mon, 12 Aug 2019 20:52:04: 9000000 INFO @ Mon, 12 Aug 2019 20:52:07: 12000000 INFO @ Mon, 12 Aug 2019 20:52:08: 11000000 INFO @ Mon, 12 Aug 2019 20:52:14: 10000000 INFO @ Mon, 12 Aug 2019 20:52:15: 13000000 INFO @ Mon, 12 Aug 2019 20:52:17: 12000000 INFO @ Mon, 12 Aug 2019 20:52:23: 14000000 INFO @ Mon, 12 Aug 2019 20:52:24: 11000000 INFO @ Mon, 12 Aug 2019 20:52:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:52:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:52:25: #1 total tags in treatment: 14280227 INFO @ Mon, 12 Aug 2019 20:52:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:52:25: #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 20:52:25: #1 tags after filtering in treatment: 14280227 INFO @ Mon, 12 Aug 2019 20:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:52:25: #1 finished! INFO @ Mon, 12 Aug 2019 20:52:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:52:26: 13000000 INFO @ Mon, 12 Aug 2019 20:52:26: #2 number of paired peaks: 317 WARNING @ Mon, 12 Aug 2019 20:52:26: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Mon, 12 Aug 2019 20:52:26: start model_add_line... INFO @ Mon, 12 Aug 2019 20:52:27: start X-correlation... INFO @ Mon, 12 Aug 2019 20:52:27: end of X-cor INFO @ Mon, 12 Aug 2019 20:52:27: #2 finished! INFO @ Mon, 12 Aug 2019 20:52:27: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:52:27: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 20:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.05_model.r WARNING @ Mon, 12 Aug 2019 20:52:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:52:27: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 20:52:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:52:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:52:34: 12000000 INFO @ Mon, 12 Aug 2019 20:52:34: 14000000 INFO @ Mon, 12 Aug 2019 20:52:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:52:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:52:37: #1 total tags in treatment: 14280227 INFO @ Mon, 12 Aug 2019 20:52:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:52:37: #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 20:52:37: #1 tags after filtering in treatment: 14280227 INFO @ Mon, 12 Aug 2019 20:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:52:37: #1 finished! INFO @ Mon, 12 Aug 2019 20:52:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:52:38: #2 number of paired peaks: 317 WARNING @ Mon, 12 Aug 2019 20:52:38: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Mon, 12 Aug 2019 20:52:38: start model_add_line... INFO @ Mon, 12 Aug 2019 20:52:38: start X-correlation... INFO @ Mon, 12 Aug 2019 20:52:38: end of X-cor INFO @ Mon, 12 Aug 2019 20:52:38: #2 finished! INFO @ Mon, 12 Aug 2019 20:52:38: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:52:38: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 20:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.20_model.r WARNING @ Mon, 12 Aug 2019 20:52:38: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:52:38: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 20:52:38: #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 20:52:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:52:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:52:44: 13000000 INFO @ Mon, 12 Aug 2019 20:52:54: 14000000 INFO @ Mon, 12 Aug 2019 20:52:56: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:52:56: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:52:56: #1 total tags in treatment: 14280227 INFO @ Mon, 12 Aug 2019 20:52:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:52:56: #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 20:52:57: #1 tags after filtering in treatment: 14280227 INFO @ Mon, 12 Aug 2019 20:52:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:52:57: #1 finished! INFO @ Mon, 12 Aug 2019 20:52:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:52:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:52:58: #2 number of paired peaks: 317 WARNING @ Mon, 12 Aug 2019 20:52:58: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Mon, 12 Aug 2019 20:52:58: start model_add_line... INFO @ Mon, 12 Aug 2019 20:52:58: start X-correlation... INFO @ Mon, 12 Aug 2019 20:52:58: end of X-cor INFO @ Mon, 12 Aug 2019 20:52:58: #2 finished! INFO @ Mon, 12 Aug 2019 20:52:58: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:52:58: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 20:52:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.10_model.r WARNING @ Mon, 12 Aug 2019 20:52:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:52:58: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 20:52:58: #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 20:52:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:52:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:53:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:53:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.05_summits.bed INFO @ Mon, 12 Aug 2019 20:53:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2198 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:53:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:53:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:53:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.20_summits.bed INFO @ Mon, 12 Aug 2019 20:53:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1435 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:53:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:53:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:53:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:53:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287765/SRX287765.10_summits.bed INFO @ Mon, 12 Aug 2019 20:53:55: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1863 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。