Job ID = 1294954 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,953,572 reads read : 18,953,572 reads written : 18,953,572 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: 00:10:20 18953572 reads; of these: 18953572 (100.00%) were unpaired; of these: 973785 (5.14%) aligned 0 times 11627678 (61.35%) aligned exactly 1 time 6352109 (33.51%) aligned >1 times 94.86% overall alignment rate Time searching: 00:10:20 Overall time: 00:10:20 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] 3038655 / 17979787 = 0.1690 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 11:17:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.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 11:17:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:17:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:17:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.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 11:17:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:17:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:17:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.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 11:17:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:17:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:18:06: 1000000 INFO @ Mon, 03 Jun 2019 11:18:07: 1000000 INFO @ Mon, 03 Jun 2019 11:18:07: 1000000 INFO @ Mon, 03 Jun 2019 11:18:13: 2000000 INFO @ Mon, 03 Jun 2019 11:18:15: 2000000 INFO @ Mon, 03 Jun 2019 11:18:16: 2000000 INFO @ Mon, 03 Jun 2019 11:18:21: 3000000 INFO @ Mon, 03 Jun 2019 11:18:23: 3000000 INFO @ Mon, 03 Jun 2019 11:18:25: 3000000 INFO @ Mon, 03 Jun 2019 11:18:28: 4000000 INFO @ Mon, 03 Jun 2019 11:18:31: 4000000 INFO @ Mon, 03 Jun 2019 11:18:33: 4000000 INFO @ Mon, 03 Jun 2019 11:18:36: 5000000 INFO @ Mon, 03 Jun 2019 11:18:39: 5000000 INFO @ Mon, 03 Jun 2019 11:18:42: 5000000 INFO @ Mon, 03 Jun 2019 11:18:44: 6000000 INFO @ Mon, 03 Jun 2019 11:18:48: 6000000 INFO @ Mon, 03 Jun 2019 11:18:51: 6000000 INFO @ Mon, 03 Jun 2019 11:18:51: 7000000 INFO @ Mon, 03 Jun 2019 11:18:56: 7000000 INFO @ Mon, 03 Jun 2019 11:18:59: 8000000 INFO @ Mon, 03 Jun 2019 11:19:00: 7000000 INFO @ Mon, 03 Jun 2019 11:19:04: 8000000 INFO @ Mon, 03 Jun 2019 11:19:07: 9000000 INFO @ Mon, 03 Jun 2019 11:19:09: 8000000 INFO @ Mon, 03 Jun 2019 11:19:13: 9000000 INFO @ Mon, 03 Jun 2019 11:19:15: 10000000 INFO @ Mon, 03 Jun 2019 11:19:18: 9000000 INFO @ Mon, 03 Jun 2019 11:19:22: 10000000 INFO @ Mon, 03 Jun 2019 11:19:23: 11000000 INFO @ Mon, 03 Jun 2019 11:19:27: 10000000 INFO @ Mon, 03 Jun 2019 11:19:30: 11000000 INFO @ Mon, 03 Jun 2019 11:19:30: 12000000 INFO @ Mon, 03 Jun 2019 11:19:35: 11000000 INFO @ Mon, 03 Jun 2019 11:19:38: 13000000 INFO @ Mon, 03 Jun 2019 11:19:38: 12000000 INFO @ Mon, 03 Jun 2019 11:19:44: 12000000 INFO @ Mon, 03 Jun 2019 11:19:45: 14000000 INFO @ Mon, 03 Jun 2019 11:19:46: 13000000 INFO @ Mon, 03 Jun 2019 11:19:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:19:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:19:53: #1 total tags in treatment: 14941132 INFO @ Mon, 03 Jun 2019 11:19:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:19:53: #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 11:19:53: 13000000 INFO @ Mon, 03 Jun 2019 11:19:53: #1 tags after filtering in treatment: 14941132 INFO @ Mon, 03 Jun 2019 11:19:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:19:53: #1 finished! INFO @ Mon, 03 Jun 2019 11:19:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:19:54: #2 number of paired peaks: 441 WARNING @ Mon, 03 Jun 2019 11:19:54: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Mon, 03 Jun 2019 11:19:54: start model_add_line... INFO @ Mon, 03 Jun 2019 11:19:54: start X-correlation... INFO @ Mon, 03 Jun 2019 11:19:54: end of X-cor INFO @ Mon, 03 Jun 2019 11:19:54: #2 finished! INFO @ Mon, 03 Jun 2019 11:19:54: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 11:19:54: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 11:19:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.20_model.r WARNING @ Mon, 03 Jun 2019 11:19:54: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:19:54: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 11:19:54: #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 11:19:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:19:54: 14000000 INFO @ Mon, 03 Jun 2019 11:20:01: 14000000 INFO @ Mon, 03 Jun 2019 11:20:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:20:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:20:02: #1 total tags in treatment: 14941132 INFO @ Mon, 03 Jun 2019 11:20:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:20:02: #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 11:20:02: #1 tags after filtering in treatment: 14941132 INFO @ Mon, 03 Jun 2019 11:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:20:02: #1 finished! INFO @ Mon, 03 Jun 2019 11:20:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:20:04: #2 number of paired peaks: 441 WARNING @ Mon, 03 Jun 2019 11:20:04: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Mon, 03 Jun 2019 11:20:04: start model_add_line... INFO @ Mon, 03 Jun 2019 11:20:04: start X-correlation... INFO @ Mon, 03 Jun 2019 11:20:04: end of X-cor INFO @ Mon, 03 Jun 2019 11:20:04: #2 finished! INFO @ Mon, 03 Jun 2019 11:20:04: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 11:20:04: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 11:20:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.05_model.r WARNING @ Mon, 03 Jun 2019 11:20:04: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:20:04: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 11:20:04: #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 11:20:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:20:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:20:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:20:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:20:10: #1 total tags in treatment: 14941132 INFO @ Mon, 03 Jun 2019 11:20:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:20:10: #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 11:20:10: #1 tags after filtering in treatment: 14941132 INFO @ Mon, 03 Jun 2019 11:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:20:10: #1 finished! INFO @ Mon, 03 Jun 2019 11:20:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:20:11: #2 number of paired peaks: 441 WARNING @ Mon, 03 Jun 2019 11:20:11: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Mon, 03 Jun 2019 11:20:11: start model_add_line... INFO @ Mon, 03 Jun 2019 11:20:11: start X-correlation... INFO @ Mon, 03 Jun 2019 11:20:11: end of X-cor INFO @ Mon, 03 Jun 2019 11:20:11: #2 finished! INFO @ Mon, 03 Jun 2019 11:20:11: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 11:20:11: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 11:20:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.10_model.r WARNING @ Mon, 03 Jun 2019 11:20:11: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:20:11: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 11:20:11: #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 11:20:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:20:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:20:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:20:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:20:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:20:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:20:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:20:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.20_summits.bed INFO @ Mon, 03 Jun 2019 11:20:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1542 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.05_summits.bed INFO @ Mon, 03 Jun 2019 11:21:03: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2197 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288016/SRX288016.10_summits.bed INFO @ Mon, 03 Jun 2019 11:21:11: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1941 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。