Job ID = 6529388 SRX = SRX2325648 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:12:45 30853192 reads; of these: 30853192 (100.00%) were unpaired; of these: 1981571 (6.42%) aligned 0 times 21554157 (69.86%) aligned exactly 1 time 7317464 (23.72%) aligned >1 times 93.58% overall alignment rate Time searching: 00:12:45 Overall time: 00:12:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4954292 / 28871621 = 0.1716 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.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, 30 Jun 2020 02:19:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:10: 1000000 INFO @ Tue, 30 Jun 2020 02:19:19: 2000000 INFO @ Tue, 30 Jun 2020 02:19:27: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.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, 30 Jun 2020 02:19:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:36: 4000000 INFO @ Tue, 30 Jun 2020 02:19:40: 1000000 INFO @ Tue, 30 Jun 2020 02:19:46: 5000000 INFO @ Tue, 30 Jun 2020 02:19:48: 2000000 INFO @ Tue, 30 Jun 2020 02:19:55: 6000000 INFO @ Tue, 30 Jun 2020 02:19:57: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.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, 30 Jun 2020 02:20:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:20:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:20:05: 7000000 INFO @ Tue, 30 Jun 2020 02:20:05: 4000000 INFO @ Tue, 30 Jun 2020 02:20:12: 1000000 INFO @ Tue, 30 Jun 2020 02:20:14: 5000000 INFO @ Tue, 30 Jun 2020 02:20:15: 8000000 INFO @ Tue, 30 Jun 2020 02:20:22: 2000000 INFO @ Tue, 30 Jun 2020 02:20:23: 6000000 INFO @ Tue, 30 Jun 2020 02:20:25: 9000000 INFO @ Tue, 30 Jun 2020 02:20:32: 7000000 INFO @ Tue, 30 Jun 2020 02:20:32: 3000000 INFO @ Tue, 30 Jun 2020 02:20:34: 10000000 INFO @ Tue, 30 Jun 2020 02:20:41: 8000000 INFO @ Tue, 30 Jun 2020 02:20:42: 4000000 INFO @ Tue, 30 Jun 2020 02:20:44: 11000000 INFO @ Tue, 30 Jun 2020 02:20:50: 9000000 INFO @ Tue, 30 Jun 2020 02:20:53: 5000000 INFO @ Tue, 30 Jun 2020 02:20:54: 12000000 INFO @ Tue, 30 Jun 2020 02:20:58: 10000000 INFO @ Tue, 30 Jun 2020 02:21:02: 6000000 INFO @ Tue, 30 Jun 2020 02:21:03: 13000000 INFO @ Tue, 30 Jun 2020 02:21:07: 11000000 INFO @ Tue, 30 Jun 2020 02:21:13: 14000000 INFO @ Tue, 30 Jun 2020 02:21:13: 7000000 INFO @ Tue, 30 Jun 2020 02:21:16: 12000000 INFO @ Tue, 30 Jun 2020 02:21:22: 15000000 INFO @ Tue, 30 Jun 2020 02:21:23: 8000000 INFO @ Tue, 30 Jun 2020 02:21:24: 13000000 INFO @ Tue, 30 Jun 2020 02:21:31: 16000000 INFO @ Tue, 30 Jun 2020 02:21:33: 14000000 INFO @ Tue, 30 Jun 2020 02:21:33: 9000000 INFO @ Tue, 30 Jun 2020 02:21:41: 17000000 INFO @ Tue, 30 Jun 2020 02:21:42: 15000000 INFO @ Tue, 30 Jun 2020 02:21:44: 10000000 INFO @ Tue, 30 Jun 2020 02:21:50: 16000000 INFO @ Tue, 30 Jun 2020 02:21:50: 18000000 INFO @ Tue, 30 Jun 2020 02:21:53: 11000000 INFO @ Tue, 30 Jun 2020 02:21:59: 17000000 INFO @ Tue, 30 Jun 2020 02:22:00: 19000000 INFO @ Tue, 30 Jun 2020 02:22:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:22:08: 18000000 INFO @ Tue, 30 Jun 2020 02:22:09: 20000000 INFO @ Tue, 30 Jun 2020 02:22:13: 13000000 INFO @ Tue, 30 Jun 2020 02:22:17: 19000000 INFO @ Tue, 30 Jun 2020 02:22:19: 21000000 INFO @ Tue, 30 Jun 2020 02:22:23: 14000000 INFO @ Tue, 30 Jun 2020 02:22:25: 20000000 INFO @ Tue, 30 Jun 2020 02:22:29: 22000000 INFO @ Tue, 30 Jun 2020 02:22:33: 15000000 INFO @ Tue, 30 Jun 2020 02:22:35: 21000000 INFO @ Tue, 30 Jun 2020 02:22:38: 23000000 INFO @ Tue, 30 Jun 2020 02:22:42: 16000000 INFO @ Tue, 30 Jun 2020 02:22:43: 22000000 INFO @ Tue, 30 Jun 2020 02:22:47: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:22:47: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:22:47: #1 total tags in treatment: 23917329 INFO @ Tue, 30 Jun 2020 02:22:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:22:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:22:48: #1 tags after filtering in treatment: 23917329 INFO @ Tue, 30 Jun 2020 02:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:22:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:22:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:22:49: #2 number of paired peaks: 176 WARNING @ Tue, 30 Jun 2020 02:22:49: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Tue, 30 Jun 2020 02:22:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:22:49: start X-correlation... INFO @ Tue, 30 Jun 2020 02:22:49: end of X-cor INFO @ Tue, 30 Jun 2020 02:22:49: #2 finished! INFO @ Tue, 30 Jun 2020 02:22:49: #2 predicted fragment length is 76 bps INFO @ Tue, 30 Jun 2020 02:22:49: #2 alternative fragment length(s) may be 3,76 bps INFO @ Tue, 30 Jun 2020 02:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.05_model.r WARNING @ Tue, 30 Jun 2020 02:22:49: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:22:49: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Tue, 30 Jun 2020 02:22:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:22:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:22:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:22:52: 23000000 INFO @ Tue, 30 Jun 2020 02:22:52: 17000000 INFO @ Tue, 30 Jun 2020 02:23:00: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:23:00: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:23:00: #1 total tags in treatment: 23917329 INFO @ Tue, 30 Jun 2020 02:23:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:23:00: #1 tags after filtering in treatment: 23917329 INFO @ Tue, 30 Jun 2020 02:23:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:00: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:02: 18000000 INFO @ Tue, 30 Jun 2020 02:23:02: #2 number of paired peaks: 176 WARNING @ Tue, 30 Jun 2020 02:23:02: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:02: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:02: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:02: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:02: #2 predicted fragment length is 76 bps INFO @ Tue, 30 Jun 2020 02:23:02: #2 alternative fragment length(s) may be 3,76 bps INFO @ Tue, 30 Jun 2020 02:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.10_model.r WARNING @ Tue, 30 Jun 2020 02:23:02: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:02: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Tue, 30 Jun 2020 02:23:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:23:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:23:10: 19000000 INFO @ Tue, 30 Jun 2020 02:23:18: 20000000 INFO @ Tue, 30 Jun 2020 02:23:27: 21000000 INFO @ Tue, 30 Jun 2020 02:23:36: 22000000 INFO @ Tue, 30 Jun 2020 02:23:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:45: 23000000 INFO @ Tue, 30 Jun 2020 02:23:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:53: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:23:53: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:23:53: #1 total tags in treatment: 23917329 INFO @ Tue, 30 Jun 2020 02:23:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:23:53: #1 tags after filtering in treatment: 23917329 INFO @ Tue, 30 Jun 2020 02:23:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:55: #2 number of paired peaks: 176 WARNING @ Tue, 30 Jun 2020 02:23:55: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:55: #2 predicted fragment length is 76 bps INFO @ Tue, 30 Jun 2020 02:23:55: #2 alternative fragment length(s) may be 3,76 bps INFO @ Tue, 30 Jun 2020 02:23:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.20_model.r WARNING @ Tue, 30 Jun 2020 02:23:55: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:55: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Tue, 30 Jun 2020 02:23:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:23:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.05_summits.bed INFO @ Tue, 30 Jun 2020 02:24:00: Done! pass1 - making usageList (838 chroms): 2 millis pass2 - checking and writing primary data (2968 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.10_summits.bed INFO @ Tue, 30 Jun 2020 02:24:14: Done! pass1 - making usageList (647 chroms): 2 millis pass2 - checking and writing primary data (1719 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:25:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325648/SRX2325648.20_summits.bed INFO @ Tue, 30 Jun 2020 02:25:03: Done! pass1 - making usageList (368 chroms): 1 millis pass2 - checking and writing primary data (688 records, 4 fields): 13 millis CompletedMACS2peakCalling