Job ID = 6529877 SRX = SRX5343141 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: 00:10:34 32207365 reads; of these: 32207365 (100.00%) were unpaired; of these: 1271699 (3.95%) aligned 0 times 21681021 (67.32%) aligned exactly 1 time 9254645 (28.73%) aligned >1 times 96.05% overall alignment rate Time searching: 00:10:34 Overall time: 00:10:34 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 16 files... [bam_rmdupse_core] 4797242 / 30935666 = 0.1551 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 03:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.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 03:08:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:00: 1000000 INFO @ Tue, 30 Jun 2020 03:09:06: 2000000 INFO @ Tue, 30 Jun 2020 03:09:12: 3000000 INFO @ Tue, 30 Jun 2020 03:09:18: 4000000 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 03:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.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 03:09:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:24: 5000000 INFO @ Tue, 30 Jun 2020 03:09:30: 1000000 INFO @ Tue, 30 Jun 2020 03:09:31: 6000000 INFO @ Tue, 30 Jun 2020 03:09:37: 2000000 INFO @ Tue, 30 Jun 2020 03:09:38: 7000000 INFO @ Tue, 30 Jun 2020 03:09:44: 3000000 INFO @ Tue, 30 Jun 2020 03:09:45: 8000000 INFO @ Tue, 30 Jun 2020 03:09:50: 4000000 INFO @ Tue, 30 Jun 2020 03:09:51: 9000000 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 03:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.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 03:09:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:58: 5000000 INFO @ Tue, 30 Jun 2020 03:09:58: 10000000 INFO @ Tue, 30 Jun 2020 03:10:01: 1000000 INFO @ Tue, 30 Jun 2020 03:10:05: 11000000 INFO @ Tue, 30 Jun 2020 03:10:05: 6000000 INFO @ Tue, 30 Jun 2020 03:10:08: 2000000 INFO @ Tue, 30 Jun 2020 03:10:12: 12000000 INFO @ Tue, 30 Jun 2020 03:10:12: 7000000 INFO @ Tue, 30 Jun 2020 03:10:15: 3000000 INFO @ Tue, 30 Jun 2020 03:10:20: 13000000 INFO @ Tue, 30 Jun 2020 03:10:20: 8000000 INFO @ Tue, 30 Jun 2020 03:10:22: 4000000 INFO @ Tue, 30 Jun 2020 03:10:27: 14000000 INFO @ Tue, 30 Jun 2020 03:10:27: 9000000 INFO @ Tue, 30 Jun 2020 03:10:28: 5000000 INFO @ Tue, 30 Jun 2020 03:10:34: 15000000 INFO @ Tue, 30 Jun 2020 03:10:34: 10000000 INFO @ Tue, 30 Jun 2020 03:10:35: 6000000 INFO @ Tue, 30 Jun 2020 03:10:41: 11000000 INFO @ Tue, 30 Jun 2020 03:10:41: 16000000 INFO @ Tue, 30 Jun 2020 03:10:42: 7000000 INFO @ Tue, 30 Jun 2020 03:10:48: 17000000 INFO @ Tue, 30 Jun 2020 03:10:48: 12000000 INFO @ Tue, 30 Jun 2020 03:10:49: 8000000 INFO @ Tue, 30 Jun 2020 03:10:55: 18000000 INFO @ Tue, 30 Jun 2020 03:10:55: 13000000 INFO @ Tue, 30 Jun 2020 03:10:55: 9000000 INFO @ Tue, 30 Jun 2020 03:11:02: 10000000 INFO @ Tue, 30 Jun 2020 03:11:02: 19000000 INFO @ Tue, 30 Jun 2020 03:11:02: 14000000 INFO @ Tue, 30 Jun 2020 03:11:09: 11000000 INFO @ Tue, 30 Jun 2020 03:11:10: 20000000 INFO @ Tue, 30 Jun 2020 03:11:10: 15000000 INFO @ Tue, 30 Jun 2020 03:11:16: 12000000 INFO @ Tue, 30 Jun 2020 03:11:17: 21000000 INFO @ Tue, 30 Jun 2020 03:11:17: 16000000 INFO @ Tue, 30 Jun 2020 03:11:22: 13000000 INFO @ Tue, 30 Jun 2020 03:11:24: 17000000 INFO @ Tue, 30 Jun 2020 03:11:24: 22000000 INFO @ Tue, 30 Jun 2020 03:11:29: 14000000 INFO @ Tue, 30 Jun 2020 03:11:31: 18000000 INFO @ Tue, 30 Jun 2020 03:11:31: 23000000 INFO @ Tue, 30 Jun 2020 03:11:36: 15000000 INFO @ Tue, 30 Jun 2020 03:11:38: 19000000 INFO @ Tue, 30 Jun 2020 03:11:39: 24000000 INFO @ Tue, 30 Jun 2020 03:11:42: 16000000 INFO @ Tue, 30 Jun 2020 03:11:46: 20000000 INFO @ Tue, 30 Jun 2020 03:11:46: 25000000 INFO @ Tue, 30 Jun 2020 03:11:49: 17000000 INFO @ Tue, 30 Jun 2020 03:11:53: 21000000 INFO @ Tue, 30 Jun 2020 03:11:54: 26000000 INFO @ Tue, 30 Jun 2020 03:11:55: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:11:55: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:11:55: #1 total tags in treatment: 26138424 INFO @ Tue, 30 Jun 2020 03:11:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:55: #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 03:11:55: #1 tags after filtering in treatment: 26138424 INFO @ Tue, 30 Jun 2020 03:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:55: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:55: 18000000 INFO @ Tue, 30 Jun 2020 03:11:57: #2 number of paired peaks: 189 WARNING @ Tue, 30 Jun 2020 03:11:57: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:57: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:57: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:57: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:57: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:11:57: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 30 Jun 2020 03:11:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.05_model.r WARNING @ Tue, 30 Jun 2020 03:11:57: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:57: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 30 Jun 2020 03:11:57: #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 03:11:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:00: 22000000 INFO @ Tue, 30 Jun 2020 03:12:02: 19000000 INFO @ Tue, 30 Jun 2020 03:12:07: 23000000 INFO @ Tue, 30 Jun 2020 03:12:09: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:14: 24000000 INFO @ Tue, 30 Jun 2020 03:12:16: 21000000 INFO @ Tue, 30 Jun 2020 03:12:22: 25000000 INFO @ Tue, 30 Jun 2020 03:12:23: 22000000 INFO @ Tue, 30 Jun 2020 03:12:29: 26000000 INFO @ Tue, 30 Jun 2020 03:12:30: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:12:30: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:12:30: #1 total tags in treatment: 26138424 INFO @ Tue, 30 Jun 2020 03:12:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:30: #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 03:12:31: 23000000 INFO @ Tue, 30 Jun 2020 03:12:31: #1 tags after filtering in treatment: 26138424 INFO @ Tue, 30 Jun 2020 03:12:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:31: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:33: #2 number of paired peaks: 189 WARNING @ Tue, 30 Jun 2020 03:12:33: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:33: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:33: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:33: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:33: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:33: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:12:33: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 30 Jun 2020 03:12:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:33: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 30 Jun 2020 03:12:33: #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 03:12:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:37: 24000000 INFO @ Tue, 30 Jun 2020 03:12:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:44: 25000000 INFO @ Tue, 30 Jun 2020 03:12:51: 26000000 INFO @ Tue, 30 Jun 2020 03:12:52: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:12:52: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:12:52: #1 total tags in treatment: 26138424 INFO @ Tue, 30 Jun 2020 03:12:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:52: #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 03:12:53: #1 tags after filtering in treatment: 26138424 INFO @ Tue, 30 Jun 2020 03:12:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:53: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:54: #2 number of paired peaks: 189 WARNING @ Tue, 30 Jun 2020 03:12:54: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:54: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:54: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:54: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:54: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:54: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:12:54: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 30 Jun 2020 03:12:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.20_model.r WARNING @ Tue, 30 Jun 2020 03:12:54: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:54: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 30 Jun 2020 03:12:54: #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 03:12:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.05_summits.bed INFO @ Tue, 30 Jun 2020 03:13:00: Done! pass1 - making usageList (766 chroms): 2 millis pass2 - checking and writing primary data (2733 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:13:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.10_summits.bed INFO @ Tue, 30 Jun 2020 03:13:37: Done! pass1 - making usageList (607 chroms): 1 millis pass2 - checking and writing primary data (1878 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343141/SRX5343141.20_summits.bed INFO @ Tue, 30 Jun 2020 03:13:55: Done! pass1 - making usageList (375 chroms): 1 millis pass2 - checking and writing primary data (799 records, 4 fields): 11 millis CompletedMACS2peakCalling