Job ID = 6529852 SRX = SRX5287826 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: 00:10:04 24665534 reads; of these: 24665534 (100.00%) were unpaired; of these: 1271710 (5.16%) aligned 0 times 16993968 (68.90%) aligned exactly 1 time 6399856 (25.95%) aligned >1 times 94.84% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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] 3687863 / 23393824 = 0.1576 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 03:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.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 03:18:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:18:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:18:38: 1000000 INFO @ Tue, 30 Jun 2020 03:18:43: 2000000 INFO @ Tue, 30 Jun 2020 03:18:49: 3000000 INFO @ Tue, 30 Jun 2020 03:18:55: 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 03:19:01: 5000000 INFO @ Tue, 30 Jun 2020 03:19:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.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 03:19:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:08: 6000000 INFO @ Tue, 30 Jun 2020 03:19:09: 1000000 INFO @ Tue, 30 Jun 2020 03:19:15: 7000000 INFO @ Tue, 30 Jun 2020 03:19:16: 2000000 INFO @ Tue, 30 Jun 2020 03:19:22: 8000000 INFO @ Tue, 30 Jun 2020 03:19:23: 3000000 INFO @ Tue, 30 Jun 2020 03:19:28: 9000000 INFO @ Tue, 30 Jun 2020 03:19:29: 4000000 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 03:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.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 03:19:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:35: 10000000 INFO @ Tue, 30 Jun 2020 03:19:35: 5000000 INFO @ Tue, 30 Jun 2020 03:19:40: 1000000 INFO @ Tue, 30 Jun 2020 03:19:41: 11000000 INFO @ Tue, 30 Jun 2020 03:19:43: 6000000 INFO @ Tue, 30 Jun 2020 03:19:48: 2000000 INFO @ Tue, 30 Jun 2020 03:19:48: 12000000 INFO @ Tue, 30 Jun 2020 03:19:50: 7000000 INFO @ Tue, 30 Jun 2020 03:19:55: 3000000 INFO @ Tue, 30 Jun 2020 03:19:55: 13000000 INFO @ Tue, 30 Jun 2020 03:19:57: 8000000 INFO @ Tue, 30 Jun 2020 03:20:02: 4000000 INFO @ Tue, 30 Jun 2020 03:20:03: 14000000 INFO @ Tue, 30 Jun 2020 03:20:04: 9000000 INFO @ Tue, 30 Jun 2020 03:20:10: 15000000 INFO @ Tue, 30 Jun 2020 03:20:10: 5000000 INFO @ Tue, 30 Jun 2020 03:20:11: 10000000 INFO @ Tue, 30 Jun 2020 03:20:17: 6000000 INFO @ Tue, 30 Jun 2020 03:20:17: 16000000 INFO @ Tue, 30 Jun 2020 03:20:18: 11000000 INFO @ Tue, 30 Jun 2020 03:20:24: 7000000 INFO @ Tue, 30 Jun 2020 03:20:25: 17000000 INFO @ Tue, 30 Jun 2020 03:20:25: 12000000 INFO @ Tue, 30 Jun 2020 03:20:31: 8000000 INFO @ Tue, 30 Jun 2020 03:20:31: 18000000 INFO @ Tue, 30 Jun 2020 03:20:33: 13000000 INFO @ Tue, 30 Jun 2020 03:20:38: 9000000 INFO @ Tue, 30 Jun 2020 03:20:38: 19000000 INFO @ Tue, 30 Jun 2020 03:20:40: 14000000 INFO @ Tue, 30 Jun 2020 03:20:44: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:20:44: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:20:44: #1 total tags in treatment: 19705961 INFO @ Tue, 30 Jun 2020 03:20:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:20:44: #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 03:20:44: #1 tags after filtering in treatment: 19705958 INFO @ Tue, 30 Jun 2020 03:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:20:44: #1 finished! INFO @ Tue, 30 Jun 2020 03:20:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:20:45: 10000000 INFO @ Tue, 30 Jun 2020 03:20:46: #2 number of paired peaks: 591 WARNING @ Tue, 30 Jun 2020 03:20:46: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 30 Jun 2020 03:20:46: start model_add_line... INFO @ Tue, 30 Jun 2020 03:20:46: start X-correlation... INFO @ Tue, 30 Jun 2020 03:20:46: end of X-cor INFO @ Tue, 30 Jun 2020 03:20:46: #2 finished! INFO @ Tue, 30 Jun 2020 03:20:46: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:20:46: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 03:20:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.05_model.r WARNING @ Tue, 30 Jun 2020 03:20:46: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:20:46: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 03:20:46: #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 03:20:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:20:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:20:47: 15000000 INFO @ Tue, 30 Jun 2020 03:20:52: 11000000 INFO @ Tue, 30 Jun 2020 03:20:54: 16000000 INFO @ Tue, 30 Jun 2020 03:20:59: 12000000 INFO @ Tue, 30 Jun 2020 03:20:59: 17000000 INFO @ Tue, 30 Jun 2020 03:21:06: 18000000 INFO @ Tue, 30 Jun 2020 03:21:06: 13000000 INFO @ Tue, 30 Jun 2020 03:21:11: 19000000 INFO @ Tue, 30 Jun 2020 03:21:13: 14000000 INFO @ Tue, 30 Jun 2020 03:21:16: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:21:16: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:21:16: #1 total tags in treatment: 19705961 INFO @ Tue, 30 Jun 2020 03:21:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:16: #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 03:21:17: #1 tags after filtering in treatment: 19705958 INFO @ Tue, 30 Jun 2020 03:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:21:18: #2 number of paired peaks: 591 WARNING @ Tue, 30 Jun 2020 03:21:18: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:19: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:19: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:19: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:21:19: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 03:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.10_model.r WARNING @ Tue, 30 Jun 2020 03:21:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:21:19: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 03:21:19: #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 03:21:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:21:20: 15000000 INFO @ Tue, 30 Jun 2020 03:21:28: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.05_summits.bed INFO @ Tue, 30 Jun 2020 03:21:34: Done! INFO @ Tue, 30 Jun 2020 03:21:34: 17000000 pass1 - making usageList (678 chroms): 2 millis pass2 - checking and writing primary data (2427 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:21:40: 18000000 INFO @ Tue, 30 Jun 2020 03:21:45: 19000000 INFO @ Tue, 30 Jun 2020 03:21:50: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:21:50: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:21:50: #1 total tags in treatment: 19705961 INFO @ Tue, 30 Jun 2020 03:21:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:50: #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 03:21:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:21:51: #1 tags after filtering in treatment: 19705958 INFO @ Tue, 30 Jun 2020 03:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:51: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:52: #2 number of paired peaks: 591 WARNING @ Tue, 30 Jun 2020 03:21:52: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:52: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:52: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:52: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:52: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:52: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:21:52: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 03:21:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.20_model.r WARNING @ Tue, 30 Jun 2020 03:21:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:21:52: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 03:21:52: #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 03:21:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.10_summits.bed INFO @ Tue, 30 Jun 2020 03:22:06: Done! pass1 - making usageList (549 chroms): 1 millis pass2 - checking and writing primary data (1736 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:22:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:22:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287826/SRX5287826.20_summits.bed INFO @ Tue, 30 Jun 2020 03:22:40: Done! pass1 - making usageList (436 chroms): 1 millis pass2 - checking and writing primary data (1327 records, 4 fields): 26 millis CompletedMACS2peakCalling