Job ID = 6530054 SRX = SRX6827253 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:46 52274882 reads; of these: 52274882 (100.00%) were unpaired; of these: 25595263 (48.96%) aligned 0 times 20817963 (39.82%) aligned exactly 1 time 5861656 (11.21%) aligned >1 times 51.04% overall alignment rate Time searching: 00:09:47 Overall time: 00:09:47 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] 4327504 / 26679619 = 0.1622 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 04:17:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.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 04:17:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 04:17:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 04:17:55: 1000000 INFO @ Tue, 30 Jun 2020 04:18:01: 2000000 INFO @ Tue, 30 Jun 2020 04:18:07: 3000000 INFO @ Tue, 30 Jun 2020 04:18:12: 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 04:18:18: 5000000 INFO @ Tue, 30 Jun 2020 04:18:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.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 04:18:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 04:18:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 04:18:24: 6000000 INFO @ Tue, 30 Jun 2020 04:18:26: 1000000 INFO @ Tue, 30 Jun 2020 04:18:30: 7000000 INFO @ Tue, 30 Jun 2020 04:18:32: 2000000 INFO @ Tue, 30 Jun 2020 04:18:36: 8000000 INFO @ Tue, 30 Jun 2020 04:18:38: 3000000 INFO @ Tue, 30 Jun 2020 04:18:42: 9000000 INFO @ Tue, 30 Jun 2020 04:18:44: 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 04:18:48: 10000000 INFO @ Tue, 30 Jun 2020 04:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.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 04:18:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 04:18:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 04:18:51: 5000000 INFO @ Tue, 30 Jun 2020 04:18:55: 11000000 INFO @ Tue, 30 Jun 2020 04:18:56: 1000000 INFO @ Tue, 30 Jun 2020 04:18:57: 6000000 INFO @ Tue, 30 Jun 2020 04:19:01: 12000000 INFO @ Tue, 30 Jun 2020 04:19:03: 2000000 INFO @ Tue, 30 Jun 2020 04:19:04: 7000000 INFO @ Tue, 30 Jun 2020 04:19:08: 13000000 INFO @ Tue, 30 Jun 2020 04:19:10: 3000000 INFO @ Tue, 30 Jun 2020 04:19:10: 8000000 INFO @ Tue, 30 Jun 2020 04:19:15: 14000000 INFO @ Tue, 30 Jun 2020 04:19:17: 4000000 INFO @ Tue, 30 Jun 2020 04:19:17: 9000000 INFO @ Tue, 30 Jun 2020 04:19:21: 15000000 INFO @ Tue, 30 Jun 2020 04:19:23: 5000000 INFO @ Tue, 30 Jun 2020 04:19:24: 10000000 INFO @ Tue, 30 Jun 2020 04:19:28: 16000000 INFO @ Tue, 30 Jun 2020 04:19:30: 6000000 INFO @ Tue, 30 Jun 2020 04:19:30: 11000000 INFO @ Tue, 30 Jun 2020 04:19:35: 17000000 INFO @ Tue, 30 Jun 2020 04:19:37: 7000000 INFO @ Tue, 30 Jun 2020 04:19:37: 12000000 INFO @ Tue, 30 Jun 2020 04:19:42: 18000000 INFO @ Tue, 30 Jun 2020 04:19:43: 8000000 INFO @ Tue, 30 Jun 2020 04:19:44: 13000000 INFO @ Tue, 30 Jun 2020 04:19:49: 19000000 INFO @ Tue, 30 Jun 2020 04:19:50: 9000000 INFO @ Tue, 30 Jun 2020 04:19:51: 14000000 INFO @ Tue, 30 Jun 2020 04:19:56: 20000000 INFO @ Tue, 30 Jun 2020 04:19:57: 10000000 INFO @ Tue, 30 Jun 2020 04:19:58: 15000000 INFO @ Tue, 30 Jun 2020 04:20:02: 21000000 INFO @ Tue, 30 Jun 2020 04:20:03: 11000000 INFO @ Tue, 30 Jun 2020 04:20:04: 16000000 INFO @ Tue, 30 Jun 2020 04:20:09: 22000000 INFO @ Tue, 30 Jun 2020 04:20:10: 12000000 INFO @ Tue, 30 Jun 2020 04:20:11: 17000000 INFO @ Tue, 30 Jun 2020 04:20:12: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 04:20:12: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 04:20:12: #1 total tags in treatment: 22352115 INFO @ Tue, 30 Jun 2020 04:20:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 04:20:12: #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 04:20:13: #1 tags after filtering in treatment: 22352114 INFO @ Tue, 30 Jun 2020 04:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 04:20:13: #1 finished! INFO @ Tue, 30 Jun 2020 04:20:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 04:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 04:20:14: #2 number of paired peaks: 316 WARNING @ Tue, 30 Jun 2020 04:20:14: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 30 Jun 2020 04:20:14: start model_add_line... INFO @ Tue, 30 Jun 2020 04:20:15: start X-correlation... INFO @ Tue, 30 Jun 2020 04:20:15: end of X-cor INFO @ Tue, 30 Jun 2020 04:20:15: #2 finished! INFO @ Tue, 30 Jun 2020 04:20:15: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 04:20:15: #2 alternative fragment length(s) may be 3,47 bps INFO @ Tue, 30 Jun 2020 04:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.05_model.r WARNING @ Tue, 30 Jun 2020 04:20:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 04:20:15: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Tue, 30 Jun 2020 04:20:15: #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 04:20:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 04:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 04:20:17: 13000000 INFO @ Tue, 30 Jun 2020 04:20:18: 18000000 INFO @ Tue, 30 Jun 2020 04:20:23: 14000000 INFO @ Tue, 30 Jun 2020 04:20:25: 19000000 INFO @ Tue, 30 Jun 2020 04:20:29: 15000000 INFO @ Tue, 30 Jun 2020 04:20:31: 20000000 INFO @ Tue, 30 Jun 2020 04:20:35: 16000000 INFO @ Tue, 30 Jun 2020 04:20:37: 21000000 INFO @ Tue, 30 Jun 2020 04:20:42: 17000000 INFO @ Tue, 30 Jun 2020 04:20:44: 22000000 INFO @ Tue, 30 Jun 2020 04:20:47: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 04:20:47: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 04:20:47: #1 total tags in treatment: 22352115 INFO @ Tue, 30 Jun 2020 04:20:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 04:20:47: #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 04:20:48: #1 tags after filtering in treatment: 22352114 INFO @ Tue, 30 Jun 2020 04:20:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 04:20:48: #1 finished! INFO @ Tue, 30 Jun 2020 04:20:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 04:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 04:20:49: 18000000 INFO @ Tue, 30 Jun 2020 04:20:49: #2 number of paired peaks: 316 WARNING @ Tue, 30 Jun 2020 04:20:49: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 30 Jun 2020 04:20:49: start model_add_line... INFO @ Tue, 30 Jun 2020 04:20:49: start X-correlation... INFO @ Tue, 30 Jun 2020 04:20:49: end of X-cor INFO @ Tue, 30 Jun 2020 04:20:49: #2 finished! INFO @ Tue, 30 Jun 2020 04:20:49: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 04:20:49: #2 alternative fragment length(s) may be 3,47 bps INFO @ Tue, 30 Jun 2020 04:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.10_model.r WARNING @ Tue, 30 Jun 2020 04:20:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 04:20:49: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Tue, 30 Jun 2020 04:20:49: #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 04:20:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 04:20:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 04:20:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 04:20:55: 19000000 INFO @ Tue, 30 Jun 2020 04:21:00: 20000000 INFO @ Tue, 30 Jun 2020 04:21:06: 21000000 INFO @ Tue, 30 Jun 2020 04:21:12: 22000000 INFO @ Tue, 30 Jun 2020 04:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.05_peaks.xls INFO @ Tue, 30 Jun 2020 04:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 04:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.05_summits.bed INFO @ Tue, 30 Jun 2020 04:21:13: Done! pass1 - making usageList (612 chroms): 2 millis pass2 - checking and writing primary data (2940 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 04:21:14: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 04:21:14: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 04:21:14: #1 total tags in treatment: 22352115 INFO @ Tue, 30 Jun 2020 04:21:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 04:21:14: #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 04:21:15: #1 tags after filtering in treatment: 22352114 INFO @ Tue, 30 Jun 2020 04:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 04:21:15: #1 finished! INFO @ Tue, 30 Jun 2020 04:21:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 04:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 04:21:17: #2 number of paired peaks: 316 WARNING @ Tue, 30 Jun 2020 04:21:17: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 30 Jun 2020 04:21:17: start model_add_line... INFO @ Tue, 30 Jun 2020 04:21:17: start X-correlation... INFO @ Tue, 30 Jun 2020 04:21:17: end of X-cor INFO @ Tue, 30 Jun 2020 04:21:17: #2 finished! INFO @ Tue, 30 Jun 2020 04:21:17: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 04:21:17: #2 alternative fragment length(s) may be 3,47 bps INFO @ Tue, 30 Jun 2020 04:21:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.20_model.r WARNING @ Tue, 30 Jun 2020 04:21:17: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 04:21:17: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Tue, 30 Jun 2020 04:21:17: #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 04:21:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 04:21:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 04:21:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 04:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.10_peaks.xls INFO @ Tue, 30 Jun 2020 04:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 04:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.10_summits.bed INFO @ Tue, 30 Jun 2020 04:21:46: Done! pass1 - making usageList (467 chroms): 2 millis pass2 - checking and writing primary data (1781 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 04:21:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 04:22:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.20_peaks.xls INFO @ Tue, 30 Jun 2020 04:22:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 04:22:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827253/SRX6827253.20_summits.bed INFO @ Tue, 30 Jun 2020 04:22:14: Done! pass1 - making usageList (359 chroms): 1 millis pass2 - checking and writing primary data (933 records, 4 fields): 21 millis CompletedMACS2peakCalling