Job ID = 16439161 SRX = SRX13227900 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: 00:16:01 34635595 reads; of these: 34635595 (100.00%) were unpaired; of these: 1063792 (3.07%) aligned 0 times 24466605 (70.64%) aligned exactly 1 time 9105198 (26.29%) aligned >1 times 96.93% overall alignment rate Time searching: 00:16:01 Overall time: 00:16:01 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] 5526481 / 33571803 = 0.1646 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.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, 02 Aug 2022 15:09:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:09:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:09:32: 1000000 INFO @ Tue, 02 Aug 2022 15:09:43: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.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, 02 Aug 2022 15:09:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:09:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:09:53: 3000000 INFO @ Tue, 02 Aug 2022 15:10:02: 1000000 INFO @ Tue, 02 Aug 2022 15:10:05: 4000000 INFO @ Tue, 02 Aug 2022 15:10:14: 2000000 INFO @ Tue, 02 Aug 2022 15:10:16: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.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, 02 Aug 2022 15:10:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:10:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:10:25: 3000000 INFO @ Tue, 02 Aug 2022 15:10:28: 6000000 INFO @ Tue, 02 Aug 2022 15:10:36: 1000000 INFO @ Tue, 02 Aug 2022 15:10:36: 4000000 INFO @ Tue, 02 Aug 2022 15:10:40: 7000000 INFO @ Tue, 02 Aug 2022 15:10:47: 5000000 INFO @ Tue, 02 Aug 2022 15:10:52: 2000000 INFO @ Tue, 02 Aug 2022 15:10:52: 8000000 INFO @ Tue, 02 Aug 2022 15:10:59: 6000000 INFO @ Tue, 02 Aug 2022 15:11:03: 9000000 INFO @ Tue, 02 Aug 2022 15:11:07: 3000000 INFO @ Tue, 02 Aug 2022 15:11:10: 7000000 INFO @ Tue, 02 Aug 2022 15:11:15: 10000000 INFO @ Tue, 02 Aug 2022 15:11:21: 4000000 INFO @ Tue, 02 Aug 2022 15:11:22: 8000000 INFO @ Tue, 02 Aug 2022 15:11:26: 11000000 INFO @ Tue, 02 Aug 2022 15:11:32: 9000000 INFO @ Tue, 02 Aug 2022 15:11:36: 5000000 INFO @ Tue, 02 Aug 2022 15:11:37: 12000000 INFO @ Tue, 02 Aug 2022 15:11:44: 10000000 INFO @ Tue, 02 Aug 2022 15:11:48: 13000000 INFO @ Tue, 02 Aug 2022 15:11:50: 6000000 INFO @ Tue, 02 Aug 2022 15:11:54: 11000000 INFO @ Tue, 02 Aug 2022 15:11:59: 14000000 INFO @ Tue, 02 Aug 2022 15:12:04: 7000000 INFO @ Tue, 02 Aug 2022 15:12:05: 12000000 INFO @ Tue, 02 Aug 2022 15:12:10: 15000000 INFO @ Tue, 02 Aug 2022 15:12:15: 13000000 INFO @ Tue, 02 Aug 2022 15:12:18: 8000000 INFO @ Tue, 02 Aug 2022 15:12:21: 16000000 INFO @ Tue, 02 Aug 2022 15:12:26: 14000000 INFO @ Tue, 02 Aug 2022 15:12:31: 17000000 INFO @ Tue, 02 Aug 2022 15:12:32: 9000000 INFO @ Tue, 02 Aug 2022 15:12:37: 15000000 INFO @ Tue, 02 Aug 2022 15:12:42: 18000000 INFO @ Tue, 02 Aug 2022 15:12:46: 10000000 INFO @ Tue, 02 Aug 2022 15:12:48: 16000000 INFO @ Tue, 02 Aug 2022 15:12:53: 19000000 INFO @ Tue, 02 Aug 2022 15:12:59: 17000000 INFO @ Tue, 02 Aug 2022 15:13:00: 11000000 INFO @ Tue, 02 Aug 2022 15:13:04: 20000000 INFO @ Tue, 02 Aug 2022 15:13:11: 18000000 INFO @ Tue, 02 Aug 2022 15:13:13: 12000000 INFO @ Tue, 02 Aug 2022 15:13:15: 21000000 INFO @ Tue, 02 Aug 2022 15:13:23: 19000000 INFO @ Tue, 02 Aug 2022 15:13:27: 22000000 INFO @ Tue, 02 Aug 2022 15:13:27: 13000000 INFO @ Tue, 02 Aug 2022 15:13:34: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:13:38: 23000000 INFO @ Tue, 02 Aug 2022 15:13:41: 14000000 INFO @ Tue, 02 Aug 2022 15:13:45: 21000000 INFO @ Tue, 02 Aug 2022 15:13:49: 24000000 INFO @ Tue, 02 Aug 2022 15:13:55: 15000000 INFO @ Tue, 02 Aug 2022 15:13:57: 22000000 INFO @ Tue, 02 Aug 2022 15:14:01: 25000000 INFO @ Tue, 02 Aug 2022 15:14:09: 23000000 INFO @ Tue, 02 Aug 2022 15:14:09: 16000000 INFO @ Tue, 02 Aug 2022 15:14:11: 26000000 INFO @ Tue, 02 Aug 2022 15:14:20: 24000000 INFO @ Tue, 02 Aug 2022 15:14:23: 27000000 INFO @ Tue, 02 Aug 2022 15:14:24: 17000000 INFO @ Tue, 02 Aug 2022 15:14:31: 25000000 INFO @ Tue, 02 Aug 2022 15:14:34: 28000000 INFO @ Tue, 02 Aug 2022 15:14:34: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:14:34: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:14:34: #1 total tags in treatment: 28045322 INFO @ Tue, 02 Aug 2022 15:14:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:14:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:14:36: #1 tags after filtering in treatment: 28045322 INFO @ Tue, 02 Aug 2022 15:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:14:36: #1 finished! INFO @ Tue, 02 Aug 2022 15:14:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:14:38: #2 number of paired peaks: 265 WARNING @ Tue, 02 Aug 2022 15:14:38: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 02 Aug 2022 15:14:38: start model_add_line... INFO @ Tue, 02 Aug 2022 15:14:38: start X-correlation... INFO @ Tue, 02 Aug 2022 15:14:38: end of X-cor INFO @ Tue, 02 Aug 2022 15:14:38: #2 finished! INFO @ Tue, 02 Aug 2022 15:14:38: #2 predicted fragment length is 35 bps INFO @ Tue, 02 Aug 2022 15:14:38: #2 alternative fragment length(s) may be 3,35,598 bps INFO @ Tue, 02 Aug 2022 15:14:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.05_model.r WARNING @ Tue, 02 Aug 2022 15:14:38: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:14:38: #2 You may need to consider one of the other alternative d(s): 3,35,598 WARNING @ Tue, 02 Aug 2022 15:14:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:14:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:14:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:14:39: 18000000 INFO @ Tue, 02 Aug 2022 15:14:42: 26000000 INFO @ Tue, 02 Aug 2022 15:14:53: 19000000 INFO @ Tue, 02 Aug 2022 15:14:54: 27000000 INFO @ Tue, 02 Aug 2022 15:15:05: 28000000 INFO @ Tue, 02 Aug 2022 15:15:06: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:15:06: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:15:06: #1 total tags in treatment: 28045322 INFO @ Tue, 02 Aug 2022 15:15:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:15:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:15:07: #1 tags after filtering in treatment: 28045322 INFO @ Tue, 02 Aug 2022 15:15:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:15:07: #1 finished! INFO @ Tue, 02 Aug 2022 15:15:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:15:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:15:08: 20000000 INFO @ Tue, 02 Aug 2022 15:15:09: #2 number of paired peaks: 265 WARNING @ Tue, 02 Aug 2022 15:15:09: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 02 Aug 2022 15:15:09: start model_add_line... INFO @ Tue, 02 Aug 2022 15:15:10: start X-correlation... INFO @ Tue, 02 Aug 2022 15:15:10: end of X-cor INFO @ Tue, 02 Aug 2022 15:15:10: #2 finished! INFO @ Tue, 02 Aug 2022 15:15:10: #2 predicted fragment length is 35 bps INFO @ Tue, 02 Aug 2022 15:15:10: #2 alternative fragment length(s) may be 3,35,598 bps INFO @ Tue, 02 Aug 2022 15:15:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.10_model.r WARNING @ Tue, 02 Aug 2022 15:15:10: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:15:10: #2 You may need to consider one of the other alternative d(s): 3,35,598 WARNING @ Tue, 02 Aug 2022 15:15:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:15:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:15:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:15:22: 21000000 INFO @ Tue, 02 Aug 2022 15:15:36: 22000000 INFO @ Tue, 02 Aug 2022 15:15:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:15:51: 23000000 INFO @ Tue, 02 Aug 2022 15:16:06: 24000000 INFO @ Tue, 02 Aug 2022 15:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.05_summits.bed INFO @ Tue, 02 Aug 2022 15:16:14: Done! pass1 - making usageList (672 chroms): 2 millis pass2 - checking and writing primary data (2220 records, 4 fields): 197 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:16:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:16:21: 25000000 INFO @ Tue, 02 Aug 2022 15:16:36: 26000000 INFO @ Tue, 02 Aug 2022 15:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.10_summits.bed INFO @ Tue, 02 Aug 2022 15:16:47: Done! pass1 - making usageList (537 chroms): 3 millis pass2 - checking and writing primary data (1686 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:16:51: 27000000 INFO @ Tue, 02 Aug 2022 15:17:06: 28000000 INFO @ Tue, 02 Aug 2022 15:17:07: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:17:07: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:17:07: #1 total tags in treatment: 28045322 INFO @ Tue, 02 Aug 2022 15:17:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:17:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:17:08: #1 tags after filtering in treatment: 28045322 INFO @ Tue, 02 Aug 2022 15:17:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:17:08: #1 finished! INFO @ Tue, 02 Aug 2022 15:17:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:17:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:17:10: #2 number of paired peaks: 265 WARNING @ Tue, 02 Aug 2022 15:17:10: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 02 Aug 2022 15:17:10: start model_add_line... INFO @ Tue, 02 Aug 2022 15:17:10: start X-correlation... INFO @ Tue, 02 Aug 2022 15:17:10: end of X-cor INFO @ Tue, 02 Aug 2022 15:17:10: #2 finished! INFO @ Tue, 02 Aug 2022 15:17:10: #2 predicted fragment length is 35 bps INFO @ Tue, 02 Aug 2022 15:17:10: #2 alternative fragment length(s) may be 3,35,598 bps INFO @ Tue, 02 Aug 2022 15:17:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.20_model.r WARNING @ Tue, 02 Aug 2022 15:17:10: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:17:10: #2 You may need to consider one of the other alternative d(s): 3,35,598 WARNING @ Tue, 02 Aug 2022 15:17:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:17:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:18:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:18:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:18:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227900/SRX13227900.20_summits.bed INFO @ Tue, 02 Aug 2022 15:18:49: Done! pass1 - making usageList (387 chroms): 3 millis pass2 - checking and writing primary data (921 records, 4 fields): 39 millis CompletedMACS2peakCalling