Job ID = 6529339 SRX = SRX191915 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: 00:07:50 32815353 reads; of these: 32815353 (100.00%) were unpaired; of these: 1085725 (3.31%) aligned 0 times 22229975 (67.74%) aligned exactly 1 time 9499653 (28.95%) aligned >1 times 96.69% overall alignment rate Time searching: 00:07:50 Overall time: 00:07:50 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 8 files... [bam_rmdupse_core] 7228125 / 31729628 = 0.2278 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 02:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.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 02:00:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:00:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:00:47: 1000000 INFO @ Tue, 30 Jun 2020 02:00:52: 2000000 INFO @ Tue, 30 Jun 2020 02:00:57: 3000000 INFO @ Tue, 30 Jun 2020 02:01:01: 4000000 INFO @ Tue, 30 Jun 2020 02:01:06: 5000000 INFO @ Tue, 30 Jun 2020 02:01:11: 6000000 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 02:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.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 02:01:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:15: 7000000 INFO @ Tue, 30 Jun 2020 02:01:18: 1000000 INFO @ Tue, 30 Jun 2020 02:01:20: 8000000 INFO @ Tue, 30 Jun 2020 02:01:22: 2000000 INFO @ Tue, 30 Jun 2020 02:01:25: 9000000 INFO @ Tue, 30 Jun 2020 02:01:27: 3000000 INFO @ Tue, 30 Jun 2020 02:01:30: 10000000 INFO @ Tue, 30 Jun 2020 02:01:32: 4000000 INFO @ Tue, 30 Jun 2020 02:01:35: 11000000 INFO @ Tue, 30 Jun 2020 02:01:37: 5000000 INFO @ Tue, 30 Jun 2020 02:01:40: 12000000 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 02:01:42: 6000000 INFO @ Tue, 30 Jun 2020 02:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.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 02:01:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:45: 13000000 INFO @ Tue, 30 Jun 2020 02:01:46: 7000000 INFO @ Tue, 30 Jun 2020 02:01:48: 1000000 INFO @ Tue, 30 Jun 2020 02:01:50: 14000000 INFO @ Tue, 30 Jun 2020 02:01:51: 8000000 INFO @ Tue, 30 Jun 2020 02:01:53: 2000000 INFO @ Tue, 30 Jun 2020 02:01:55: 15000000 INFO @ Tue, 30 Jun 2020 02:01:56: 9000000 INFO @ Tue, 30 Jun 2020 02:01:58: 3000000 INFO @ Tue, 30 Jun 2020 02:01:59: 16000000 INFO @ Tue, 30 Jun 2020 02:02:01: 10000000 INFO @ Tue, 30 Jun 2020 02:02:03: 4000000 INFO @ Tue, 30 Jun 2020 02:02:04: 17000000 INFO @ Tue, 30 Jun 2020 02:02:06: 11000000 INFO @ Tue, 30 Jun 2020 02:02:07: 5000000 INFO @ Tue, 30 Jun 2020 02:02:09: 18000000 INFO @ Tue, 30 Jun 2020 02:02:11: 12000000 INFO @ Tue, 30 Jun 2020 02:02:12: 6000000 INFO @ Tue, 30 Jun 2020 02:02:14: 19000000 INFO @ Tue, 30 Jun 2020 02:02:15: 13000000 INFO @ Tue, 30 Jun 2020 02:02:17: 7000000 INFO @ Tue, 30 Jun 2020 02:02:19: 20000000 INFO @ Tue, 30 Jun 2020 02:02:20: 14000000 INFO @ Tue, 30 Jun 2020 02:02:22: 8000000 INFO @ Tue, 30 Jun 2020 02:02:24: 21000000 INFO @ Tue, 30 Jun 2020 02:02:25: 15000000 INFO @ Tue, 30 Jun 2020 02:02:27: 9000000 INFO @ Tue, 30 Jun 2020 02:02:29: 22000000 INFO @ Tue, 30 Jun 2020 02:02:30: 16000000 INFO @ Tue, 30 Jun 2020 02:02:32: 10000000 INFO @ Tue, 30 Jun 2020 02:02:34: 17000000 INFO @ Tue, 30 Jun 2020 02:02:34: 23000000 INFO @ Tue, 30 Jun 2020 02:02:37: 11000000 INFO @ Tue, 30 Jun 2020 02:02:39: 18000000 INFO @ Tue, 30 Jun 2020 02:02:39: 24000000 INFO @ Tue, 30 Jun 2020 02:02:42: 12000000 INFO @ Tue, 30 Jun 2020 02:02:42: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:02:42: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:02:42: #1 total tags in treatment: 24501503 INFO @ Tue, 30 Jun 2020 02:02:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:42: #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 02:02:43: #1 tags after filtering in treatment: 24501455 INFO @ Tue, 30 Jun 2020 02:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:44: 19000000 INFO @ Tue, 30 Jun 2020 02:02:44: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:02:44: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:44: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 02:02:44: #2 alternative fragment length(s) may be 2,37,542 bps INFO @ Tue, 30 Jun 2020 02:02:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.05_model.r WARNING @ Tue, 30 Jun 2020 02:02:44: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:02:44: #2 You may need to consider one of the other alternative d(s): 2,37,542 WARNING @ Tue, 30 Jun 2020 02:02:44: #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 02:02:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:02:47: 13000000 INFO @ Tue, 30 Jun 2020 02:02:49: 20000000 INFO @ Tue, 30 Jun 2020 02:02:52: 14000000 INFO @ Tue, 30 Jun 2020 02:02:54: 21000000 INFO @ Tue, 30 Jun 2020 02:02:56: 15000000 INFO @ Tue, 30 Jun 2020 02:02:59: 22000000 INFO @ Tue, 30 Jun 2020 02:03:01: 16000000 INFO @ Tue, 30 Jun 2020 02:03:04: 23000000 INFO @ Tue, 30 Jun 2020 02:03:06: 17000000 INFO @ Tue, 30 Jun 2020 02:03:08: 24000000 INFO @ Tue, 30 Jun 2020 02:03:11: 18000000 INFO @ Tue, 30 Jun 2020 02:03:11: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:03:11: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:03:11: #1 total tags in treatment: 24501503 INFO @ Tue, 30 Jun 2020 02:03:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:11: #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 02:03:12: #1 tags after filtering in treatment: 24501455 INFO @ Tue, 30 Jun 2020 02:03:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:12: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:13: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:03:13: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:13: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 02:03:13: #2 alternative fragment length(s) may be 2,37,542 bps INFO @ Tue, 30 Jun 2020 02:03:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.10_model.r WARNING @ Tue, 30 Jun 2020 02:03:13: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:03:13: #2 You may need to consider one of the other alternative d(s): 2,37,542 WARNING @ Tue, 30 Jun 2020 02:03:13: #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 02:03:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:15: 19000000 INFO @ Tue, 30 Jun 2020 02:03:20: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:03:25: 21000000 INFO @ Tue, 30 Jun 2020 02:03:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:03:30: 22000000 INFO @ Tue, 30 Jun 2020 02:03:34: 23000000 INFO @ Tue, 30 Jun 2020 02:03:39: 24000000 INFO @ Tue, 30 Jun 2020 02:03:42: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:03:42: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:03:42: #1 total tags in treatment: 24501503 INFO @ Tue, 30 Jun 2020 02:03:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:42: #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 02:03:42: #1 tags after filtering in treatment: 24501455 INFO @ Tue, 30 Jun 2020 02:03:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:42: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:44: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:03:44: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:44: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 02:03:44: #2 alternative fragment length(s) may be 2,37,542 bps INFO @ Tue, 30 Jun 2020 02:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.20_model.r WARNING @ Tue, 30 Jun 2020 02:03:44: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:03:44: #2 You may need to consider one of the other alternative d(s): 2,37,542 WARNING @ Tue, 30 Jun 2020 02:03:44: #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 02:03:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.05_summits.bed INFO @ Tue, 30 Jun 2020 02:03:47: Done! pass1 - making usageList (421 chroms): 1 millis pass2 - checking and writing primary data (2880 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:03:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:04:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.10_summits.bed INFO @ Tue, 30 Jun 2020 02:04:15: Done! pass1 - making usageList (241 chroms): 1 millis pass2 - checking and writing primary data (919 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:04:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:04:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191915/SRX191915.20_summits.bed INFO @ Tue, 30 Jun 2020 02:04:48: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (344 records, 4 fields): 5 millis CompletedMACS2peakCalling