Job ID = 6529441 SRX = SRX2804221 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: 00:08:45 31702050 reads; of these: 31702050 (100.00%) were unpaired; of these: 3361088 (10.60%) aligned 0 times 19324919 (60.96%) aligned exactly 1 time 9016043 (28.44%) aligned >1 times 89.40% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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] 5130883 / 28340962 = 0.1810 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 02:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.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 02:09:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:26: 1000000 INFO @ Tue, 30 Jun 2020 02:09:33: 2000000 INFO @ Tue, 30 Jun 2020 02:09:40: 3000000 INFO @ Tue, 30 Jun 2020 02:09:47: 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 02:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.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 02:09:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:54: 5000000 INFO @ Tue, 30 Jun 2020 02:09:56: 1000000 INFO @ Tue, 30 Jun 2020 02:10:02: 6000000 INFO @ Tue, 30 Jun 2020 02:10:04: 2000000 INFO @ Tue, 30 Jun 2020 02:10:10: 7000000 INFO @ Tue, 30 Jun 2020 02:10:12: 3000000 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 02:10:18: 8000000 INFO @ Tue, 30 Jun 2020 02:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.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 02:10:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:10:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:10:20: 4000000 INFO @ Tue, 30 Jun 2020 02:10:26: 9000000 INFO @ Tue, 30 Jun 2020 02:10:27: 1000000 INFO @ Tue, 30 Jun 2020 02:10:28: 5000000 INFO @ Tue, 30 Jun 2020 02:10:34: 10000000 INFO @ Tue, 30 Jun 2020 02:10:35: 2000000 INFO @ Tue, 30 Jun 2020 02:10:36: 6000000 INFO @ Tue, 30 Jun 2020 02:10:42: 11000000 INFO @ Tue, 30 Jun 2020 02:10:44: 7000000 INFO @ Tue, 30 Jun 2020 02:10:44: 3000000 INFO @ Tue, 30 Jun 2020 02:10:50: 12000000 INFO @ Tue, 30 Jun 2020 02:10:52: 8000000 INFO @ Tue, 30 Jun 2020 02:10:52: 4000000 INFO @ Tue, 30 Jun 2020 02:10:58: 13000000 INFO @ Tue, 30 Jun 2020 02:11:00: 9000000 INFO @ Tue, 30 Jun 2020 02:11:00: 5000000 INFO @ Tue, 30 Jun 2020 02:11:06: 14000000 INFO @ Tue, 30 Jun 2020 02:11:08: 10000000 INFO @ Tue, 30 Jun 2020 02:11:09: 6000000 INFO @ Tue, 30 Jun 2020 02:11:14: 15000000 INFO @ Tue, 30 Jun 2020 02:11:16: 11000000 INFO @ Tue, 30 Jun 2020 02:11:17: 7000000 INFO @ Tue, 30 Jun 2020 02:11:22: 16000000 INFO @ Tue, 30 Jun 2020 02:11:24: 12000000 INFO @ Tue, 30 Jun 2020 02:11:26: 8000000 INFO @ Tue, 30 Jun 2020 02:11:30: 17000000 INFO @ Tue, 30 Jun 2020 02:11:32: 13000000 INFO @ Tue, 30 Jun 2020 02:11:34: 9000000 INFO @ Tue, 30 Jun 2020 02:11:38: 18000000 INFO @ Tue, 30 Jun 2020 02:11:40: 14000000 INFO @ Tue, 30 Jun 2020 02:11:42: 10000000 INFO @ Tue, 30 Jun 2020 02:11:47: 19000000 INFO @ Tue, 30 Jun 2020 02:11:48: 15000000 INFO @ Tue, 30 Jun 2020 02:11:51: 11000000 INFO @ Tue, 30 Jun 2020 02:11:55: 20000000 INFO @ Tue, 30 Jun 2020 02:11:56: 16000000 INFO @ Tue, 30 Jun 2020 02:11:59: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:12:04: 21000000 INFO @ Tue, 30 Jun 2020 02:12:04: 17000000 INFO @ Tue, 30 Jun 2020 02:12:07: 13000000 INFO @ Tue, 30 Jun 2020 02:12:12: 22000000 INFO @ Tue, 30 Jun 2020 02:12:12: 18000000 INFO @ Tue, 30 Jun 2020 02:12:16: 14000000 INFO @ Tue, 30 Jun 2020 02:12:20: 23000000 INFO @ Tue, 30 Jun 2020 02:12:21: 19000000 INFO @ Tue, 30 Jun 2020 02:12:22: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:12:22: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:12:22: #1 total tags in treatment: 23210079 INFO @ Tue, 30 Jun 2020 02:12:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:22: #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 02:12:23: #1 tags after filtering in treatment: 23210079 INFO @ Tue, 30 Jun 2020 02:12:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:24: 15000000 INFO @ Tue, 30 Jun 2020 02:12:24: #2 number of paired peaks: 549 WARNING @ Tue, 30 Jun 2020 02:12:24: Fewer paired peaks (549) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 549 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:24: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 02:12:24: #2 alternative fragment length(s) may be 2,47,588,593 bps INFO @ Tue, 30 Jun 2020 02:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.05_model.r WARNING @ Tue, 30 Jun 2020 02:12:24: #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 02:12:24: #2 You may need to consider one of the other alternative d(s): 2,47,588,593 WARNING @ Tue, 30 Jun 2020 02:12:24: #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 02:12:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:12:29: 20000000 INFO @ Tue, 30 Jun 2020 02:12:32: 16000000 INFO @ Tue, 30 Jun 2020 02:12:37: 21000000 INFO @ Tue, 30 Jun 2020 02:12:40: 17000000 INFO @ Tue, 30 Jun 2020 02:12:45: 22000000 INFO @ Tue, 30 Jun 2020 02:12:48: 18000000 INFO @ Tue, 30 Jun 2020 02:12:53: 23000000 INFO @ Tue, 30 Jun 2020 02:12:55: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:12:55: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:12:55: #1 total tags in treatment: 23210079 INFO @ Tue, 30 Jun 2020 02:12:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:55: #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 02:12:56: #1 tags after filtering in treatment: 23210079 INFO @ Tue, 30 Jun 2020 02:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:56: 19000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:12:57: #2 number of paired peaks: 549 WARNING @ Tue, 30 Jun 2020 02:12:57: Fewer paired peaks (549) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 549 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:57: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 02:12:57: #2 alternative fragment length(s) may be 2,47,588,593 bps INFO @ Tue, 30 Jun 2020 02:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.10_model.r WARNING @ Tue, 30 Jun 2020 02:12:57: #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 02:12:57: #2 You may need to consider one of the other alternative d(s): 2,47,588,593 WARNING @ Tue, 30 Jun 2020 02:12:57: #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 02:12:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:04: 20000000 INFO @ Tue, 30 Jun 2020 02:13:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:11: 21000000 INFO @ Tue, 30 Jun 2020 02:13:18: 22000000 INFO @ Tue, 30 Jun 2020 02:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.05_summits.bed INFO @ Tue, 30 Jun 2020 02:13:25: Done! pass1 - making usageList (742 chroms): 2 millis pass2 - checking and writing primary data (4116 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:13:26: 23000000 INFO @ Tue, 30 Jun 2020 02:13:27: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:13:27: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:13:27: #1 total tags in treatment: 23210079 INFO @ Tue, 30 Jun 2020 02:13:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:13:27: #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 02:13:28: #1 tags after filtering in treatment: 23210079 INFO @ Tue, 30 Jun 2020 02:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:29: #2 number of paired peaks: 549 WARNING @ Tue, 30 Jun 2020 02:13:29: Fewer paired peaks (549) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 549 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:29: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:30: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 02:13:30: #2 alternative fragment length(s) may be 2,47,588,593 bps INFO @ Tue, 30 Jun 2020 02:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.20_model.r WARNING @ Tue, 30 Jun 2020 02:13:30: #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 02:13:30: #2 You may need to consider one of the other alternative d(s): 2,47,588,593 WARNING @ Tue, 30 Jun 2020 02:13:30: #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 02:13:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.10_summits.bed INFO @ Tue, 30 Jun 2020 02:13:58: Done! pass1 - making usageList (629 chroms): 1 millis pass2 - checking and writing primary data (2799 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:14:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804221/SRX2804221.20_summits.bed INFO @ Tue, 30 Jun 2020 02:14:29: Done! pass1 - making usageList (429 chroms): 1 millis pass2 - checking and writing primary data (1381 records, 4 fields): 14 millis CompletedMACS2peakCalling