Job ID = 6529701 SRX = SRX3981697 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: 00:08:21 32829976 reads; of these: 32829976 (100.00%) were unpaired; of these: 952966 (2.90%) aligned 0 times 24772710 (75.46%) aligned exactly 1 time 7104300 (21.64%) aligned >1 times 97.10% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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] 4304192 / 31877010 = 0.1350 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 03:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.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 03:13:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:22: 1000000 INFO @ Tue, 30 Jun 2020 03:13:28: 2000000 INFO @ Tue, 30 Jun 2020 03:13:34: 3000000 INFO @ Tue, 30 Jun 2020 03:13:41: 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 03:13:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.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 03:13:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:47: 5000000 INFO @ Tue, 30 Jun 2020 03:13:52: 1000000 INFO @ Tue, 30 Jun 2020 03:13:54: 6000000 INFO @ Tue, 30 Jun 2020 03:13:57: 2000000 INFO @ Tue, 30 Jun 2020 03:14:01: 7000000 INFO @ Tue, 30 Jun 2020 03:14:03: 3000000 INFO @ Tue, 30 Jun 2020 03:14:07: 8000000 INFO @ Tue, 30 Jun 2020 03:14:09: 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 03:14:14: 9000000 INFO @ Tue, 30 Jun 2020 03:14:15: 5000000 INFO @ Tue, 30 Jun 2020 03:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.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 03:14:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:14:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:21: 6000000 INFO @ Tue, 30 Jun 2020 03:14:21: 10000000 INFO @ Tue, 30 Jun 2020 03:14:22: 1000000 INFO @ Tue, 30 Jun 2020 03:14:26: 7000000 INFO @ Tue, 30 Jun 2020 03:14:27: 11000000 INFO @ Tue, 30 Jun 2020 03:14:28: 2000000 INFO @ Tue, 30 Jun 2020 03:14:32: 8000000 INFO @ Tue, 30 Jun 2020 03:14:34: 12000000 INFO @ Tue, 30 Jun 2020 03:14:35: 3000000 INFO @ Tue, 30 Jun 2020 03:14:38: 9000000 INFO @ Tue, 30 Jun 2020 03:14:41: 4000000 INFO @ Tue, 30 Jun 2020 03:14:41: 13000000 INFO @ Tue, 30 Jun 2020 03:14:44: 10000000 INFO @ Tue, 30 Jun 2020 03:14:47: 5000000 INFO @ Tue, 30 Jun 2020 03:14:47: 14000000 INFO @ Tue, 30 Jun 2020 03:14:50: 11000000 INFO @ Tue, 30 Jun 2020 03:14:54: 6000000 INFO @ Tue, 30 Jun 2020 03:14:54: 15000000 INFO @ Tue, 30 Jun 2020 03:14:55: 12000000 INFO @ Tue, 30 Jun 2020 03:15:00: 7000000 INFO @ Tue, 30 Jun 2020 03:15:01: 16000000 INFO @ Tue, 30 Jun 2020 03:15:01: 13000000 INFO @ Tue, 30 Jun 2020 03:15:06: 8000000 INFO @ Tue, 30 Jun 2020 03:15:07: 14000000 INFO @ Tue, 30 Jun 2020 03:15:07: 17000000 INFO @ Tue, 30 Jun 2020 03:15:13: 9000000 INFO @ Tue, 30 Jun 2020 03:15:13: 15000000 INFO @ Tue, 30 Jun 2020 03:15:14: 18000000 INFO @ Tue, 30 Jun 2020 03:15:19: 16000000 INFO @ Tue, 30 Jun 2020 03:15:19: 10000000 INFO @ Tue, 30 Jun 2020 03:15:21: 19000000 INFO @ Tue, 30 Jun 2020 03:15:25: 17000000 INFO @ Tue, 30 Jun 2020 03:15:26: 11000000 INFO @ Tue, 30 Jun 2020 03:15:27: 20000000 INFO @ Tue, 30 Jun 2020 03:15:31: 18000000 INFO @ Tue, 30 Jun 2020 03:15:32: 12000000 INFO @ Tue, 30 Jun 2020 03:15:34: 21000000 INFO @ Tue, 30 Jun 2020 03:15:37: 19000000 INFO @ Tue, 30 Jun 2020 03:15:38: 13000000 INFO @ Tue, 30 Jun 2020 03:15:41: 22000000 INFO @ Tue, 30 Jun 2020 03:15:42: 20000000 INFO @ Tue, 30 Jun 2020 03:15:45: 14000000 INFO @ Tue, 30 Jun 2020 03:15:48: 23000000 INFO @ Tue, 30 Jun 2020 03:15:48: 21000000 INFO @ Tue, 30 Jun 2020 03:15:51: 15000000 INFO @ Tue, 30 Jun 2020 03:15:54: 22000000 INFO @ Tue, 30 Jun 2020 03:15:55: 24000000 INFO @ Tue, 30 Jun 2020 03:15:58: 16000000 INFO @ Tue, 30 Jun 2020 03:16:00: 23000000 INFO @ Tue, 30 Jun 2020 03:16:02: 25000000 INFO @ Tue, 30 Jun 2020 03:16:04: 17000000 INFO @ Tue, 30 Jun 2020 03:16:06: 24000000 INFO @ Tue, 30 Jun 2020 03:16:08: 26000000 INFO @ Tue, 30 Jun 2020 03:16:11: 18000000 INFO @ Tue, 30 Jun 2020 03:16:12: 25000000 INFO @ Tue, 30 Jun 2020 03:16:15: 27000000 INFO @ Tue, 30 Jun 2020 03:16:17: 19000000 INFO @ Tue, 30 Jun 2020 03:16:19: 26000000 INFO @ Tue, 30 Jun 2020 03:16:19: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:16:19: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:16:19: #1 total tags in treatment: 27572818 INFO @ Tue, 30 Jun 2020 03:16:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:19: #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 03:16:20: #1 tags after filtering in treatment: 27572762 INFO @ Tue, 30 Jun 2020 03:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:20: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:16:22: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 03:16:22: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:22: start model_add_line... INFO @ Tue, 30 Jun 2020 03:16:22: start X-correlation... INFO @ Tue, 30 Jun 2020 03:16:22: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:22: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:22: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:16:22: #2 alternative fragment length(s) may be 2,52,511,575 bps INFO @ Tue, 30 Jun 2020 03:16:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.05_model.r WARNING @ Tue, 30 Jun 2020 03:16:22: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:22: #2 You may need to consider one of the other alternative d(s): 2,52,511,575 WARNING @ Tue, 30 Jun 2020 03:16:22: #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 03:16:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:16:24: 20000000 INFO @ Tue, 30 Jun 2020 03:16:25: 27000000 INFO @ Tue, 30 Jun 2020 03:16:28: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:16:28: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:16:28: #1 total tags in treatment: 27572818 INFO @ Tue, 30 Jun 2020 03:16:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:28: #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 03:16:29: #1 tags after filtering in treatment: 27572762 INFO @ Tue, 30 Jun 2020 03:16:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:29: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:29: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:16:30: 21000000 INFO @ Tue, 30 Jun 2020 03:16:31: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 03:16:31: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:16:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:16:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:31: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:16:31: #2 alternative fragment length(s) may be 2,52,511,575 bps INFO @ Tue, 30 Jun 2020 03:16:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.10_model.r WARNING @ Tue, 30 Jun 2020 03:16:31: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:31: #2 You may need to consider one of the other alternative d(s): 2,52,511,575 WARNING @ Tue, 30 Jun 2020 03:16:31: #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 03:16:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:16:37: 22000000 INFO @ Tue, 30 Jun 2020 03:16:43: 23000000 INFO @ Tue, 30 Jun 2020 03:16:49: 24000000 INFO @ Tue, 30 Jun 2020 03:16:55: 25000000 INFO @ Tue, 30 Jun 2020 03:17:02: 26000000 INFO @ Tue, 30 Jun 2020 03:17:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:08: 27000000 INFO @ Tue, 30 Jun 2020 03:17:12: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:17:12: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:17:12: #1 total tags in treatment: 27572818 INFO @ Tue, 30 Jun 2020 03:17:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:17:12: #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 03:17:12: #1 tags after filtering in treatment: 27572762 INFO @ Tue, 30 Jun 2020 03:17:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:17:12: #1 finished! INFO @ Tue, 30 Jun 2020 03:17:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:17:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:17:14: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 03:17:14: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 03:17:14: start model_add_line... INFO @ Tue, 30 Jun 2020 03:17:14: start X-correlation... INFO @ Tue, 30 Jun 2020 03:17:14: end of X-cor INFO @ Tue, 30 Jun 2020 03:17:14: #2 finished! INFO @ Tue, 30 Jun 2020 03:17:14: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:17:14: #2 alternative fragment length(s) may be 2,52,511,575 bps INFO @ Tue, 30 Jun 2020 03:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.20_model.r WARNING @ Tue, 30 Jun 2020 03:17:14: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:17:14: #2 You may need to consider one of the other alternative d(s): 2,52,511,575 WARNING @ Tue, 30 Jun 2020 03:17:14: #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 03:17:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:17:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:17:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:17:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.05_summits.bed INFO @ Tue, 30 Jun 2020 03:17:29: Done! pass1 - making usageList (627 chroms): 1 millis pass2 - checking and writing primary data (3167 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:17:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.10_summits.bed INFO @ Tue, 30 Jun 2020 03:17:40: Done! pass1 - making usageList (377 chroms): 1 millis pass2 - checking and writing primary data (1280 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:18:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:18:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981697/SRX3981697.20_summits.bed INFO @ Tue, 30 Jun 2020 03:18:25: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (399 records, 4 fields): 6 millis CompletedMACS2peakCalling