Job ID = 6529762 SRX = SRX467100 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: 00:05:11 18393353 reads; of these: 18393353 (100.00%) were unpaired; of these: 1212982 (6.59%) aligned 0 times 13406024 (72.89%) aligned exactly 1 time 3774347 (20.52%) aligned >1 times 93.41% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 1474916 / 17180371 = 0.0858 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 02:50:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.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 02:50:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:39: 1000000 INFO @ Tue, 30 Jun 2020 02:50:46: 2000000 INFO @ Tue, 30 Jun 2020 02:50:53: 3000000 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 02:51:00: 4000000 INFO @ Tue, 30 Jun 2020 02:51:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.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 02:51:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:08: 5000000 INFO @ Tue, 30 Jun 2020 02:51:08: 1000000 INFO @ Tue, 30 Jun 2020 02:51:15: 6000000 INFO @ Tue, 30 Jun 2020 02:51:15: 2000000 INFO @ Tue, 30 Jun 2020 02:51:22: 3000000 INFO @ Tue, 30 Jun 2020 02:51:23: 7000000 INFO @ Tue, 30 Jun 2020 02:51:29: 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 02:51:31: 8000000 INFO @ Tue, 30 Jun 2020 02:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.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 02:51:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:36: 5000000 INFO @ Tue, 30 Jun 2020 02:51:39: 9000000 INFO @ Tue, 30 Jun 2020 02:51:39: 1000000 INFO @ Tue, 30 Jun 2020 02:51:43: 6000000 INFO @ Tue, 30 Jun 2020 02:51:46: 10000000 INFO @ Tue, 30 Jun 2020 02:51:47: 2000000 INFO @ Tue, 30 Jun 2020 02:51:50: 7000000 INFO @ Tue, 30 Jun 2020 02:51:54: 11000000 INFO @ Tue, 30 Jun 2020 02:51:54: 3000000 INFO @ Tue, 30 Jun 2020 02:51:57: 8000000 INFO @ Tue, 30 Jun 2020 02:52:02: 12000000 INFO @ Tue, 30 Jun 2020 02:52:02: 4000000 INFO @ Tue, 30 Jun 2020 02:52:04: 9000000 INFO @ Tue, 30 Jun 2020 02:52:10: 5000000 INFO @ Tue, 30 Jun 2020 02:52:10: 13000000 INFO @ Tue, 30 Jun 2020 02:52:11: 10000000 INFO @ Tue, 30 Jun 2020 02:52:17: 6000000 INFO @ Tue, 30 Jun 2020 02:52:18: 14000000 INFO @ Tue, 30 Jun 2020 02:52:18: 11000000 INFO @ Tue, 30 Jun 2020 02:52:25: 7000000 INFO @ Tue, 30 Jun 2020 02:52:25: 12000000 INFO @ Tue, 30 Jun 2020 02:52:25: 15000000 INFO @ Tue, 30 Jun 2020 02:52:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:52:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:52:31: #1 total tags in treatment: 15705455 INFO @ Tue, 30 Jun 2020 02:52:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:31: #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 02:52:31: #1 tags after filtering in treatment: 15705454 INFO @ Tue, 30 Jun 2020 02:52:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:32: 13000000 INFO @ Tue, 30 Jun 2020 02:52:32: #2 number of paired peaks: 339 WARNING @ Tue, 30 Jun 2020 02:52:32: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:32: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:32: 8000000 INFO @ Tue, 30 Jun 2020 02:52:32: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:32: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:32: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:32: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:52:32: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 02:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.05_model.r WARNING @ Tue, 30 Jun 2020 02:52:32: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:32: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 02:52:32: #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 02:52:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:39: 14000000 INFO @ Tue, 30 Jun 2020 02:52:40: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:52:46: 15000000 INFO @ Tue, 30 Jun 2020 02:52:47: 10000000 INFO @ Tue, 30 Jun 2020 02:52:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:52:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:52:51: #1 total tags in treatment: 15705455 INFO @ Tue, 30 Jun 2020 02:52:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:51: #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 02:52:52: #1 tags after filtering in treatment: 15705454 INFO @ Tue, 30 Jun 2020 02:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:53: #2 number of paired peaks: 339 WARNING @ Tue, 30 Jun 2020 02:52:53: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:53: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:52:53: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 02:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.10_model.r WARNING @ Tue, 30 Jun 2020 02:52:53: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:53: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 02:52:53: #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 02:52:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:55: 11000000 INFO @ Tue, 30 Jun 2020 02:53:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:02: 12000000 INFO @ Tue, 30 Jun 2020 02:53:09: 13000000 INFO @ Tue, 30 Jun 2020 02:53:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.05_summits.bed INFO @ Tue, 30 Jun 2020 02:53:16: Done! pass1 - making usageList (520 chroms): 1 millis pass2 - checking and writing primary data (2058 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:16: 14000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:53:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:23: 15000000 INFO @ Tue, 30 Jun 2020 02:53:28: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:53:28: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:53:28: #1 total tags in treatment: 15705455 INFO @ Tue, 30 Jun 2020 02:53:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:28: #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 02:53:29: #1 tags after filtering in treatment: 15705454 INFO @ Tue, 30 Jun 2020 02:53:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:30: #2 number of paired peaks: 339 WARNING @ Tue, 30 Jun 2020 02:53:30: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:30: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:53:30: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 02:53:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.20_model.r WARNING @ Tue, 30 Jun 2020 02:53:30: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:30: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 02:53:30: #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 02:53:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.10_summits.bed INFO @ Tue, 30 Jun 2020 02:53:36: Done! pass1 - making usageList (461 chroms): 1 millis pass2 - checking and writing primary data (1695 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467100/SRX467100.20_summits.bed INFO @ Tue, 30 Jun 2020 02:54:13: Done! pass1 - making usageList (281 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 9 millis CompletedMACS2peakCalling