Job ID = 6529854 SRX = SRX5287828 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: 00:00:01 Multiseed full-index search: 00:07:04 17954539 reads; of these: 17954539 (100.00%) were unpaired; of these: 725745 (4.04%) aligned 0 times 12894711 (71.82%) aligned exactly 1 time 4334083 (24.14%) aligned >1 times 95.96% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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] 2182143 / 17228794 = 0.1267 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 03:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.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 03:04:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:04:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:04:10: 1000000 INFO @ Tue, 30 Jun 2020 03:04:17: 2000000 INFO @ Tue, 30 Jun 2020 03:04:25: 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 03:04:32: 4000000 INFO @ Tue, 30 Jun 2020 03:04:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.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 03:04:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:04:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:04:39: 5000000 INFO @ Tue, 30 Jun 2020 03:04:41: 1000000 INFO @ Tue, 30 Jun 2020 03:04:46: 6000000 INFO @ Tue, 30 Jun 2020 03:04:49: 2000000 INFO @ Tue, 30 Jun 2020 03:04:53: 7000000 INFO @ Tue, 30 Jun 2020 03:04:57: 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 03:05:01: 8000000 INFO @ Tue, 30 Jun 2020 03:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.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 03:05:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:05:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:05:04: 4000000 INFO @ Tue, 30 Jun 2020 03:05:08: 9000000 INFO @ Tue, 30 Jun 2020 03:05:10: 1000000 INFO @ Tue, 30 Jun 2020 03:05:12: 5000000 INFO @ Tue, 30 Jun 2020 03:05:15: 10000000 INFO @ Tue, 30 Jun 2020 03:05:18: 2000000 INFO @ Tue, 30 Jun 2020 03:05:20: 6000000 INFO @ Tue, 30 Jun 2020 03:05:22: 11000000 INFO @ Tue, 30 Jun 2020 03:05:26: 3000000 INFO @ Tue, 30 Jun 2020 03:05:27: 7000000 INFO @ Tue, 30 Jun 2020 03:05:29: 12000000 INFO @ Tue, 30 Jun 2020 03:05:34: 4000000 INFO @ Tue, 30 Jun 2020 03:05:35: 8000000 INFO @ Tue, 30 Jun 2020 03:05:37: 13000000 INFO @ Tue, 30 Jun 2020 03:05:41: 5000000 INFO @ Tue, 30 Jun 2020 03:05:42: 9000000 INFO @ Tue, 30 Jun 2020 03:05:45: 14000000 INFO @ Tue, 30 Jun 2020 03:05:49: 6000000 INFO @ Tue, 30 Jun 2020 03:05:50: 10000000 INFO @ Tue, 30 Jun 2020 03:05:52: 15000000 INFO @ Tue, 30 Jun 2020 03:05:53: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:05:53: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:05:53: #1 total tags in treatment: 15046651 INFO @ Tue, 30 Jun 2020 03:05:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:05:53: #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 03:05:54: #1 tags after filtering in treatment: 15046651 INFO @ Tue, 30 Jun 2020 03:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:05:54: #1 finished! INFO @ Tue, 30 Jun 2020 03:05:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:05:55: #2 number of paired peaks: 496 WARNING @ Tue, 30 Jun 2020 03:05:55: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 30 Jun 2020 03:05:55: start model_add_line... INFO @ Tue, 30 Jun 2020 03:05:55: start X-correlation... INFO @ Tue, 30 Jun 2020 03:05:55: end of X-cor INFO @ Tue, 30 Jun 2020 03:05:55: #2 finished! INFO @ Tue, 30 Jun 2020 03:05:55: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 03:05:55: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 30 Jun 2020 03:05:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.05_model.r WARNING @ Tue, 30 Jun 2020 03:05:55: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:05:55: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 30 Jun 2020 03:05:55: #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 03:05:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:05:56: 7000000 INFO @ Tue, 30 Jun 2020 03:05:57: 11000000 INFO @ Tue, 30 Jun 2020 03:06:03: 8000000 INFO @ Tue, 30 Jun 2020 03:06:04: 12000000 INFO @ Tue, 30 Jun 2020 03:06:10: 9000000 INFO @ Tue, 30 Jun 2020 03:06:12: 13000000 INFO @ Tue, 30 Jun 2020 03:06:17: 10000000 INFO @ Tue, 30 Jun 2020 03:06:19: 14000000 INFO @ Tue, 30 Jun 2020 03:06:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:06:23: 11000000 INFO @ Tue, 30 Jun 2020 03:06:28: 15000000 INFO @ Tue, 30 Jun 2020 03:06:28: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:06:28: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:06:28: #1 total tags in treatment: 15046651 INFO @ Tue, 30 Jun 2020 03:06:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:06:28: #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 03:06:29: #1 tags after filtering in treatment: 15046651 INFO @ Tue, 30 Jun 2020 03:06:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:06:29: #1 finished! INFO @ Tue, 30 Jun 2020 03:06:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:06:30: #2 number of paired peaks: 496 WARNING @ Tue, 30 Jun 2020 03:06:30: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 30 Jun 2020 03:06:30: start model_add_line... INFO @ Tue, 30 Jun 2020 03:06:30: start X-correlation... INFO @ Tue, 30 Jun 2020 03:06:30: 12000000 INFO @ Tue, 30 Jun 2020 03:06:30: end of X-cor INFO @ Tue, 30 Jun 2020 03:06:30: #2 finished! INFO @ Tue, 30 Jun 2020 03:06:30: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 03:06:30: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 30 Jun 2020 03:06:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.10_model.r WARNING @ Tue, 30 Jun 2020 03:06:30: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:06:30: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 30 Jun 2020 03:06:30: #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 03:06:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:06:30: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.05_summits.bed INFO @ Tue, 30 Jun 2020 03:06:37: Done! pass1 - making usageList (650 chroms): 2 millis pass2 - checking and writing primary data (3043 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:06:38: 13000000 INFO @ Tue, 30 Jun 2020 03:06:44: 14000000 INFO @ Tue, 30 Jun 2020 03:06:51: 15000000 INFO @ Tue, 30 Jun 2020 03:06:51: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:06:51: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:06:51: #1 total tags in treatment: 15046651 INFO @ Tue, 30 Jun 2020 03:06:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:06:51: #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 03:06:52: #1 tags after filtering in treatment: 15046651 INFO @ Tue, 30 Jun 2020 03:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:06:52: #1 finished! INFO @ Tue, 30 Jun 2020 03:06:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:06:53: #2 number of paired peaks: 496 WARNING @ Tue, 30 Jun 2020 03:06:53: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 30 Jun 2020 03:06:53: start model_add_line... INFO @ Tue, 30 Jun 2020 03:06:53: start X-correlation... INFO @ Tue, 30 Jun 2020 03:06:53: end of X-cor INFO @ Tue, 30 Jun 2020 03:06:53: #2 finished! INFO @ Tue, 30 Jun 2020 03:06:53: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 03:06:53: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 30 Jun 2020 03:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.20_model.r WARNING @ Tue, 30 Jun 2020 03:06:53: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:06:53: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 30 Jun 2020 03:06:53: #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 03:06:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:06:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.10_summits.bed INFO @ Tue, 30 Jun 2020 03:07:12: Done! pass1 - making usageList (548 chroms): 2 millis pass2 - checking and writing primary data (1857 records, 4 fields): 31 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:07:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:07:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:07:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287828/SRX5287828.20_summits.bed INFO @ Tue, 30 Jun 2020 03:07:35: Done! pass1 - making usageList (407 chroms): 2 millis pass2 - checking and writing primary data (1062 records, 4 fields): 23 millis CompletedMACS2peakCalling