Job ID = 6529615 SRX = SRX3511944 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: 00:05:22 12066483 reads; of these: 12066483 (100.00%) were unpaired; of these: 1508794 (12.50%) aligned 0 times 8806483 (72.98%) aligned exactly 1 time 1751206 (14.51%) aligned >1 times 87.50% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 525118 / 10557689 = 0.0497 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 02:38:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.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 02:38:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:38:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:38:55: 1000000 INFO @ Tue, 30 Jun 2020 02:39:02: 2000000 INFO @ Tue, 30 Jun 2020 02:39:09: 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 02:39:17: 4000000 INFO @ Tue, 30 Jun 2020 02:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.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 02:39:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:39:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:39:25: 5000000 INFO @ Tue, 30 Jun 2020 02:39:26: 1000000 INFO @ Tue, 30 Jun 2020 02:39:34: 6000000 INFO @ Tue, 30 Jun 2020 02:39:34: 2000000 INFO @ Tue, 30 Jun 2020 02:39:42: 7000000 INFO @ Tue, 30 Jun 2020 02:39:43: 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 02:39:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.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 02:39:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:39:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:39:51: 8000000 INFO @ Tue, 30 Jun 2020 02:39:51: 4000000 INFO @ Tue, 30 Jun 2020 02:39:57: 1000000 INFO @ Tue, 30 Jun 2020 02:40:00: 5000000 INFO @ Tue, 30 Jun 2020 02:40:01: 9000000 INFO @ Tue, 30 Jun 2020 02:40:06: 2000000 INFO @ Tue, 30 Jun 2020 02:40:10: 6000000 INFO @ Tue, 30 Jun 2020 02:40:10: 10000000 INFO @ Tue, 30 Jun 2020 02:40:11: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:40:11: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:40:11: #1 total tags in treatment: 10032571 INFO @ Tue, 30 Jun 2020 02:40:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:40:11: #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 02:40:11: #1 tags after filtering in treatment: 10032550 INFO @ Tue, 30 Jun 2020 02:40:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:40:11: #1 finished! INFO @ Tue, 30 Jun 2020 02:40:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:40:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:40:12: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:40:12: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:40:12: start model_add_line... INFO @ Tue, 30 Jun 2020 02:40:12: start X-correlation... INFO @ Tue, 30 Jun 2020 02:40:12: end of X-cor INFO @ Tue, 30 Jun 2020 02:40:12: #2 finished! INFO @ Tue, 30 Jun 2020 02:40:12: #2 predicted fragment length is 110 bps INFO @ Tue, 30 Jun 2020 02:40:12: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 30 Jun 2020 02:40:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.05_model.r WARNING @ Tue, 30 Jun 2020 02:40:12: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:40:12: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 30 Jun 2020 02:40:12: #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 02:40:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:40:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:40:15: 3000000 INFO @ Tue, 30 Jun 2020 02:40:18: 7000000 INFO @ Tue, 30 Jun 2020 02:40:23: 4000000 INFO @ Tue, 30 Jun 2020 02:40:26: 8000000 INFO @ Tue, 30 Jun 2020 02:40:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:40:32: 5000000 INFO @ Tue, 30 Jun 2020 02:40:36: 9000000 INFO @ Tue, 30 Jun 2020 02:40:40: 6000000 INFO @ Tue, 30 Jun 2020 02:40:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:40:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:40:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.05_summits.bed INFO @ Tue, 30 Jun 2020 02:40:41: Done! pass1 - making usageList (371 chroms): 1 millis pass2 - checking and writing primary data (800 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:40:44: 10000000 INFO @ Tue, 30 Jun 2020 02:40:45: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:40:45: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:40:45: #1 total tags in treatment: 10032571 INFO @ Tue, 30 Jun 2020 02:40:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:40:45: #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 02:40:45: #1 tags after filtering in treatment: 10032550 INFO @ Tue, 30 Jun 2020 02:40:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:40:45: #1 finished! INFO @ Tue, 30 Jun 2020 02:40:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:40:46: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:40:46: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:40:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:40:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:40:46: end of X-cor INFO @ Tue, 30 Jun 2020 02:40:46: #2 finished! INFO @ Tue, 30 Jun 2020 02:40:46: #2 predicted fragment length is 110 bps INFO @ Tue, 30 Jun 2020 02:40:46: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 30 Jun 2020 02:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.10_model.r WARNING @ Tue, 30 Jun 2020 02:40:46: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:40:46: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 30 Jun 2020 02:40:46: #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 02:40:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:40:48: 7000000 INFO @ Tue, 30 Jun 2020 02:40:55: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:41:03: 9000000 INFO @ Tue, 30 Jun 2020 02:41:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:41:11: 10000000 INFO @ Tue, 30 Jun 2020 02:41:11: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:41:11: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:41:11: #1 total tags in treatment: 10032571 INFO @ Tue, 30 Jun 2020 02:41:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:11: #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 02:41:12: #1 tags after filtering in treatment: 10032550 INFO @ Tue, 30 Jun 2020 02:41:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:12: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:13: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:41:13: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:13: #2 predicted fragment length is 110 bps INFO @ Tue, 30 Jun 2020 02:41:13: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 30 Jun 2020 02:41:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.20_model.r WARNING @ Tue, 30 Jun 2020 02:41:13: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:13: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 30 Jun 2020 02:41:13: #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 02:41:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:41:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:41:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.10_summits.bed INFO @ Tue, 30 Jun 2020 02:41:15: Done! pass1 - making usageList (227 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:41:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511944/SRX3511944.20_summits.bed INFO @ Tue, 30 Jun 2020 02:41:41: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 7 millis CompletedMACS2peakCalling