Job ID = 6529409 SRX = SRX2564140 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: 00:11:08 34336563 reads; of these: 34336563 (100.00%) were unpaired; of these: 8697166 (25.33%) aligned 0 times 19525891 (56.87%) aligned exactly 1 time 6113506 (17.80%) aligned >1 times 74.67% overall alignment rate Time searching: 00:11:08 Overall time: 00:11:08 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] 7625429 / 25639397 = 0.2974 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 02:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.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 02:15:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:15:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:15:37: 1000000 INFO @ Tue, 30 Jun 2020 02:15:44: 2000000 INFO @ Tue, 30 Jun 2020 02:15:50: 3000000 INFO @ Tue, 30 Jun 2020 02:15:57: 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 02:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.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 02:16:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:04: 5000000 INFO @ Tue, 30 Jun 2020 02:16:08: 1000000 INFO @ Tue, 30 Jun 2020 02:16:11: 6000000 INFO @ Tue, 30 Jun 2020 02:16:15: 2000000 INFO @ Tue, 30 Jun 2020 02:16:18: 7000000 INFO @ Tue, 30 Jun 2020 02:16:23: 3000000 INFO @ Tue, 30 Jun 2020 02:16:26: 8000000 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 02:16:30: 4000000 INFO @ Tue, 30 Jun 2020 02:16:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.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 02:16:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:33: 9000000 INFO @ Tue, 30 Jun 2020 02:16:38: 5000000 INFO @ Tue, 30 Jun 2020 02:16:41: 1000000 INFO @ Tue, 30 Jun 2020 02:16:42: 10000000 INFO @ Tue, 30 Jun 2020 02:16:46: 6000000 INFO @ Tue, 30 Jun 2020 02:16:50: 2000000 INFO @ Tue, 30 Jun 2020 02:16:51: 11000000 INFO @ Tue, 30 Jun 2020 02:16:54: 7000000 INFO @ Tue, 30 Jun 2020 02:16:59: 12000000 INFO @ Tue, 30 Jun 2020 02:16:59: 3000000 INFO @ Tue, 30 Jun 2020 02:17:03: 8000000 INFO @ Tue, 30 Jun 2020 02:17:07: 13000000 INFO @ Tue, 30 Jun 2020 02:17:09: 4000000 INFO @ Tue, 30 Jun 2020 02:17:11: 9000000 INFO @ Tue, 30 Jun 2020 02:17:15: 14000000 INFO @ Tue, 30 Jun 2020 02:17:18: 5000000 INFO @ Tue, 30 Jun 2020 02:17:19: 10000000 INFO @ Tue, 30 Jun 2020 02:17:24: 15000000 INFO @ Tue, 30 Jun 2020 02:17:27: 6000000 INFO @ Tue, 30 Jun 2020 02:17:28: 11000000 INFO @ Tue, 30 Jun 2020 02:17:32: 16000000 INFO @ Tue, 30 Jun 2020 02:17:36: 12000000 INFO @ Tue, 30 Jun 2020 02:17:36: 7000000 INFO @ Tue, 30 Jun 2020 02:17:40: 17000000 INFO @ Tue, 30 Jun 2020 02:17:44: 13000000 INFO @ Tue, 30 Jun 2020 02:17:45: 8000000 INFO @ Tue, 30 Jun 2020 02:17:48: 18000000 INFO @ Tue, 30 Jun 2020 02:17:49: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 02:17:49: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 02:17:49: #1 total tags in treatment: 18013968 INFO @ Tue, 30 Jun 2020 02:17:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:49: #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 02:17:49: #1 tags after filtering in treatment: 18013967 INFO @ Tue, 30 Jun 2020 02:17:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:50: #2 number of paired peaks: 720 WARNING @ Tue, 30 Jun 2020 02:17:50: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:51: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:17:51: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 30 Jun 2020 02:17:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.05_model.r WARNING @ Tue, 30 Jun 2020 02:17:51: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:17:51: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 30 Jun 2020 02:17:51: #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 02:17:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:17:52: 14000000 INFO @ Tue, 30 Jun 2020 02:17:54: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:18:01: 15000000 INFO @ Tue, 30 Jun 2020 02:18:03: 10000000 INFO @ Tue, 30 Jun 2020 02:18:10: 16000000 INFO @ Tue, 30 Jun 2020 02:18:12: 11000000 INFO @ Tue, 30 Jun 2020 02:18:18: 17000000 INFO @ Tue, 30 Jun 2020 02:18:21: 12000000 INFO @ Tue, 30 Jun 2020 02:18:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:27: 18000000 INFO @ Tue, 30 Jun 2020 02:18:27: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 02:18:27: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 02:18:27: #1 total tags in treatment: 18013968 INFO @ Tue, 30 Jun 2020 02:18:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:27: #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 02:18:28: #1 tags after filtering in treatment: 18013967 INFO @ Tue, 30 Jun 2020 02:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:29: #2 number of paired peaks: 720 WARNING @ Tue, 30 Jun 2020 02:18:29: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:29: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:29: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:29: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:29: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:29: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:18:29: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 30 Jun 2020 02:18:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.10_model.r WARNING @ Tue, 30 Jun 2020 02:18:29: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:18:29: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 30 Jun 2020 02:18:29: #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 02:18:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:30: 13000000 INFO @ Tue, 30 Jun 2020 02:18:37: 14000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:18:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.05_summits.bed INFO @ Tue, 30 Jun 2020 02:18:40: Done! pass1 - making usageList (608 chroms): 2 millis pass2 - checking and writing primary data (1867 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:18:46: 15000000 INFO @ Tue, 30 Jun 2020 02:18:53: 16000000 INFO @ Tue, 30 Jun 2020 02:19:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:01: 17000000 INFO @ Tue, 30 Jun 2020 02:19:10: 18000000 INFO @ Tue, 30 Jun 2020 02:19:10: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 02:19:10: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 02:19:10: #1 total tags in treatment: 18013968 INFO @ Tue, 30 Jun 2020 02:19:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:10: #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 02:19:10: #1 tags after filtering in treatment: 18013967 INFO @ Tue, 30 Jun 2020 02:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:12: #2 number of paired peaks: 720 WARNING @ Tue, 30 Jun 2020 02:19:12: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:12: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:12: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:12: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:12: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:12: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:19:12: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 30 Jun 2020 02:19:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.20_model.r WARNING @ Tue, 30 Jun 2020 02:19:12: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:12: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 30 Jun 2020 02:19:12: #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 02:19:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.10_summits.bed INFO @ Tue, 30 Jun 2020 02:19:17: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (1526 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:19:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:20:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564140/SRX2564140.20_summits.bed INFO @ Tue, 30 Jun 2020 02:20:00: Done! pass1 - making usageList (462 chroms): 1 millis pass2 - checking and writing primary data (1321 records, 4 fields): 14 millis CompletedMACS2peakCalling