Job ID = 6529397 SRX = SRX245834 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: 00:05:55 24191836 reads; of these: 24191836 (100.00%) were unpaired; of these: 1579814 (6.53%) aligned 0 times 17507949 (72.37%) aligned exactly 1 time 5104073 (21.10%) aligned >1 times 93.47% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 2510198 / 22612022 = 0.1110 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 02:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.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 02:16:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:43: 1000000 INFO @ Tue, 30 Jun 2020 02:16:49: 2000000 INFO @ Tue, 30 Jun 2020 02:16:54: 3000000 INFO @ Tue, 30 Jun 2020 02:16:59: 4000000 INFO @ Tue, 30 Jun 2020 02:17:04: 5000000 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 02:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.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 02:17:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:09: 6000000 INFO @ Tue, 30 Jun 2020 02:17:13: 1000000 INFO @ Tue, 30 Jun 2020 02:17:15: 7000000 INFO @ Tue, 30 Jun 2020 02:17:19: 2000000 INFO @ Tue, 30 Jun 2020 02:17:21: 8000000 INFO @ Tue, 30 Jun 2020 02:17:25: 3000000 INFO @ Tue, 30 Jun 2020 02:17:27: 9000000 INFO @ Tue, 30 Jun 2020 02:17:31: 4000000 INFO @ Tue, 30 Jun 2020 02:17:32: 10000000 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 02:17:36: 5000000 INFO @ Tue, 30 Jun 2020 02:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.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 02:17:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:38: 11000000 INFO @ Tue, 30 Jun 2020 02:17:42: 6000000 INFO @ Tue, 30 Jun 2020 02:17:44: 1000000 INFO @ Tue, 30 Jun 2020 02:17:44: 12000000 INFO @ Tue, 30 Jun 2020 02:17:49: 7000000 INFO @ Tue, 30 Jun 2020 02:17:50: 2000000 INFO @ Tue, 30 Jun 2020 02:17:50: 13000000 INFO @ Tue, 30 Jun 2020 02:17:54: 8000000 INFO @ Tue, 30 Jun 2020 02:17:56: 3000000 INFO @ Tue, 30 Jun 2020 02:17:56: 14000000 INFO @ Tue, 30 Jun 2020 02:18:00: 9000000 INFO @ Tue, 30 Jun 2020 02:18:02: 4000000 INFO @ Tue, 30 Jun 2020 02:18:02: 15000000 INFO @ Tue, 30 Jun 2020 02:18:07: 10000000 INFO @ Tue, 30 Jun 2020 02:18:08: 5000000 INFO @ Tue, 30 Jun 2020 02:18:09: 16000000 INFO @ Tue, 30 Jun 2020 02:18:13: 11000000 INFO @ Tue, 30 Jun 2020 02:18:15: 6000000 INFO @ Tue, 30 Jun 2020 02:18:15: 17000000 INFO @ Tue, 30 Jun 2020 02:18:19: 12000000 INFO @ Tue, 30 Jun 2020 02:18:21: 7000000 INFO @ Tue, 30 Jun 2020 02:18:21: 18000000 INFO @ Tue, 30 Jun 2020 02:18:25: 13000000 INFO @ Tue, 30 Jun 2020 02:18:27: 8000000 INFO @ Tue, 30 Jun 2020 02:18:27: 19000000 INFO @ Tue, 30 Jun 2020 02:18:31: 14000000 INFO @ Tue, 30 Jun 2020 02:18:33: 9000000 INFO @ Tue, 30 Jun 2020 02:18:33: 20000000 INFO @ Tue, 30 Jun 2020 02:18:34: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 02:18:34: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 02:18:34: #1 total tags in treatment: 20101824 INFO @ Tue, 30 Jun 2020 02:18:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:34: #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 02:18:35: #1 tags after filtering in treatment: 20101768 INFO @ Tue, 30 Jun 2020 02:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:36: 15000000 INFO @ Tue, 30 Jun 2020 02:18:36: #2 number of paired peaks: 229 WARNING @ Tue, 30 Jun 2020 02:18:36: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:36: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:37: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:18:37: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.05_model.r WARNING @ Tue, 30 Jun 2020 02:18:37: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:18:37: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:18:37: #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 02:18:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:38: 10000000 INFO @ Tue, 30 Jun 2020 02:18:42: 16000000 INFO @ Tue, 30 Jun 2020 02:18:44: 11000000 INFO @ Tue, 30 Jun 2020 02:18:48: 17000000 INFO @ Tue, 30 Jun 2020 02:18:49: 12000000 INFO @ Tue, 30 Jun 2020 02:18:53: 18000000 INFO @ Tue, 30 Jun 2020 02:18:54: 13000000 INFO @ Tue, 30 Jun 2020 02:18:59: 19000000 INFO @ Tue, 30 Jun 2020 02:19:00: 14000000 INFO @ Tue, 30 Jun 2020 02:19:05: 20000000 INFO @ Tue, 30 Jun 2020 02:19:06: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 02:19:06: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 02:19:06: #1 total tags in treatment: 20101824 INFO @ Tue, 30 Jun 2020 02:19:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:06: #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 02:19:06: 15000000 INFO @ Tue, 30 Jun 2020 02:19:07: #1 tags after filtering in treatment: 20101768 INFO @ Tue, 30 Jun 2020 02:19:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:08: #2 number of paired peaks: 229 WARNING @ Tue, 30 Jun 2020 02:19:08: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:08: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:19:08: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:19:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.10_model.r WARNING @ Tue, 30 Jun 2020 02:19:08: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:08: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:19:08: #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 02:19:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:13: 16000000 INFO @ Tue, 30 Jun 2020 02:19:18: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:19:24: 18000000 INFO @ Tue, 30 Jun 2020 02:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.05_summits.bed INFO @ Tue, 30 Jun 2020 02:19:27: Done! pass1 - making usageList (569 chroms): 2 millis pass2 - checking and writing primary data (2757 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:19:30: 19000000 INFO @ Tue, 30 Jun 2020 02:19:36: 20000000 INFO @ Tue, 30 Jun 2020 02:19:37: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 02:19:37: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 02:19:37: #1 total tags in treatment: 20101824 INFO @ Tue, 30 Jun 2020 02:19:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:37: #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 02:19:37: #1 tags after filtering in treatment: 20101768 INFO @ Tue, 30 Jun 2020 02:19:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:39: #2 number of paired peaks: 229 WARNING @ Tue, 30 Jun 2020 02:19:39: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:39: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:39: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:39: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:39: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:39: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:19:39: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.20_model.r WARNING @ Tue, 30 Jun 2020 02:19:39: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:39: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:19:39: #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 02:19:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.10_summits.bed INFO @ Tue, 30 Jun 2020 02:19:59: Done! pass1 - making usageList (368 chroms): 1 millis pass2 - checking and writing primary data (1108 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:20:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:20:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX245834/SRX245834.20_summits.bed INFO @ Tue, 30 Jun 2020 02:20:29: Done! pass1 - making usageList (148 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 10 millis CompletedMACS2peakCalling