Job ID = 6529853 SRX = SRX5287827 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: 00:10:19 28304229 reads; of these: 28304229 (100.00%) were unpaired; of these: 1034407 (3.65%) aligned 0 times 20699694 (73.13%) aligned exactly 1 time 6570128 (23.21%) aligned >1 times 96.35% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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] 3467806 / 27269822 = 0.1272 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 03:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.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 03:19:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:20: 1000000 INFO @ Tue, 30 Jun 2020 03:19:28: 2000000 INFO @ Tue, 30 Jun 2020 03:19:35: 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 03:19:42: 4000000 INFO @ Tue, 30 Jun 2020 03:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.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 03:19:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:49: 1000000 INFO @ Tue, 30 Jun 2020 03:19:50: 5000000 INFO @ Tue, 30 Jun 2020 03:19:57: 2000000 INFO @ Tue, 30 Jun 2020 03:19:57: 6000000 INFO @ Tue, 30 Jun 2020 03:20:04: 3000000 INFO @ Tue, 30 Jun 2020 03:20:05: 7000000 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 03:20:11: 4000000 INFO @ Tue, 30 Jun 2020 03:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.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 03:20:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:13: 8000000 INFO @ Tue, 30 Jun 2020 03:20:18: 5000000 INFO @ Tue, 30 Jun 2020 03:20:20: 1000000 INFO @ Tue, 30 Jun 2020 03:20:21: 9000000 INFO @ Tue, 30 Jun 2020 03:20:26: 6000000 INFO @ Tue, 30 Jun 2020 03:20:28: 2000000 INFO @ Tue, 30 Jun 2020 03:20:29: 10000000 INFO @ Tue, 30 Jun 2020 03:20:33: 7000000 INFO @ Tue, 30 Jun 2020 03:20:36: 3000000 INFO @ Tue, 30 Jun 2020 03:20:36: 11000000 INFO @ Tue, 30 Jun 2020 03:20:40: 8000000 INFO @ Tue, 30 Jun 2020 03:20:44: 4000000 INFO @ Tue, 30 Jun 2020 03:20:44: 12000000 INFO @ Tue, 30 Jun 2020 03:20:47: 9000000 INFO @ Tue, 30 Jun 2020 03:20:51: 5000000 INFO @ Tue, 30 Jun 2020 03:20:52: 13000000 INFO @ Tue, 30 Jun 2020 03:20:54: 10000000 INFO @ Tue, 30 Jun 2020 03:20:59: 6000000 INFO @ Tue, 30 Jun 2020 03:21:00: 14000000 INFO @ Tue, 30 Jun 2020 03:21:01: 11000000 INFO @ Tue, 30 Jun 2020 03:21:06: 7000000 INFO @ Tue, 30 Jun 2020 03:21:08: 15000000 INFO @ Tue, 30 Jun 2020 03:21:08: 12000000 INFO @ Tue, 30 Jun 2020 03:21:14: 8000000 INFO @ Tue, 30 Jun 2020 03:21:15: 13000000 INFO @ Tue, 30 Jun 2020 03:21:16: 16000000 INFO @ Tue, 30 Jun 2020 03:21:22: 9000000 INFO @ Tue, 30 Jun 2020 03:21:22: 14000000 INFO @ Tue, 30 Jun 2020 03:21:24: 17000000 INFO @ Tue, 30 Jun 2020 03:21:29: 15000000 INFO @ Tue, 30 Jun 2020 03:21:30: 10000000 INFO @ Tue, 30 Jun 2020 03:21:32: 18000000 INFO @ Tue, 30 Jun 2020 03:21:37: 16000000 INFO @ Tue, 30 Jun 2020 03:21:37: 11000000 INFO @ Tue, 30 Jun 2020 03:21:40: 19000000 INFO @ Tue, 30 Jun 2020 03:21:44: 17000000 INFO @ Tue, 30 Jun 2020 03:21:45: 12000000 INFO @ Tue, 30 Jun 2020 03:21:48: 20000000 INFO @ Tue, 30 Jun 2020 03:21:51: 18000000 INFO @ Tue, 30 Jun 2020 03:21:52: 13000000 INFO @ Tue, 30 Jun 2020 03:21:56: 21000000 INFO @ Tue, 30 Jun 2020 03:21:58: 19000000 INFO @ Tue, 30 Jun 2020 03:22:00: 14000000 INFO @ Tue, 30 Jun 2020 03:22:04: 22000000 INFO @ Tue, 30 Jun 2020 03:22:05: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:22:08: 15000000 INFO @ Tue, 30 Jun 2020 03:22:11: 23000000 INFO @ Tue, 30 Jun 2020 03:22:12: 21000000 INFO @ Tue, 30 Jun 2020 03:22:15: 16000000 INFO @ Tue, 30 Jun 2020 03:22:18: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:22:18: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:22:18: #1 total tags in treatment: 23802016 INFO @ Tue, 30 Jun 2020 03:22:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:18: #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 03:22:18: #1 tags after filtering in treatment: 23802016 INFO @ Tue, 30 Jun 2020 03:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:18: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:19: 22000000 INFO @ Tue, 30 Jun 2020 03:22:20: #2 number of paired peaks: 320 WARNING @ Tue, 30 Jun 2020 03:22:20: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:20: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:20: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:20: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:20: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:20: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 03:22:20: #2 alternative fragment length(s) may be 3,57,585 bps INFO @ Tue, 30 Jun 2020 03:22:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.05_model.r WARNING @ Tue, 30 Jun 2020 03:22:20: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:22:20: #2 You may need to consider one of the other alternative d(s): 3,57,585 WARNING @ Tue, 30 Jun 2020 03:22:20: #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 03:22:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:23: 17000000 INFO @ Tue, 30 Jun 2020 03:22:26: 23000000 INFO @ Tue, 30 Jun 2020 03:22:30: 18000000 INFO @ Tue, 30 Jun 2020 03:22:31: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:22:31: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:22:31: #1 total tags in treatment: 23802016 INFO @ Tue, 30 Jun 2020 03:22:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:31: #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 03:22:32: #1 tags after filtering in treatment: 23802016 INFO @ Tue, 30 Jun 2020 03:22:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:32: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:34: #2 number of paired peaks: 320 WARNING @ Tue, 30 Jun 2020 03:22:34: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:34: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:34: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:34: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:34: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:34: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 03:22:34: #2 alternative fragment length(s) may be 3,57,585 bps INFO @ Tue, 30 Jun 2020 03:22:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.10_model.r WARNING @ Tue, 30 Jun 2020 03:22:34: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:22:34: #2 You may need to consider one of the other alternative d(s): 3,57,585 WARNING @ Tue, 30 Jun 2020 03:22:34: #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 03:22:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:37: 19000000 INFO @ Tue, 30 Jun 2020 03:22:45: 20000000 INFO @ Tue, 30 Jun 2020 03:22:52: 21000000 INFO @ Tue, 30 Jun 2020 03:22:59: 22000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:23:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:23:06: 23000000 INFO @ Tue, 30 Jun 2020 03:23:12: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:23:12: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:23:12: #1 total tags in treatment: 23802016 INFO @ Tue, 30 Jun 2020 03:23:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:23:12: #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 03:23:12: #1 tags after filtering in treatment: 23802016 INFO @ Tue, 30 Jun 2020 03:23:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:23:12: #1 finished! INFO @ Tue, 30 Jun 2020 03:23:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:23:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:23:14: #2 number of paired peaks: 320 WARNING @ Tue, 30 Jun 2020 03:23:14: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Tue, 30 Jun 2020 03:23:14: start model_add_line... INFO @ Tue, 30 Jun 2020 03:23:14: start X-correlation... INFO @ Tue, 30 Jun 2020 03:23:14: end of X-cor INFO @ Tue, 30 Jun 2020 03:23:14: #2 finished! INFO @ Tue, 30 Jun 2020 03:23:14: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 03:23:14: #2 alternative fragment length(s) may be 3,57,585 bps INFO @ Tue, 30 Jun 2020 03:23:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.20_model.r WARNING @ Tue, 30 Jun 2020 03:23:14: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:23:14: #2 You may need to consider one of the other alternative d(s): 3,57,585 WARNING @ Tue, 30 Jun 2020 03:23:14: #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 03:23:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:23:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.05_summits.bed INFO @ Tue, 30 Jun 2020 03:23:21: Done! pass1 - making usageList (713 chroms): 1 millis pass2 - checking and writing primary data (2398 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.10_summits.bed INFO @ Tue, 30 Jun 2020 03:23:34: Done! pass1 - making usageList (572 chroms): 1 millis pass2 - checking and writing primary data (1724 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:23:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:24:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:24:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:24:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287827/SRX5287827.20_summits.bed INFO @ Tue, 30 Jun 2020 03:24:13: Done! pass1 - making usageList (424 chroms): 1 millis pass2 - checking and writing primary data (1130 records, 4 fields): 13 millis CompletedMACS2peakCalling