Job ID = 6529585 SRX = SRX331365 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: 00:05:02 19200904 reads; of these: 19200904 (100.00%) were unpaired; of these: 1306449 (6.80%) aligned 0 times 13670284 (71.20%) aligned exactly 1 time 4224171 (22.00%) aligned >1 times 93.20% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 1808467 / 17894455 = 0.1011 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 02:30:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.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 02:30:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:30:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:30:32: 1000000 INFO @ Tue, 30 Jun 2020 02:30:38: 2000000 INFO @ Tue, 30 Jun 2020 02:30:44: 3000000 INFO @ Tue, 30 Jun 2020 02:30:49: 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 02:30:55: 5000000 INFO @ Tue, 30 Jun 2020 02:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.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 02:30:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:30:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:01: 6000000 INFO @ Tue, 30 Jun 2020 02:31:03: 1000000 INFO @ Tue, 30 Jun 2020 02:31:08: 7000000 INFO @ Tue, 30 Jun 2020 02:31:10: 2000000 INFO @ Tue, 30 Jun 2020 02:31:15: 8000000 INFO @ Tue, 30 Jun 2020 02:31:17: 3000000 INFO @ Tue, 30 Jun 2020 02:31:21: 9000000 INFO @ Tue, 30 Jun 2020 02:31:23: 4000000 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 02:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.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 02:31:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:28: 10000000 INFO @ Tue, 30 Jun 2020 02:31:30: 5000000 INFO @ Tue, 30 Jun 2020 02:31:35: 1000000 INFO @ Tue, 30 Jun 2020 02:31:35: 11000000 INFO @ Tue, 30 Jun 2020 02:31:38: 6000000 INFO @ Tue, 30 Jun 2020 02:31:43: 12000000 INFO @ Tue, 30 Jun 2020 02:31:43: 2000000 INFO @ Tue, 30 Jun 2020 02:31:45: 7000000 INFO @ Tue, 30 Jun 2020 02:31:50: 13000000 INFO @ Tue, 30 Jun 2020 02:31:51: 3000000 INFO @ Tue, 30 Jun 2020 02:31:53: 8000000 INFO @ Tue, 30 Jun 2020 02:31:58: 14000000 INFO @ Tue, 30 Jun 2020 02:31:59: 4000000 INFO @ Tue, 30 Jun 2020 02:32:00: 9000000 INFO @ Tue, 30 Jun 2020 02:32:06: 15000000 INFO @ Tue, 30 Jun 2020 02:32:08: 5000000 INFO @ Tue, 30 Jun 2020 02:32:08: 10000000 INFO @ Tue, 30 Jun 2020 02:32:14: 16000000 INFO @ Tue, 30 Jun 2020 02:32:15: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:32:15: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:32:15: #1 total tags in treatment: 16085988 INFO @ Tue, 30 Jun 2020 02:32:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:15: #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 02:32:16: #1 tags after filtering in treatment: 16085988 INFO @ Tue, 30 Jun 2020 02:32:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:16: 11000000 INFO @ Tue, 30 Jun 2020 02:32:17: 6000000 INFO @ Tue, 30 Jun 2020 02:32:17: #2 number of paired peaks: 296 WARNING @ Tue, 30 Jun 2020 02:32:17: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:17: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:17: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:17: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:17: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:17: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 02:32:17: #2 alternative fragment length(s) may be 3,38 bps INFO @ Tue, 30 Jun 2020 02:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.05_model.r WARNING @ Tue, 30 Jun 2020 02:32:17: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:17: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Tue, 30 Jun 2020 02:32:17: #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 02:32:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:24: 12000000 INFO @ Tue, 30 Jun 2020 02:32:25: 7000000 INFO @ Tue, 30 Jun 2020 02:32:32: 13000000 INFO @ Tue, 30 Jun 2020 02:32:34: 8000000 INFO @ Tue, 30 Jun 2020 02:32:41: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:32:43: 9000000 INFO @ Tue, 30 Jun 2020 02:32:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:32:49: 15000000 INFO @ Tue, 30 Jun 2020 02:32:53: 10000000 INFO @ Tue, 30 Jun 2020 02:32:58: 16000000 INFO @ Tue, 30 Jun 2020 02:32:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:32:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:32:58: #1 total tags in treatment: 16085988 INFO @ Tue, 30 Jun 2020 02:32:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:58: #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 02:32:59: #1 tags after filtering in treatment: 16085988 INFO @ Tue, 30 Jun 2020 02:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:59: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:00: #2 number of paired peaks: 296 WARNING @ Tue, 30 Jun 2020 02:33:00: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:00: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:00: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:00: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:00: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:00: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 02:33:00: #2 alternative fragment length(s) may be 3,38 bps INFO @ Tue, 30 Jun 2020 02:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.10_model.r WARNING @ Tue, 30 Jun 2020 02:33:00: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:33:00: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Tue, 30 Jun 2020 02:33:00: #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 02:33:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:33:01: 11000000 INFO @ Tue, 30 Jun 2020 02:33:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.05_summits.bed INFO @ Tue, 30 Jun 2020 02:33:02: Done! pass1 - making usageList (539 chroms): 1 millis pass2 - checking and writing primary data (2270 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:33:09: 12000000 INFO @ Tue, 30 Jun 2020 02:33:17: 13000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:33:26: 14000000 INFO @ Tue, 30 Jun 2020 02:33:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:33: 15000000 INFO @ Tue, 30 Jun 2020 02:33:42: 16000000 INFO @ Tue, 30 Jun 2020 02:33:43: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:33:43: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:33:43: #1 total tags in treatment: 16085988 INFO @ Tue, 30 Jun 2020 02:33:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:33:43: #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 02:33:43: #1 tags after filtering in treatment: 16085988 INFO @ Tue, 30 Jun 2020 02:33:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:33:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:33:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:44: #2 number of paired peaks: 296 WARNING @ Tue, 30 Jun 2020 02:33:44: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:45: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 02:33:45: #2 alternative fragment length(s) may be 3,38 bps INFO @ Tue, 30 Jun 2020 02:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.20_model.r WARNING @ Tue, 30 Jun 2020 02:33:45: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:33:45: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Tue, 30 Jun 2020 02:33:45: #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 02:33:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.10_summits.bed INFO @ Tue, 30 Jun 2020 02:33:46: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (1503 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:34:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:34:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:34:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331365/SRX331365.20_summits.bed INFO @ Tue, 30 Jun 2020 02:34:34: Done! pass1 - making usageList (234 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 8 millis CompletedMACS2peakCalling