Job ID = 6529270 SRX = SRX1150333 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:51 25518805 reads; of these: 25518805 (100.00%) were unpaired; of these: 531777 (2.08%) aligned 0 times 16396899 (64.25%) aligned exactly 1 time 8590129 (33.66%) aligned >1 times 97.92% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 5347912 / 24987028 = 0.2140 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 01:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.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 01:40:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:42: 1000000 INFO @ Tue, 30 Jun 2020 01:40:50: 2000000 INFO @ Tue, 30 Jun 2020 01:40:58: 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 01:41:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.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 01:41:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:41:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:41:07: 4000000 INFO @ Tue, 30 Jun 2020 01:41:12: 1000000 INFO @ Tue, 30 Jun 2020 01:41:16: 5000000 INFO @ Tue, 30 Jun 2020 01:41:21: 2000000 INFO @ Tue, 30 Jun 2020 01:41:25: 6000000 INFO @ Tue, 30 Jun 2020 01:41:30: 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 01:41:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.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 01:41:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:41:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:41:34: 7000000 INFO @ Tue, 30 Jun 2020 01:41:40: 4000000 INFO @ Tue, 30 Jun 2020 01:41:41: 1000000 INFO @ Tue, 30 Jun 2020 01:41:43: 8000000 INFO @ Tue, 30 Jun 2020 01:41:48: 2000000 INFO @ Tue, 30 Jun 2020 01:41:49: 5000000 INFO @ Tue, 30 Jun 2020 01:41:52: 9000000 INFO @ Tue, 30 Jun 2020 01:41:55: 3000000 INFO @ Tue, 30 Jun 2020 01:41:58: 6000000 INFO @ Tue, 30 Jun 2020 01:42:01: 10000000 INFO @ Tue, 30 Jun 2020 01:42:02: 4000000 INFO @ Tue, 30 Jun 2020 01:42:08: 7000000 INFO @ Tue, 30 Jun 2020 01:42:09: 5000000 INFO @ Tue, 30 Jun 2020 01:42:11: 11000000 INFO @ Tue, 30 Jun 2020 01:42:16: 6000000 INFO @ Tue, 30 Jun 2020 01:42:17: 8000000 INFO @ Tue, 30 Jun 2020 01:42:21: 12000000 INFO @ Tue, 30 Jun 2020 01:42:24: 7000000 INFO @ Tue, 30 Jun 2020 01:42:27: 9000000 INFO @ Tue, 30 Jun 2020 01:42:30: 13000000 INFO @ Tue, 30 Jun 2020 01:42:31: 8000000 INFO @ Tue, 30 Jun 2020 01:42:36: 10000000 INFO @ Tue, 30 Jun 2020 01:42:38: 9000000 INFO @ Tue, 30 Jun 2020 01:42:39: 14000000 INFO @ Tue, 30 Jun 2020 01:42:45: 10000000 INFO @ Tue, 30 Jun 2020 01:42:46: 11000000 INFO @ Tue, 30 Jun 2020 01:42:49: 15000000 INFO @ Tue, 30 Jun 2020 01:42:53: 11000000 INFO @ Tue, 30 Jun 2020 01:42:55: 12000000 INFO @ Tue, 30 Jun 2020 01:42:59: 16000000 INFO @ Tue, 30 Jun 2020 01:43:01: 12000000 INFO @ Tue, 30 Jun 2020 01:43:04: 13000000 INFO @ Tue, 30 Jun 2020 01:43:08: 17000000 INFO @ Tue, 30 Jun 2020 01:43:09: 13000000 INFO @ Tue, 30 Jun 2020 01:43:14: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:43:17: 14000000 INFO @ Tue, 30 Jun 2020 01:43:18: 18000000 INFO @ Tue, 30 Jun 2020 01:43:24: 15000000 INFO @ Tue, 30 Jun 2020 01:43:25: 15000000 INFO @ Tue, 30 Jun 2020 01:43:27: 19000000 INFO @ Tue, 30 Jun 2020 01:43:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:43:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:43:33: #1 total tags in treatment: 19639116 INFO @ Tue, 30 Jun 2020 01:43:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:43:33: 16000000 INFO @ Tue, 30 Jun 2020 01:43:33: #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 01:43:34: 16000000 INFO @ Tue, 30 Jun 2020 01:43:34: #1 tags after filtering in treatment: 19639075 INFO @ Tue, 30 Jun 2020 01:43:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:43:34: #1 finished! INFO @ Tue, 30 Jun 2020 01:43:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:43:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:43:36: #2 number of paired peaks: 924 WARNING @ Tue, 30 Jun 2020 01:43:36: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Tue, 30 Jun 2020 01:43:36: start model_add_line... INFO @ Tue, 30 Jun 2020 01:43:36: start X-correlation... INFO @ Tue, 30 Jun 2020 01:43:36: end of X-cor INFO @ Tue, 30 Jun 2020 01:43:36: #2 finished! INFO @ Tue, 30 Jun 2020 01:43:36: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 01:43:36: #2 alternative fragment length(s) may be 2,43,597 bps INFO @ Tue, 30 Jun 2020 01:43:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.05_model.r WARNING @ Tue, 30 Jun 2020 01:43:36: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:43:36: #2 You may need to consider one of the other alternative d(s): 2,43,597 WARNING @ Tue, 30 Jun 2020 01:43:36: #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 01:43:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:43:43: 17000000 INFO @ Tue, 30 Jun 2020 01:43:43: 17000000 INFO @ Tue, 30 Jun 2020 01:43:51: 18000000 INFO @ Tue, 30 Jun 2020 01:43:52: 18000000 INFO @ Tue, 30 Jun 2020 01:43:59: 19000000 INFO @ Tue, 30 Jun 2020 01:44:02: 19000000 INFO @ Tue, 30 Jun 2020 01:44:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:44:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:44:05: #1 total tags in treatment: 19639116 INFO @ Tue, 30 Jun 2020 01:44:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:44:05: #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 01:44:06: #1 tags after filtering in treatment: 19639075 INFO @ Tue, 30 Jun 2020 01:44:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:44:06: #1 finished! INFO @ Tue, 30 Jun 2020 01:44:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:44:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:44:07: #2 number of paired peaks: 924 WARNING @ Tue, 30 Jun 2020 01:44:07: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Tue, 30 Jun 2020 01:44:07: start model_add_line... INFO @ Tue, 30 Jun 2020 01:44:07: start X-correlation... INFO @ Tue, 30 Jun 2020 01:44:07: end of X-cor INFO @ Tue, 30 Jun 2020 01:44:07: #2 finished! INFO @ Tue, 30 Jun 2020 01:44:07: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 01:44:07: #2 alternative fragment length(s) may be 2,43,597 bps INFO @ Tue, 30 Jun 2020 01:44:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.20_model.r WARNING @ Tue, 30 Jun 2020 01:44:07: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:44:07: #2 You may need to consider one of the other alternative d(s): 2,43,597 WARNING @ Tue, 30 Jun 2020 01:44:07: #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 01:44:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:44:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:44:08: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:44:08: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:44:08: #1 total tags in treatment: 19639116 INFO @ Tue, 30 Jun 2020 01:44:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:44:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:44:09: #1 tags after filtering in treatment: 19639075 INFO @ Tue, 30 Jun 2020 01:44:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:44:09: #1 finished! INFO @ Tue, 30 Jun 2020 01:44:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:44:10: #2 number of paired peaks: 924 WARNING @ Tue, 30 Jun 2020 01:44:10: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Tue, 30 Jun 2020 01:44:10: start model_add_line... INFO @ Tue, 30 Jun 2020 01:44:10: start X-correlation... INFO @ Tue, 30 Jun 2020 01:44:10: end of X-cor INFO @ Tue, 30 Jun 2020 01:44:10: #2 finished! INFO @ Tue, 30 Jun 2020 01:44:10: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 01:44:10: #2 alternative fragment length(s) may be 2,43,597 bps INFO @ Tue, 30 Jun 2020 01:44:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.10_model.r WARNING @ Tue, 30 Jun 2020 01:44:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:44:10: #2 You may need to consider one of the other alternative d(s): 2,43,597 WARNING @ Tue, 30 Jun 2020 01:44:10: #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 01:44:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:44:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:44:11: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:44:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:44:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:44:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.05_summits.bed INFO @ Tue, 30 Jun 2020 01:44:29: Done! pass1 - making usageList (712 chroms): 1 millis pass2 - checking and writing primary data (3157 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:44:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:44:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.20_summits.bed INFO @ Tue, 30 Jun 2020 01:45:00: Done! pass1 - making usageList (494 chroms): 2 millis pass2 - checking and writing primary data (1579 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1150333/SRX1150333.10_summits.bed INFO @ Tue, 30 Jun 2020 01:45:03: Done! pass1 - making usageList (594 chroms): 1 millis pass2 - checking and writing primary data (2499 records, 4 fields): 36 millis CompletedMACS2peakCalling