Job ID = 6529859 SRX = SRX5287833 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: 00:11:38 32714133 reads; of these: 32714133 (100.00%) were unpaired; of these: 1089621 (3.33%) aligned 0 times 23648936 (72.29%) aligned exactly 1 time 7975576 (24.38%) aligned >1 times 96.67% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 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 16 files... [bam_rmdupse_core] 4549134 / 31624512 = 0.1438 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 03:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.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 03:12:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:14: 1000000 INFO @ Tue, 30 Jun 2020 03:12:21: 2000000 INFO @ Tue, 30 Jun 2020 03:12:27: 3000000 INFO @ Tue, 30 Jun 2020 03:12:34: 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 03:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.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 03:12:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:40: 5000000 INFO @ Tue, 30 Jun 2020 03:12:45: 1000000 INFO @ Tue, 30 Jun 2020 03:12:47: 6000000 INFO @ Tue, 30 Jun 2020 03:12:51: 2000000 INFO @ Tue, 30 Jun 2020 03:12:54: 7000000 INFO @ Tue, 30 Jun 2020 03:12:58: 3000000 INFO @ Tue, 30 Jun 2020 03:13:00: 8000000 INFO @ Tue, 30 Jun 2020 03:13:05: 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 03:13:07: 9000000 INFO @ Tue, 30 Jun 2020 03:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.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 03:13:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:12: 5000000 INFO @ Tue, 30 Jun 2020 03:13:13: 10000000 INFO @ Tue, 30 Jun 2020 03:13:14: 1000000 INFO @ Tue, 30 Jun 2020 03:13:19: 6000000 INFO @ Tue, 30 Jun 2020 03:13:20: 11000000 INFO @ Tue, 30 Jun 2020 03:13:21: 2000000 INFO @ Tue, 30 Jun 2020 03:13:25: 7000000 INFO @ Tue, 30 Jun 2020 03:13:27: 12000000 INFO @ Tue, 30 Jun 2020 03:13:27: 3000000 INFO @ Tue, 30 Jun 2020 03:13:32: 8000000 INFO @ Tue, 30 Jun 2020 03:13:34: 13000000 INFO @ Tue, 30 Jun 2020 03:13:34: 4000000 INFO @ Tue, 30 Jun 2020 03:13:39: 9000000 INFO @ Tue, 30 Jun 2020 03:13:40: 14000000 INFO @ Tue, 30 Jun 2020 03:13:41: 5000000 INFO @ Tue, 30 Jun 2020 03:13:46: 10000000 INFO @ Tue, 30 Jun 2020 03:13:47: 15000000 INFO @ Tue, 30 Jun 2020 03:13:48: 6000000 INFO @ Tue, 30 Jun 2020 03:13:53: 11000000 INFO @ Tue, 30 Jun 2020 03:13:54: 16000000 INFO @ Tue, 30 Jun 2020 03:13:54: 7000000 INFO @ Tue, 30 Jun 2020 03:13:59: 12000000 INFO @ Tue, 30 Jun 2020 03:14:00: 17000000 INFO @ Tue, 30 Jun 2020 03:14:01: 8000000 INFO @ Tue, 30 Jun 2020 03:14:06: 13000000 INFO @ Tue, 30 Jun 2020 03:14:07: 18000000 INFO @ Tue, 30 Jun 2020 03:14:07: 9000000 INFO @ Tue, 30 Jun 2020 03:14:13: 14000000 INFO @ Tue, 30 Jun 2020 03:14:14: 19000000 INFO @ Tue, 30 Jun 2020 03:14:14: 10000000 INFO @ Tue, 30 Jun 2020 03:14:19: 15000000 INFO @ Tue, 30 Jun 2020 03:14:21: 20000000 INFO @ Tue, 30 Jun 2020 03:14:21: 11000000 INFO @ Tue, 30 Jun 2020 03:14:26: 16000000 INFO @ Tue, 30 Jun 2020 03:14:27: 12000000 INFO @ Tue, 30 Jun 2020 03:14:27: 21000000 INFO @ Tue, 30 Jun 2020 03:14:33: 17000000 INFO @ Tue, 30 Jun 2020 03:14:34: 13000000 INFO @ Tue, 30 Jun 2020 03:14:35: 22000000 INFO @ Tue, 30 Jun 2020 03:14:39: 18000000 INFO @ Tue, 30 Jun 2020 03:14:40: 14000000 INFO @ Tue, 30 Jun 2020 03:14:41: 23000000 INFO @ Tue, 30 Jun 2020 03:14:46: 19000000 INFO @ Tue, 30 Jun 2020 03:14:47: 15000000 INFO @ Tue, 30 Jun 2020 03:14:48: 24000000 INFO @ Tue, 30 Jun 2020 03:14:53: 20000000 INFO @ Tue, 30 Jun 2020 03:14:53: 16000000 INFO @ Tue, 30 Jun 2020 03:14:55: 25000000 INFO @ Tue, 30 Jun 2020 03:15:00: 17000000 INFO @ Tue, 30 Jun 2020 03:15:00: 21000000 INFO @ Tue, 30 Jun 2020 03:15:02: 26000000 INFO @ Tue, 30 Jun 2020 03:15:06: 18000000 INFO @ Tue, 30 Jun 2020 03:15:07: 22000000 INFO @ Tue, 30 Jun 2020 03:15:09: 27000000 INFO @ Tue, 30 Jun 2020 03:15:09: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:15:09: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:15:09: #1 total tags in treatment: 27075378 INFO @ Tue, 30 Jun 2020 03:15:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:15:09: #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 03:15:10: #1 tags after filtering in treatment: 27075378 INFO @ Tue, 30 Jun 2020 03:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:15:10: #1 finished! INFO @ Tue, 30 Jun 2020 03:15:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:15:12: #2 number of paired peaks: 222 WARNING @ Tue, 30 Jun 2020 03:15:12: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 30 Jun 2020 03:15:12: start model_add_line... INFO @ Tue, 30 Jun 2020 03:15:12: start X-correlation... INFO @ Tue, 30 Jun 2020 03:15:12: end of X-cor INFO @ Tue, 30 Jun 2020 03:15:12: #2 finished! INFO @ Tue, 30 Jun 2020 03:15:12: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 03:15:12: #2 alternative fragment length(s) may be 2,36,51,55,63 bps INFO @ Tue, 30 Jun 2020 03:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.05_model.r WARNING @ Tue, 30 Jun 2020 03:15:12: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:15:12: #2 You may need to consider one of the other alternative d(s): 2,36,51,55,63 WARNING @ Tue, 30 Jun 2020 03:15:12: #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 03:15:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:15:13: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:15:14: 23000000 INFO @ Tue, 30 Jun 2020 03:15:19: 20000000 INFO @ Tue, 30 Jun 2020 03:15:21: 24000000 INFO @ Tue, 30 Jun 2020 03:15:26: 21000000 INFO @ Tue, 30 Jun 2020 03:15:27: 25000000 INFO @ Tue, 30 Jun 2020 03:15:33: 22000000 INFO @ Tue, 30 Jun 2020 03:15:34: 26000000 INFO @ Tue, 30 Jun 2020 03:15:39: 23000000 INFO @ Tue, 30 Jun 2020 03:15:41: 27000000 INFO @ Tue, 30 Jun 2020 03:15:41: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:15:41: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:15:41: #1 total tags in treatment: 27075378 INFO @ Tue, 30 Jun 2020 03:15:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:15:41: #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 03:15:42: #1 tags after filtering in treatment: 27075378 INFO @ Tue, 30 Jun 2020 03:15:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:15:42: #1 finished! INFO @ Tue, 30 Jun 2020 03:15:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:15:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:15:44: #2 number of paired peaks: 222 WARNING @ Tue, 30 Jun 2020 03:15:44: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 30 Jun 2020 03:15:44: start model_add_line... INFO @ Tue, 30 Jun 2020 03:15:44: start X-correlation... INFO @ Tue, 30 Jun 2020 03:15:44: end of X-cor INFO @ Tue, 30 Jun 2020 03:15:44: #2 finished! INFO @ Tue, 30 Jun 2020 03:15:44: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 03:15:44: #2 alternative fragment length(s) may be 2,36,51,55,63 bps INFO @ Tue, 30 Jun 2020 03:15:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.10_model.r WARNING @ Tue, 30 Jun 2020 03:15:44: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:15:44: #2 You may need to consider one of the other alternative d(s): 2,36,51,55,63 WARNING @ Tue, 30 Jun 2020 03:15:44: #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 03:15:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:15:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:15:45: 24000000 INFO @ Tue, 30 Jun 2020 03:15:52: 25000000 INFO @ Tue, 30 Jun 2020 03:15:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:15:58: 26000000 INFO @ Tue, 30 Jun 2020 03:16:04: 27000000 INFO @ Tue, 30 Jun 2020 03:16:05: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:16:05: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:16:05: #1 total tags in treatment: 27075378 INFO @ Tue, 30 Jun 2020 03:16:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:05: #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 03:16:06: #1 tags after filtering in treatment: 27075378 INFO @ Tue, 30 Jun 2020 03:16:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:06: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:16:07: #2 number of paired peaks: 222 WARNING @ Tue, 30 Jun 2020 03:16:07: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:07: start model_add_line... INFO @ Tue, 30 Jun 2020 03:16:08: start X-correlation... INFO @ Tue, 30 Jun 2020 03:16:08: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:08: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:08: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 03:16:08: #2 alternative fragment length(s) may be 2,36,51,55,63 bps INFO @ Tue, 30 Jun 2020 03:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.20_model.r WARNING @ Tue, 30 Jun 2020 03:16:08: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:08: #2 You may need to consider one of the other alternative d(s): 2,36,51,55,63 WARNING @ Tue, 30 Jun 2020 03:16:08: #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 03:16:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.05_summits.bed INFO @ Tue, 30 Jun 2020 03:16:19: Done! pass1 - making usageList (678 chroms): 1 millis pass2 - checking and writing primary data (2688 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:16:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.10_summits.bed INFO @ Tue, 30 Jun 2020 03:16:50: Done! pass1 - making usageList (573 chroms): 2 millis pass2 - checking and writing primary data (1715 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:16:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287833/SRX5287833.20_summits.bed INFO @ Tue, 30 Jun 2020 03:17:17: Done! pass1 - making usageList (278 chroms): 1 millis pass2 - checking and writing primary data (507 records, 4 fields): 9 millis CompletedMACS2peakCalling