Job ID = 6530010 SRX = SRX6386756 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: 00:06:05 20172098 reads; of these: 20172098 (100.00%) were unpaired; of these: 981967 (4.87%) aligned 0 times 13537105 (67.11%) aligned exactly 1 time 5653026 (28.02%) aligned >1 times 95.13% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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] 4778730 / 19190131 = 0.2490 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 03:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.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 03:19:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:49: 1000000 INFO @ Tue, 30 Jun 2020 03:19:56: 2000000 INFO @ Tue, 30 Jun 2020 03:20:02: 3000000 INFO @ Tue, 30 Jun 2020 03:20:08: 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 03:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.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 03:20:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:15: 5000000 INFO @ Tue, 30 Jun 2020 03:20:21: 1000000 INFO @ Tue, 30 Jun 2020 03:20:23: 6000000 INFO @ Tue, 30 Jun 2020 03:20:28: 2000000 INFO @ Tue, 30 Jun 2020 03:20:30: 7000000 INFO @ Tue, 30 Jun 2020 03:20:36: 3000000 INFO @ Tue, 30 Jun 2020 03:20:38: 8000000 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 03:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.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 03:20:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:44: 4000000 INFO @ Tue, 30 Jun 2020 03:20:45: 9000000 INFO @ Tue, 30 Jun 2020 03:20:51: 1000000 INFO @ Tue, 30 Jun 2020 03:20:52: 5000000 INFO @ Tue, 30 Jun 2020 03:20:53: 10000000 INFO @ Tue, 30 Jun 2020 03:20:59: 2000000 INFO @ Tue, 30 Jun 2020 03:21:00: 6000000 INFO @ Tue, 30 Jun 2020 03:21:01: 11000000 INFO @ Tue, 30 Jun 2020 03:21:07: 3000000 INFO @ Tue, 30 Jun 2020 03:21:08: 7000000 INFO @ Tue, 30 Jun 2020 03:21:10: 12000000 INFO @ Tue, 30 Jun 2020 03:21:14: 4000000 INFO @ Tue, 30 Jun 2020 03:21:16: 8000000 INFO @ Tue, 30 Jun 2020 03:21:18: 13000000 INFO @ Tue, 30 Jun 2020 03:21:22: 5000000 INFO @ Tue, 30 Jun 2020 03:21:23: 9000000 INFO @ Tue, 30 Jun 2020 03:21:26: 14000000 INFO @ Tue, 30 Jun 2020 03:21:29: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:21:29: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:21:29: #1 total tags in treatment: 14411401 INFO @ Tue, 30 Jun 2020 03:21:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:29: #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 03:21:29: 6000000 INFO @ Tue, 30 Jun 2020 03:21:30: #1 tags after filtering in treatment: 14411401 INFO @ Tue, 30 Jun 2020 03:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:31: #2 number of paired peaks: 651 WARNING @ Tue, 30 Jun 2020 03:21:31: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:31: 10000000 INFO @ Tue, 30 Jun 2020 03:21:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:31: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 03:21:31: #2 alternative fragment length(s) may be 2,43,556 bps INFO @ Tue, 30 Jun 2020 03:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.05_model.r WARNING @ Tue, 30 Jun 2020 03:21:31: #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 03:21:31: #2 You may need to consider one of the other alternative d(s): 2,43,556 WARNING @ Tue, 30 Jun 2020 03:21:31: #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 03:21:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:21:37: 7000000 INFO @ Tue, 30 Jun 2020 03:21:38: 11000000 INFO @ Tue, 30 Jun 2020 03:21:44: 8000000 INFO @ Tue, 30 Jun 2020 03:21:46: 12000000 INFO @ Tue, 30 Jun 2020 03:21:51: 9000000 INFO @ Tue, 30 Jun 2020 03:21:53: 13000000 INFO @ Tue, 30 Jun 2020 03:21:58: 10000000 INFO @ Tue, 30 Jun 2020 03:21:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:01: 14000000 INFO @ Tue, 30 Jun 2020 03:22:04: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:22:04: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:22:04: #1 total tags in treatment: 14411401 INFO @ Tue, 30 Jun 2020 03:22:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:04: #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 03:22:05: #1 tags after filtering in treatment: 14411401 INFO @ Tue, 30 Jun 2020 03:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:06: #2 number of paired peaks: 651 WARNING @ Tue, 30 Jun 2020 03:22:06: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:06: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 03:22:06: #2 alternative fragment length(s) may be 2,43,556 bps INFO @ Tue, 30 Jun 2020 03:22:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.10_model.r WARNING @ Tue, 30 Jun 2020 03:22:06: #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 03:22:06: #2 You may need to consider one of the other alternative d(s): 2,43,556 WARNING @ Tue, 30 Jun 2020 03:22:06: #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 03:22:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:06: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:22:13: 12000000 INFO @ Tue, 30 Jun 2020 03:22:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.05_summits.bed INFO @ Tue, 30 Jun 2020 03:22:14: Done! pass1 - making usageList (754 chroms): 1 millis pass2 - checking and writing primary data (2953 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:22:19: 13000000 INFO @ Tue, 30 Jun 2020 03:22:26: 14000000 INFO @ Tue, 30 Jun 2020 03:22:28: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:22:28: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:22:28: #1 total tags in treatment: 14411401 INFO @ Tue, 30 Jun 2020 03:22:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:28: #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 03:22:29: #1 tags after filtering in treatment: 14411401 INFO @ Tue, 30 Jun 2020 03:22:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:29: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:30: #2 number of paired peaks: 651 WARNING @ Tue, 30 Jun 2020 03:22:30: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:30: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:30: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:30: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:30: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:30: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 03:22:30: #2 alternative fragment length(s) may be 2,43,556 bps INFO @ Tue, 30 Jun 2020 03:22:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.20_model.r WARNING @ Tue, 30 Jun 2020 03:22:30: #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 03:22:30: #2 You may need to consider one of the other alternative d(s): 2,43,556 WARNING @ Tue, 30 Jun 2020 03:22:30: #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 03:22:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:22:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.10_summits.bed INFO @ Tue, 30 Jun 2020 03:22:47: Done! pass1 - making usageList (584 chroms): 1 millis pass2 - checking and writing primary data (2068 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:22:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:23:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:23:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:23:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386756/SRX6386756.20_summits.bed INFO @ Tue, 30 Jun 2020 03:23:11: Done! pass1 - making usageList (371 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 11 millis CompletedMACS2peakCalling