Job ID = 6459099 SRX = SRX6386771 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:06:02 prefetch.2.10.7: 1) Downloading 'SRR9624503'... 2020-06-21T13:06:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:07:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:07:37 prefetch.2.10.7: 'SRR9624503' is valid 2020-06-21T13:07:37 prefetch.2.10.7: 1) 'SRR9624503' was downloaded successfully Read 14463775 spots for SRR9624503/SRR9624503.sra Written 14463775 spots for SRR9624503/SRR9624503.sra 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: 00:04:38 14463775 reads; of these: 14463775 (100.00%) were unpaired; of these: 860769 (5.95%) aligned 0 times 9375907 (64.82%) aligned exactly 1 time 4227099 (29.23%) aligned >1 times 94.05% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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 8 files... [bam_rmdupse_core] 2263594 / 13603006 = 0.1664 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 @ Sun, 21 Jun 2020 22:17:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.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 @ Sun, 21 Jun 2020 22:17:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:56: 1000000 INFO @ Sun, 21 Jun 2020 22:18:03: 2000000 INFO @ Sun, 21 Jun 2020 22:18:09: 3000000 INFO @ Sun, 21 Jun 2020 22:18:15: 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 @ Sun, 21 Jun 2020 22:18:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.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 @ Sun, 21 Jun 2020 22:18:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:21: 5000000 INFO @ Sun, 21 Jun 2020 22:18:27: 1000000 INFO @ Sun, 21 Jun 2020 22:18:27: 6000000 INFO @ Sun, 21 Jun 2020 22:18:34: 2000000 INFO @ Sun, 21 Jun 2020 22:18:34: 7000000 INFO @ Sun, 21 Jun 2020 22:18:40: 3000000 INFO @ Sun, 21 Jun 2020 22:18:41: 8000000 INFO @ Sun, 21 Jun 2020 22:18:47: 4000000 INFO @ Sun, 21 Jun 2020 22:18:48: 9000000 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 @ Sun, 21 Jun 2020 22:18:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.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 @ Sun, 21 Jun 2020 22:18:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:54: 5000000 INFO @ Sun, 21 Jun 2020 22:18:55: 10000000 INFO @ Sun, 21 Jun 2020 22:18:58: 1000000 INFO @ Sun, 21 Jun 2020 22:19:00: 6000000 INFO @ Sun, 21 Jun 2020 22:19:02: 11000000 INFO @ Sun, 21 Jun 2020 22:19:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:19:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:19:05: #1 total tags in treatment: 11339412 INFO @ Sun, 21 Jun 2020 22:19:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:19:05: 2000000 INFO @ Sun, 21 Jun 2020 22:19:05: #1 tags after filtering in treatment: 11339412 INFO @ Sun, 21 Jun 2020 22:19:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:05: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:06: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 22:19:06: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 22:19:06: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:06: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:06: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:06: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:06: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 22:19:06: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 22:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.05_model.r WARNING @ Sun, 21 Jun 2020 22:19:06: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:19:06: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 22:19:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:19:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:07: 7000000 INFO @ Sun, 21 Jun 2020 22:19:12: 3000000 INFO @ Sun, 21 Jun 2020 22:19:13: 8000000 INFO @ Sun, 21 Jun 2020 22:19:19: 4000000 INFO @ Sun, 21 Jun 2020 22:19:19: 9000000 INFO @ Sun, 21 Jun 2020 22:19:26: 5000000 INFO @ Sun, 21 Jun 2020 22:19:26: 10000000 INFO @ Sun, 21 Jun 2020 22:19:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:33: 11000000 INFO @ Sun, 21 Jun 2020 22:19:34: 6000000 INFO @ Sun, 21 Jun 2020 22:19:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:19:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:19:35: #1 total tags in treatment: 11339412 INFO @ Sun, 21 Jun 2020 22:19:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:19:36: #1 tags after filtering in treatment: 11339412 INFO @ Sun, 21 Jun 2020 22:19:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:36: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:37: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 22:19:37: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 22:19:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:37: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 22:19:37: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 22:19:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.10_model.r WARNING @ Sun, 21 Jun 2020 22:19:37: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:19:37: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 22:19:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:19:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.05_summits.bed INFO @ Sun, 21 Jun 2020 22:19:38: Done! pass1 - making usageList (709 chroms): 2 millis pass2 - checking and writing primary data (2661 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:19:41: 7000000 INFO @ Sun, 21 Jun 2020 22:19:48: 8000000 INFO @ Sun, 21 Jun 2020 22:19:55: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:19:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:03: 10000000 INFO @ Sun, 21 Jun 2020 22:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.10_summits.bed INFO @ Sun, 21 Jun 2020 22:20:09: Done! pass1 - making usageList (546 chroms): 2 millis pass2 - checking and writing primary data (1850 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:20:10: 11000000 INFO @ Sun, 21 Jun 2020 22:20:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:20:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:20:13: #1 total tags in treatment: 11339412 INFO @ Sun, 21 Jun 2020 22:20:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:20:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:20:13: #1 tags after filtering in treatment: 11339412 INFO @ Sun, 21 Jun 2020 22:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:20:13: #1 finished! INFO @ Sun, 21 Jun 2020 22:20:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:20:14: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 22:20:14: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 22:20:14: start model_add_line... INFO @ Sun, 21 Jun 2020 22:20:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:20:14: end of X-cor INFO @ Sun, 21 Jun 2020 22:20:14: #2 finished! INFO @ Sun, 21 Jun 2020 22:20:14: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 22:20:14: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 22:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.20_model.r WARNING @ Sun, 21 Jun 2020 22:20:14: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:20:14: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 22:20:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:20:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:20:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:20:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386771/SRX6386771.20_summits.bed INFO @ Sun, 21 Jun 2020 22:20:46: Done! pass1 - making usageList (273 chroms): 1 millis pass2 - checking and writing primary data (530 records, 4 fields): 16 millis CompletedMACS2peakCalling