Job ID = 6458549 SRX = SRX5343086 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:32:04 prefetch.2.10.7: 1) Downloading 'SRR8540863'... 2020-06-21T12:32:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:07 prefetch.2.10.7: 1) 'SRR8540863' was downloaded successfully 2020-06-21T12:35:07 prefetch.2.10.7: 'SRR8540863' has 0 unresolved dependencies Read 24058556 spots for SRR8540863/SRR8540863.sra Written 24058556 spots for SRR8540863/SRR8540863.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: 00:06:59 24058556 reads; of these: 24058556 (100.00%) were unpaired; of these: 2095959 (8.71%) aligned 0 times 19189045 (79.76%) aligned exactly 1 time 2773552 (11.53%) aligned >1 times 91.29% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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] 8538906 / 21962597 = 0.3888 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 21:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.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 21:50:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:54: 1000000 INFO @ Sun, 21 Jun 2020 21:51:00: 2000000 INFO @ Sun, 21 Jun 2020 21:51:05: 3000000 INFO @ Sun, 21 Jun 2020 21:51:11: 4000000 INFO @ Sun, 21 Jun 2020 21:51:16: 5000000 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 21:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.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 21:51:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:22: 6000000 INFO @ Sun, 21 Jun 2020 21:51:25: 1000000 INFO @ Sun, 21 Jun 2020 21:51:28: 7000000 INFO @ Sun, 21 Jun 2020 21:51:31: 2000000 INFO @ Sun, 21 Jun 2020 21:51:34: 8000000 INFO @ Sun, 21 Jun 2020 21:51:37: 3000000 INFO @ Sun, 21 Jun 2020 21:51:40: 9000000 INFO @ Sun, 21 Jun 2020 21:51:44: 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 @ Sun, 21 Jun 2020 21:51:47: 10000000 INFO @ Sun, 21 Jun 2020 21:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.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 21:51:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:50: 5000000 INFO @ Sun, 21 Jun 2020 21:51:53: 11000000 INFO @ Sun, 21 Jun 2020 21:51:54: 1000000 INFO @ Sun, 21 Jun 2020 21:51:56: 6000000 INFO @ Sun, 21 Jun 2020 21:52:00: 2000000 INFO @ Sun, 21 Jun 2020 21:52:00: 12000000 INFO @ Sun, 21 Jun 2020 21:52:02: 7000000 INFO @ Sun, 21 Jun 2020 21:52:06: 3000000 INFO @ Sun, 21 Jun 2020 21:52:07: 13000000 INFO @ Sun, 21 Jun 2020 21:52:08: 8000000 INFO @ Sun, 21 Jun 2020 21:52:10: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:52:10: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:52:10: #1 total tags in treatment: 13423691 INFO @ Sun, 21 Jun 2020 21:52:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:10: #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 21:52:11: #1 tags after filtering in treatment: 13423690 INFO @ Sun, 21 Jun 2020 21:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:11: 4000000 INFO @ Sun, 21 Jun 2020 21:52:12: #2 number of paired peaks: 303 WARNING @ Sun, 21 Jun 2020 21:52:12: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Sun, 21 Jun 2020 21:52:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:12: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 21:52:12: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 21:52:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.05_model.r WARNING @ Sun, 21 Jun 2020 21:52:12: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:12: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sun, 21 Jun 2020 21:52:12: #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 21:52:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:14: 9000000 INFO @ Sun, 21 Jun 2020 21:52:17: 5000000 INFO @ Sun, 21 Jun 2020 21:52:20: 10000000 INFO @ Sun, 21 Jun 2020 21:52:23: 6000000 INFO @ Sun, 21 Jun 2020 21:52:25: 11000000 INFO @ Sun, 21 Jun 2020 21:52:28: 7000000 INFO @ Sun, 21 Jun 2020 21:52:32: 12000000 INFO @ Sun, 21 Jun 2020 21:52:34: 8000000 INFO @ Sun, 21 Jun 2020 21:52:37: 13000000 INFO @ Sun, 21 Jun 2020 21:52:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:40: 9000000 INFO @ Sun, 21 Jun 2020 21:52:40: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:52:40: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:52:40: #1 total tags in treatment: 13423691 INFO @ Sun, 21 Jun 2020 21:52:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:40: #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 21:52:41: #1 tags after filtering in treatment: 13423690 INFO @ Sun, 21 Jun 2020 21:52:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:42: #2 number of paired peaks: 303 WARNING @ Sun, 21 Jun 2020 21:52:42: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Sun, 21 Jun 2020 21:52:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:42: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 21:52:42: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 21:52:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.10_model.r WARNING @ Sun, 21 Jun 2020 21:52:42: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:42: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sun, 21 Jun 2020 21:52:42: #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 21:52:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:45: 10000000 INFO @ Sun, 21 Jun 2020 21:52:51: 11000000 INFO @ Sun, 21 Jun 2020 21:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.05_summits.bed INFO @ Sun, 21 Jun 2020 21:52:53: Done! pass1 - making usageList (192 chroms): 2 millis pass2 - checking and writing primary data (5280 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:57: 12000000 INFO @ Sun, 21 Jun 2020 21:53:03: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:53:07: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:53:07: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:53:07: #1 total tags in treatment: 13423691 INFO @ Sun, 21 Jun 2020 21:53:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:07: #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 21:53:07: #1 tags after filtering in treatment: 13423690 INFO @ Sun, 21 Jun 2020 21:53:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:53:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:08: #2 number of paired peaks: 303 WARNING @ Sun, 21 Jun 2020 21:53:08: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Sun, 21 Jun 2020 21:53:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:53:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:53:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:53:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:53:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:53:08: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 21:53:08: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 21:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.20_model.r WARNING @ Sun, 21 Jun 2020 21:53:08: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:53:08: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sun, 21 Jun 2020 21:53:08: #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 21:53:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:53:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:53:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:53:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.10_summits.bed INFO @ Sun, 21 Jun 2020 21:53:22: Done! pass1 - making usageList (129 chroms): 2 millis pass2 - checking and writing primary data (2972 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:53:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343086/SRX5343086.20_summits.bed INFO @ Sun, 21 Jun 2020 21:53:50: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (973 records, 4 fields): 8 millis CompletedMACS2peakCalling