Job ID = 6458353 SRX = SRX5011094 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:25:22 prefetch.2.10.7: 1) Downloading 'SRR8191543'... 2020-06-21T12:25:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:28:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:28:32 prefetch.2.10.7: 1) 'SRR8191543' was downloaded successfully 2020-06-21T12:28:32 prefetch.2.10.7: 'SRR8191543' has 0 unresolved dependencies Read 37150247 spots for SRR8191543/SRR8191543.sra Written 37150247 spots for SRR8191543/SRR8191543.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: 00:08:52 37150247 reads; of these: 37150247 (100.00%) were unpaired; of these: 6268689 (16.87%) aligned 0 times 23351539 (62.86%) aligned exactly 1 time 7530019 (20.27%) aligned >1 times 83.13% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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 16 files... [bam_rmdupse_core] 20100099 / 30881558 = 0.6509 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 21:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.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 21:43:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:43:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:43:43: 1000000 INFO @ Sun, 21 Jun 2020 21:43:48: 2000000 INFO @ Sun, 21 Jun 2020 21:43:53: 3000000 INFO @ Sun, 21 Jun 2020 21:43:58: 4000000 INFO @ Sun, 21 Jun 2020 21:44:03: 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 21:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.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 21:44:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:44:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:44:08: 6000000 INFO @ Sun, 21 Jun 2020 21:44:13: 1000000 INFO @ Sun, 21 Jun 2020 21:44:14: 7000000 INFO @ Sun, 21 Jun 2020 21:44:19: 2000000 INFO @ Sun, 21 Jun 2020 21:44:19: 8000000 INFO @ Sun, 21 Jun 2020 21:44:25: 3000000 INFO @ Sun, 21 Jun 2020 21:44:25: 9000000 INFO @ Sun, 21 Jun 2020 21:44:30: 4000000 INFO @ Sun, 21 Jun 2020 21:44:31: 10000000 INFO @ Sun, 21 Jun 2020 21:44:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:44:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:44:36: #1 total tags in treatment: 10781459 INFO @ Sun, 21 Jun 2020 21:44:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 21:44:36: 5000000 INFO @ Sun, 21 Jun 2020 21:44:36: #1 tags after filtering in treatment: 10781386 INFO @ Sun, 21 Jun 2020 21:44:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:37: #2 number of paired peaks: 3647 INFO @ Sun, 21 Jun 2020 21:44:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:37: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:44:37: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:44:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.05_model.r INFO @ Sun, 21 Jun 2020 21:44:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.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 21:44:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:44:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:44:42: 6000000 INFO @ Sun, 21 Jun 2020 21:44:43: 1000000 INFO @ Sun, 21 Jun 2020 21:44:47: 7000000 INFO @ Sun, 21 Jun 2020 21:44:49: 2000000 INFO @ Sun, 21 Jun 2020 21:44:53: 8000000 INFO @ Sun, 21 Jun 2020 21:44:54: 3000000 INFO @ Sun, 21 Jun 2020 21:44:59: 9000000 INFO @ Sun, 21 Jun 2020 21:45:00: 4000000 INFO @ Sun, 21 Jun 2020 21:45:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:45:05: 10000000 INFO @ Sun, 21 Jun 2020 21:45:06: 5000000 INFO @ Sun, 21 Jun 2020 21:45:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:45:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:45:09: #1 total tags in treatment: 10781459 INFO @ Sun, 21 Jun 2020 21:45:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:09: #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 21:45:10: #1 tags after filtering in treatment: 10781386 INFO @ Sun, 21 Jun 2020 21:45:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:45:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:45:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:45:11: #2 number of paired peaks: 3647 INFO @ Sun, 21 Jun 2020 21:45:11: start model_add_line... INFO @ Sun, 21 Jun 2020 21:45:11: start X-correlation... INFO @ Sun, 21 Jun 2020 21:45:11: end of X-cor INFO @ Sun, 21 Jun 2020 21:45:11: #2 finished! INFO @ Sun, 21 Jun 2020 21:45:11: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:45:11: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.10_model.r INFO @ Sun, 21 Jun 2020 21:45:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:45:11: 6000000 INFO @ Sun, 21 Jun 2020 21:45:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:45:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.05_summits.bed INFO @ Sun, 21 Jun 2020 21:45:15: Done! pass1 - making usageList (814 chroms): 2 millis pass2 - checking and writing primary data (6841 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:45:17: 7000000 INFO @ Sun, 21 Jun 2020 21:45:22: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:45:28: 9000000 INFO @ Sun, 21 Jun 2020 21:45:33: 10000000 INFO @ Sun, 21 Jun 2020 21:45:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:45:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:45:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:45:37: #1 total tags in treatment: 10781459 INFO @ Sun, 21 Jun 2020 21:45:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:37: #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 21:45:37: #1 tags after filtering in treatment: 10781386 INFO @ Sun, 21 Jun 2020 21:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:45:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:45:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:45:38: #2 number of paired peaks: 3647 INFO @ Sun, 21 Jun 2020 21:45:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:45:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:45:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:45:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:45:39: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:45:39: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.20_model.r INFO @ Sun, 21 Jun 2020 21:45:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:45:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.10_summits.bed INFO @ Sun, 21 Jun 2020 21:45:49: Done! pass1 - making usageList (727 chroms): 2 millis pass2 - checking and writing primary data (4745 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:46:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011094/SRX5011094.20_summits.bed INFO @ Sun, 21 Jun 2020 21:46:17: Done! pass1 - making usageList (615 chroms): 2 millis pass2 - checking and writing primary data (3138 records, 4 fields): 18 millis CompletedMACS2peakCalling