Job ID = 6455812 SRX = SRX3009519 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:51 prefetch.2.10.7: 1) Downloading 'SRR5832220'... 2020-06-21T10:15:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:46 prefetch.2.10.7: 1) 'SRR5832220' was downloaded successfully Read 16011581 spots for SRR5832220/SRR5832220.sra Written 16011581 spots for SRR5832220/SRR5832220.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: 00:05:07 16011581 reads; of these: 16011581 (100.00%) were unpaired; of these: 2536072 (15.84%) aligned 0 times 9423196 (58.85%) aligned exactly 1 time 4052313 (25.31%) aligned >1 times 84.16% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 6656088 / 13475509 = 0.4939 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 19:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.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 19:28:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:11: 1000000 INFO @ Sun, 21 Jun 2020 19:28:17: 2000000 INFO @ Sun, 21 Jun 2020 19:28:23: 3000000 INFO @ Sun, 21 Jun 2020 19:28:28: 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 19:28:34: 5000000 INFO @ Sun, 21 Jun 2020 19:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.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 19:28:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:40: 6000000 INFO @ Sun, 21 Jun 2020 19:28:42: 1000000 INFO @ Sun, 21 Jun 2020 19:28:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:28:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:28:45: #1 total tags in treatment: 6819421 INFO @ Sun, 21 Jun 2020 19:28:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:45: #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 19:28:46: #1 tags after filtering in treatment: 6819312 INFO @ Sun, 21 Jun 2020 19:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:46: #2 number of paired peaks: 1338 INFO @ Sun, 21 Jun 2020 19:28:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:47: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:28:47: #2 alternative fragment length(s) may be 4,58,140 bps INFO @ Sun, 21 Jun 2020 19:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.05_model.r INFO @ Sun, 21 Jun 2020 19:28:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:48: 2000000 INFO @ Sun, 21 Jun 2020 19:28:54: 3000000 INFO @ Sun, 21 Jun 2020 19:29:00: 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 19:29:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:06: 5000000 INFO @ Sun, 21 Jun 2020 19:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.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 19:29:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.05_summits.bed INFO @ Sun, 21 Jun 2020 19:29:12: Done! INFO @ Sun, 21 Jun 2020 19:29:12: 6000000 pass1 - making usageList (688 chroms): 2 millis pass2 - checking and writing primary data (2244 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:13: 1000000 INFO @ Sun, 21 Jun 2020 19:29:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:29:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:29:18: #1 total tags in treatment: 6819421 INFO @ Sun, 21 Jun 2020 19:29:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:18: #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 19:29:18: #1 tags after filtering in treatment: 6819312 INFO @ Sun, 21 Jun 2020 19:29:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:19: #2 number of paired peaks: 1338 INFO @ Sun, 21 Jun 2020 19:29:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:19: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:29:19: #2 alternative fragment length(s) may be 4,58,140 bps INFO @ Sun, 21 Jun 2020 19:29:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.10_model.r INFO @ Sun, 21 Jun 2020 19:29:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:20: 2000000 INFO @ Sun, 21 Jun 2020 19:29:26: 3000000 INFO @ Sun, 21 Jun 2020 19:29:33: 4000000 INFO @ Sun, 21 Jun 2020 19:29:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:39: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:29:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.10_summits.bed INFO @ Sun, 21 Jun 2020 19:29:44: Done! pass1 - making usageList (590 chroms): 1 millis pass2 - checking and writing primary data (1448 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:46: 6000000 INFO @ Sun, 21 Jun 2020 19:29:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:29:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:29:52: #1 total tags in treatment: 6819421 INFO @ Sun, 21 Jun 2020 19:29:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:52: #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 19:29:52: #1 tags after filtering in treatment: 6819312 INFO @ Sun, 21 Jun 2020 19:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:53: #2 number of paired peaks: 1338 INFO @ Sun, 21 Jun 2020 19:29:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:53: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:29:53: #2 alternative fragment length(s) may be 4,58,140 bps INFO @ Sun, 21 Jun 2020 19:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.20_model.r INFO @ Sun, 21 Jun 2020 19:29:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:30:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009519/SRX3009519.20_summits.bed INFO @ Sun, 21 Jun 2020 19:30:18: Done! pass1 - making usageList (458 chroms): 1 millis pass2 - checking and writing primary data (904 records, 4 fields): 15 millis CompletedMACS2peakCalling