Job ID = 6459919 SRX = SRX994749 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:51:20 prefetch.2.10.7: 1) Downloading 'SRR1973467'... 2020-06-21T13:51:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:52:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:52:25 prefetch.2.10.7: 'SRR1973467' is valid 2020-06-21T13:52:25 prefetch.2.10.7: 1) 'SRR1973467' was downloaded successfully 2020-06-21T13:52:25 prefetch.2.10.7: 'SRR1973467' has 0 unresolved dependencies Read 8573437 spots for SRR1973467/SRR1973467.sra Written 8573437 spots for SRR1973467/SRR1973467.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: 00:03:14 8573437 reads; of these: 8573437 (100.00%) were unpaired; of these: 446607 (5.21%) aligned 0 times 6035146 (70.39%) aligned exactly 1 time 2091684 (24.40%) aligned >1 times 94.79% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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_rmdupse_core] 2096904 / 8126830 = 0.2580 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 22:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.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 22:58:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:58:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:58:32: 1000000 INFO @ Sun, 21 Jun 2020 22:58:38: 2000000 INFO @ Sun, 21 Jun 2020 22:58:44: 3000000 INFO @ Sun, 21 Jun 2020 22:58:50: 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 22:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.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 22:58:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:58:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:58:56: 5000000 INFO @ Sun, 21 Jun 2020 22:59:02: 1000000 INFO @ Sun, 21 Jun 2020 22:59:02: 6000000 INFO @ Sun, 21 Jun 2020 22:59:03: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:59:03: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:59:03: #1 total tags in treatment: 6029926 INFO @ Sun, 21 Jun 2020 22:59:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:03: #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 22:59:03: #1 tags after filtering in treatment: 6029830 INFO @ Sun, 21 Jun 2020 22:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:03: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:04: #2 number of paired peaks: 1431 INFO @ Sun, 21 Jun 2020 22:59:04: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:04: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:04: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:04: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:04: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 22:59:04: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 22:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.05_model.r INFO @ Sun, 21 Jun 2020 22:59:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:08: 2000000 INFO @ Sun, 21 Jun 2020 22:59:14: 3000000 INFO @ Sun, 21 Jun 2020 22:59:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:59:20: 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 22:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.05_summits.bed INFO @ Sun, 21 Jun 2020 22:59:25: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (2732 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.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 22:59:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:59:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:59:26: 5000000 INFO @ Sun, 21 Jun 2020 22:59:31: 1000000 INFO @ Sun, 21 Jun 2020 22:59:33: 6000000 INFO @ Sun, 21 Jun 2020 22:59:33: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:59:33: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:59:33: #1 total tags in treatment: 6029926 INFO @ Sun, 21 Jun 2020 22:59:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:33: #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 22:59:33: #1 tags after filtering in treatment: 6029830 INFO @ Sun, 21 Jun 2020 22:59:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:34: #2 number of paired peaks: 1431 INFO @ Sun, 21 Jun 2020 22:59:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:34: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 22:59:34: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 22:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.10_model.r INFO @ Sun, 21 Jun 2020 22:59:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:37: 2000000 INFO @ Sun, 21 Jun 2020 22:59:42: 3000000 INFO @ Sun, 21 Jun 2020 22:59:47: 4000000 INFO @ Sun, 21 Jun 2020 22:59:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:59:52: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.10_summits.bed INFO @ Sun, 21 Jun 2020 22:59:55: Done! pass1 - making usageList (310 chroms): 1 millis pass2 - checking and writing primary data (1293 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:59:57: 6000000 INFO @ Sun, 21 Jun 2020 22:59:58: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:59:58: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:59:58: #1 total tags in treatment: 6029926 INFO @ Sun, 21 Jun 2020 22:59:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:58: #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 22:59:58: #1 tags after filtering in treatment: 6029830 INFO @ Sun, 21 Jun 2020 22:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:58: #2 number of paired peaks: 1431 INFO @ Sun, 21 Jun 2020 22:59:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:58: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 22:59:58: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 22:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.20_model.r INFO @ Sun, 21 Jun 2020 22:59:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:00:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:00:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX994749/SRX994749.20_summits.bed INFO @ Sun, 21 Jun 2020 23:00:19: Done! pass1 - making usageList (181 chroms): 1 millis pass2 - checking and writing primary data (642 records, 4 fields): 6 millis CompletedMACS2peakCalling