Job ID = 6458506 SRX = SRX5247956 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:29:37 prefetch.2.10.7: 1) Downloading 'SRR8440603'... 2020-06-21T12:29:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:31:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:31:22 prefetch.2.10.7: 'SRR8440603' is valid 2020-06-21T12:31:22 prefetch.2.10.7: 1) 'SRR8440603' was downloaded successfully Read 9923737 spots for SRR8440603/SRR8440603.sra Written 9923737 spots for SRR8440603/SRR8440603.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: 00:02:41 9923737 reads; of these: 9923737 (100.00%) were unpaired; of these: 510276 (5.14%) aligned 0 times 5956127 (60.02%) aligned exactly 1 time 3457334 (34.84%) aligned >1 times 94.86% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 618492 / 9413461 = 0.0657 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 21:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.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 21:37:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:11: 1000000 INFO @ Sun, 21 Jun 2020 21:37:15: 2000000 INFO @ Sun, 21 Jun 2020 21:37:20: 3000000 INFO @ Sun, 21 Jun 2020 21:37:25: 4000000 INFO @ Sun, 21 Jun 2020 21:37:29: 5000000 INFO @ Sun, 21 Jun 2020 21:37:34: 6000000 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 21:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.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 21:37:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:39: 7000000 INFO @ Sun, 21 Jun 2020 21:37:41: 1000000 INFO @ Sun, 21 Jun 2020 21:37:44: 8000000 INFO @ Sun, 21 Jun 2020 21:37:46: 2000000 INFO @ Sun, 21 Jun 2020 21:37:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:37:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:37:48: #1 total tags in treatment: 8794969 INFO @ Sun, 21 Jun 2020 21:37:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:48: #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 21:37:48: #1 tags after filtering in treatment: 8794896 INFO @ Sun, 21 Jun 2020 21:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:49: #2 number of paired peaks: 1413 INFO @ Sun, 21 Jun 2020 21:37:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:49: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:37:49: #2 alternative fragment length(s) may be 3,129,151 bps INFO @ Sun, 21 Jun 2020 21:37:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.05_model.r INFO @ Sun, 21 Jun 2020 21:37:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:51: 3000000 INFO @ Sun, 21 Jun 2020 21:37:56: 4000000 INFO @ Sun, 21 Jun 2020 21:38:01: 5000000 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 21:38:05: 6000000 INFO @ Sun, 21 Jun 2020 21:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.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 21:38:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:38:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:38:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:38:10: 7000000 INFO @ Sun, 21 Jun 2020 21:38:11: 1000000 INFO @ Sun, 21 Jun 2020 21:38:15: 8000000 INFO @ Sun, 21 Jun 2020 21:38:16: 2000000 INFO @ Sun, 21 Jun 2020 21:38:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:38:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:38:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.05_summits.bed INFO @ Sun, 21 Jun 2020 21:38:17: Done! pass1 - making usageList (390 chroms): 1 millis pass2 - checking and writing primary data (2299 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:38:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:38:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:38:19: #1 total tags in treatment: 8794969 INFO @ Sun, 21 Jun 2020 21:38:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:38:19: #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 21:38:20: #1 tags after filtering in treatment: 8794896 INFO @ Sun, 21 Jun 2020 21:38:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:38:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:38:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:38:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:38:20: 3000000 INFO @ Sun, 21 Jun 2020 21:38:20: #2 number of paired peaks: 1413 INFO @ Sun, 21 Jun 2020 21:38:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:38:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:38:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:38:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:38:21: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:38:21: #2 alternative fragment length(s) may be 3,129,151 bps INFO @ Sun, 21 Jun 2020 21:38:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.10_model.r INFO @ Sun, 21 Jun 2020 21:38:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:38:25: 4000000 INFO @ Sun, 21 Jun 2020 21:38:30: 5000000 INFO @ Sun, 21 Jun 2020 21:38:34: 6000000 INFO @ Sun, 21 Jun 2020 21:38:39: 7000000 INFO @ Sun, 21 Jun 2020 21:38:40: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:38:44: 8000000 INFO @ Sun, 21 Jun 2020 21:38:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:38:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:38:48: #1 total tags in treatment: 8794969 INFO @ Sun, 21 Jun 2020 21:38:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:38:48: #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 21:38:48: #1 tags after filtering in treatment: 8794896 INFO @ Sun, 21 Jun 2020 21:38:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:38:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:38:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:38:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:38:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:38:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.10_summits.bed INFO @ Sun, 21 Jun 2020 21:38:49: Done! pass1 - making usageList (179 chroms): 1 millis pass2 - checking and writing primary data (821 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:38:49: #2 number of paired peaks: 1413 INFO @ Sun, 21 Jun 2020 21:38:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:38:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:38:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:38:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:38:49: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:38:49: #2 alternative fragment length(s) may be 3,129,151 bps INFO @ Sun, 21 Jun 2020 21:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.20_model.r INFO @ Sun, 21 Jun 2020 21:38:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:38:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:39:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247956/SRX5247956.20_summits.bed INFO @ Sun, 21 Jun 2020 21:39:18: Done! pass1 - making usageList (95 chroms): 3 millis pass2 - checking and writing primary data (264 records, 4 fields): 5 millis CompletedMACS2peakCalling