Job ID = 6455127 SRX = SRX2748311 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:43:40 prefetch.2.10.7: 1) Downloading 'SRR5460298'... 2020-06-21T09:43:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:44:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:44:14 prefetch.2.10.7: 'SRR5460298' is valid 2020-06-21T09:44:14 prefetch.2.10.7: 1) 'SRR5460298' was downloaded successfully Read 5542137 spots for SRR5460298/SRR5460298.sra Written 5542137 spots for SRR5460298/SRR5460298.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: 00:00:54 5542137 reads; of these: 5542137 (100.00%) were unpaired; of these: 562748 (10.15%) aligned 0 times 3960901 (71.47%) aligned exactly 1 time 1018488 (18.38%) aligned >1 times 89.85% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 1870446 / 4979389 = 0.3756 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 18:46:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.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 18:46:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:03: 1000000 INFO @ Sun, 21 Jun 2020 18:47:11: 2000000 INFO @ Sun, 21 Jun 2020 18:47:20: 3000000 INFO @ Sun, 21 Jun 2020 18:47:20: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 18:47:20: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 18:47:20: #1 total tags in treatment: 3108943 INFO @ Sun, 21 Jun 2020 18:47:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:20: #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 18:47:21: #1 tags after filtering in treatment: 3108923 INFO @ Sun, 21 Jun 2020 18:47:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:21: #2 number of paired peaks: 1491 INFO @ Sun, 21 Jun 2020 18:47:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:21: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:47:21: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 18:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.05_model.r INFO @ Sun, 21 Jun 2020 18:47:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:21: #3 Pre-compute pvalue-qvalue table... 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 18:47:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.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 18:47:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.05_summits.bed INFO @ Sun, 21 Jun 2020 18:47:33: Done! pass1 - making usageList (292 chroms): 2 millis pass2 - checking and writing primary data (3252 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:47:34: 1000000 INFO @ Sun, 21 Jun 2020 18:47:43: 2000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 18:47:52: 3000000 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 18:47:53: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 18:47:53: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 18:47:53: #1 total tags in treatment: 3108943 INFO @ Sun, 21 Jun 2020 18:47:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:53: #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 18:47:54: #1 tags after filtering in treatment: 3108923 INFO @ Sun, 21 Jun 2020 18:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:54: #2 number of paired peaks: 1491 INFO @ Sun, 21 Jun 2020 18:47:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:54: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:47:54: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 18:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.10_model.r INFO @ Sun, 21 Jun 2020 18:47:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.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 18:47:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:03: 1000000 INFO @ Sun, 21 Jun 2020 18:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.10_summits.bed INFO @ Sun, 21 Jun 2020 18:48:06: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (1477 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:48:11: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:48:20: 3000000 INFO @ Sun, 21 Jun 2020 18:48:21: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 18:48:21: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 18:48:21: #1 total tags in treatment: 3108943 INFO @ Sun, 21 Jun 2020 18:48:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:21: #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 18:48:21: #1 tags after filtering in treatment: 3108923 INFO @ Sun, 21 Jun 2020 18:48:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:22: #2 number of paired peaks: 1491 INFO @ Sun, 21 Jun 2020 18:48:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:22: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:48:22: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 18:48:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.20_model.r INFO @ Sun, 21 Jun 2020 18:48:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2748311/SRX2748311.20_summits.bed INFO @ Sun, 21 Jun 2020 18:48:33: Done! pass1 - making usageList (103 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 8 millis CompletedMACS2peakCalling