Job ID = 6458008 SRX = SRX4933910 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:15:07 prefetch.2.10.7: 1) Downloading 'SRR8107301'... 2020-06-21T12:15:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:19:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:19:24 prefetch.2.10.7: 1) 'SRR8107301' was downloaded successfully Read 28445635 spots for SRR8107301/SRR8107301.sra Written 28445635 spots for SRR8107301/SRR8107301.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: 00:04:02 28445635 reads; of these: 28445635 (100.00%) were unpaired; of these: 20351910 (71.55%) aligned 0 times 7034794 (24.73%) aligned exactly 1 time 1058931 (3.72%) aligned >1 times 28.45% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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] 4444973 / 8093725 = 0.5492 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 21:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.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 21:27:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:59: 1000000 INFO @ Sun, 21 Jun 2020 21:28:05: 2000000 INFO @ Sun, 21 Jun 2020 21:28:12: 3000000 INFO @ Sun, 21 Jun 2020 21:28:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:17: #1 total tags in treatment: 3648752 INFO @ Sun, 21 Jun 2020 21:28:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:17: #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 21:28:17: #1 tags after filtering in treatment: 3648525 INFO @ Sun, 21 Jun 2020 21:28:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:18: #2 number of paired peaks: 6451 INFO @ Sun, 21 Jun 2020 21:28:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:18: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:28:18: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 21:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.05_model.r INFO @ Sun, 21 Jun 2020 21:28:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:18: #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 21:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.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 21:28:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:30: 1000000 INFO @ Sun, 21 Jun 2020 21:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.05_summits.bed INFO @ Sun, 21 Jun 2020 21:28:34: Done! pass1 - making usageList (274 chroms): 2 millis pass2 - checking and writing primary data (5712 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:28:37: 2000000 INFO @ Sun, 21 Jun 2020 21:28:45: 3000000 INFO @ Sun, 21 Jun 2020 21:28:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:50: #1 total tags in treatment: 3648752 INFO @ Sun, 21 Jun 2020 21:28:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:50: #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 21:28:50: #1 tags after filtering in treatment: 3648525 INFO @ Sun, 21 Jun 2020 21:28:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:51: #2 number of paired peaks: 6451 INFO @ Sun, 21 Jun 2020 21:28:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:51: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:28:51: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 21:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.10_model.r INFO @ Sun, 21 Jun 2020 21:28:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.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 21:28:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:00: 1000000 INFO @ Sun, 21 Jun 2020 21:29:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:07: 2000000 INFO @ Sun, 21 Jun 2020 21:29:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.10_summits.bed INFO @ Sun, 21 Jun 2020 21:29:07: Done! pass1 - making usageList (203 chroms): 1 millis pass2 - checking and writing primary data (2602 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:29:14: 3000000 INFO @ Sun, 21 Jun 2020 21:29:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:19: #1 total tags in treatment: 3648752 INFO @ Sun, 21 Jun 2020 21:29:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:19: #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 21:29:19: #1 tags after filtering in treatment: 3648525 INFO @ Sun, 21 Jun 2020 21:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:20: #2 number of paired peaks: 6451 INFO @ Sun, 21 Jun 2020 21:29:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:20: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:29:20: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 21:29:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.20_model.r INFO @ Sun, 21 Jun 2020 21:29:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:29:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933910/SRX4933910.20_summits.bed INFO @ Sun, 21 Jun 2020 21:29:36: Done! pass1 - making usageList (78 chroms): 1 millis pass2 - checking and writing primary data (775 records, 4 fields): 7 millis CompletedMACS2peakCalling