Job ID = 6454100 SRX = SRX181442 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:02:34 prefetch.2.10.7: 1) Downloading 'SRR548179'... 2020-06-21T09:02:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:04:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:04:34 prefetch.2.10.7: 'SRR548179' is valid 2020-06-21T09:04:34 prefetch.2.10.7: 1) 'SRR548179' was downloaded successfully Read 12876202 spots for SRR548179/SRR548179.sra Written 12876202 spots for SRR548179/SRR548179.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: 00:02:15 12876202 reads; of these: 12876202 (100.00%) were unpaired; of these: 5449883 (42.33%) aligned 0 times 6303321 (48.95%) aligned exactly 1 time 1122998 (8.72%) aligned >1 times 57.67% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 6625154 / 7426319 = 0.8921 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 18:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.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 18:08:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:08:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:08:49: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:08:49: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:08:49: #1 total tags in treatment: 801165 INFO @ Sun, 21 Jun 2020 18:08:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:49: #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 18:08:49: #1 tags after filtering in treatment: 800804 INFO @ Sun, 21 Jun 2020 18:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:49: #2 number of paired peaks: 1716 INFO @ Sun, 21 Jun 2020 18:08:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:49: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 18:08:49: #2 alternative fragment length(s) may be 126,189,239 bps INFO @ Sun, 21 Jun 2020 18:08:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.05_model.r INFO @ Sun, 21 Jun 2020 18:08:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.05_summits.bed INFO @ Sun, 21 Jun 2020 18:08:52: Done! pass1 - making usageList (236 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 18:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.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 18:09:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:19: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:09:19: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:09:19: #1 total tags in treatment: 801165 INFO @ Sun, 21 Jun 2020 18:09:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:19: #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 18:09:19: #1 tags after filtering in treatment: 800804 INFO @ Sun, 21 Jun 2020 18:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:20: #2 number of paired peaks: 1716 INFO @ Sun, 21 Jun 2020 18:09:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:20: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 18:09:20: #2 alternative fragment length(s) may be 126,189,239 bps INFO @ Sun, 21 Jun 2020 18:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.10_model.r INFO @ Sun, 21 Jun 2020 18:09:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:09:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.10_summits.bed INFO @ Sun, 21 Jun 2020 18:09:23: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 18:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.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 18:09:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:45: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:09:49: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:09:49: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:09:49: #1 total tags in treatment: 801165 INFO @ Sun, 21 Jun 2020 18:09:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:49: #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 18:09:49: #1 tags after filtering in treatment: 800804 INFO @ Sun, 21 Jun 2020 18:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:49: #2 number of paired peaks: 1716 INFO @ Sun, 21 Jun 2020 18:09:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:49: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 18:09:49: #2 alternative fragment length(s) may be 126,189,239 bps INFO @ Sun, 21 Jun 2020 18:09:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.20_model.r INFO @ Sun, 21 Jun 2020 18:09:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:09:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181442/SRX181442.20_summits.bed INFO @ Sun, 21 Jun 2020 18:09:52: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling