Job ID = 6459040 SRX = SRX6370204 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:08:49 prefetch.2.10.7: 1) Downloading 'SRR9606653'... 2020-06-21T13:08:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:09:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:09:53 prefetch.2.10.7: 'SRR9606653' is valid 2020-06-21T13:09:53 prefetch.2.10.7: 1) 'SRR9606653' was downloaded successfully 2020-06-21T13:09:53 prefetch.2.10.7: 'SRR9606653' has 0 unresolved dependencies Read 7152969 spots for SRR9606653/SRR9606653.sra Written 7152969 spots for SRR9606653/SRR9606653.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: 00:01:09 7152969 reads; of these: 7152969 (100.00%) were unpaired; of these: 7076905 (98.94%) aligned 0 times 27707 (0.39%) aligned exactly 1 time 48357 (0.68%) aligned >1 times 1.06% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 14694 / 76064 = 0.1932 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 22:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.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 22:12:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:01: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 22:12:01: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 22:12:01: #1 total tags in treatment: 61370 INFO @ Sun, 21 Jun 2020 22:12:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:01: #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 22:12:01: #1 tags after filtering in treatment: 60922 INFO @ Sun, 21 Jun 2020 22:12:01: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 22:12:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:01: #2 number of paired peaks: 1934 INFO @ Sun, 21 Jun 2020 22:12:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:02: #2 predicted fragment length is 294 bps INFO @ Sun, 21 Jun 2020 22:12:02: #2 alternative fragment length(s) may be 294 bps INFO @ Sun, 21 Jun 2020 22:12:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.05_model.r INFO @ Sun, 21 Jun 2020 22:12:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.05_summits.bed INFO @ Sun, 21 Jun 2020 22:12:02: Done! pass1 - making usageList (41 chroms): 0 millis pass2 - checking and writing primary data (77 records, 4 fields): 2 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 22:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.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 22:12:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:31: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 22:12:31: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 22:12:31: #1 total tags in treatment: 61370 INFO @ Sun, 21 Jun 2020 22:12:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:31: #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 22:12:31: #1 tags after filtering in treatment: 60922 INFO @ Sun, 21 Jun 2020 22:12:31: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 22:12:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:32: #2 number of paired peaks: 1934 INFO @ Sun, 21 Jun 2020 22:12:32: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:32: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:32: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:32: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:32: #2 predicted fragment length is 294 bps INFO @ Sun, 21 Jun 2020 22:12:32: #2 alternative fragment length(s) may be 294 bps INFO @ Sun, 21 Jun 2020 22:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.10_model.r INFO @ Sun, 21 Jun 2020 22:12:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.10_summits.bed INFO @ Sun, 21 Jun 2020 22:12:32: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (49 records, 4 fields): 2 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 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 22:13:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.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 22:13:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:13:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:13:01: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 22:13:01: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 22:13:01: #1 total tags in treatment: 61370 INFO @ Sun, 21 Jun 2020 22:13:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:01: #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 22:13:01: #1 tags after filtering in treatment: 60922 INFO @ Sun, 21 Jun 2020 22:13:01: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 22:13:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:02: #2 number of paired peaks: 1934 INFO @ Sun, 21 Jun 2020 22:13:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:02: #2 predicted fragment length is 294 bps INFO @ Sun, 21 Jun 2020 22:13:02: #2 alternative fragment length(s) may be 294 bps INFO @ Sun, 21 Jun 2020 22:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.20_model.r INFO @ Sun, 21 Jun 2020 22:13:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6370204/SRX6370204.20_summits.bed INFO @ Sun, 21 Jun 2020 22:13:02: Done! pass1 - making usageList (18 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 2 millis CompletedMACS2peakCalling