Job ID = 6452486 SRX = SRX013094 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:38:52 prefetch.2.10.7: 1) Downloading 'SRR030360'... 2020-06-21T07:38:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:39:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:39:07 prefetch.2.10.7: 'SRR030360' is valid 2020-06-21T07:39:07 prefetch.2.10.7: 1) 'SRR030360' was downloaded successfully Read 695909 spots for SRR030360/SRR030360.sra Written 695909 spots for SRR030360/SRR030360.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: 00:00:09 695909 reads; of these: 695909 (100.00%) were unpaired; of these: 119127 (17.12%) aligned 0 times 451349 (64.86%) aligned exactly 1 time 125433 (18.02%) aligned >1 times 82.88% overall alignment rate Time searching: 00:00:09 Overall time: 00:00:09 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] 34246 / 576782 = 0.0594 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 16:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.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 16:39:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:39:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:02: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:40:02: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:40:02: #1 total tags in treatment: 542536 INFO @ Sun, 21 Jun 2020 16:40:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:02: #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 16:40:02: #1 tags after filtering in treatment: 541865 INFO @ Sun, 21 Jun 2020 16:40:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:02: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:02: #2 number of paired peaks: 3576 INFO @ Sun, 21 Jun 2020 16:40:02: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:02: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:02: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:02: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:02: #2 predicted fragment length is 235 bps INFO @ Sun, 21 Jun 2020 16:40:02: #2 alternative fragment length(s) may be 235 bps INFO @ Sun, 21 Jun 2020 16:40:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.05_model.r INFO @ Sun, 21 Jun 2020 16:40:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:40:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.05_summits.bed INFO @ Sun, 21 Jun 2020 16:40:04: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 4 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 16:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.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 16:40:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:40:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:40:31: #1 total tags in treatment: 542536 INFO @ Sun, 21 Jun 2020 16:40:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:31: #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 16:40:31: #1 tags after filtering in treatment: 541865 INFO @ Sun, 21 Jun 2020 16:40:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:31: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:32: #2 number of paired peaks: 3576 INFO @ Sun, 21 Jun 2020 16:40:32: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:32: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:32: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:32: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:32: #2 predicted fragment length is 235 bps INFO @ Sun, 21 Jun 2020 16:40:32: #2 alternative fragment length(s) may be 235 bps INFO @ Sun, 21 Jun 2020 16:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.10_model.r INFO @ Sun, 21 Jun 2020 16:40:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:40:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.10_summits.bed INFO @ Sun, 21 Jun 2020 16:40:34: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (38 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... INFO @ Sun, 21 Jun 2020 16:41:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.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 16:41:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:00: #1 read treatment tags... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:41:03: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:03: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:03: #1 total tags in treatment: 542536 INFO @ Sun, 21 Jun 2020 16:41:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:03: #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 16:41:03: #1 tags after filtering in treatment: 541865 INFO @ Sun, 21 Jun 2020 16:41:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:03: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:03: #2 number of paired peaks: 3576 INFO @ Sun, 21 Jun 2020 16:41:03: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:03: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:03: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:03: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:03: #2 predicted fragment length is 235 bps INFO @ Sun, 21 Jun 2020 16:41:03: #2 alternative fragment length(s) may be 235 bps INFO @ Sun, 21 Jun 2020 16:41:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.20_model.r INFO @ Sun, 21 Jun 2020 16:41:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:41:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013094/SRX013094.20_summits.bed INFO @ Sun, 21 Jun 2020 16:41:06: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling