Job ID = 6366338 SRX = SRX113616 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:31 prefetch.2.10.7: 1) Downloading 'SRR393716'... 2020-06-15T23:10:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:05 prefetch.2.10.7: 'SRR393716' is valid 2020-06-15T23:11:05 prefetch.2.10.7: 1) 'SRR393716' was downloaded successfully Read 7097223 spots for SRR393716/SRR393716.sra Written 7097223 spots for SRR393716/SRR393716.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: 00:01:35 7097223 reads; of these: 7097223 (100.00%) were unpaired; of these: 306375 (4.32%) aligned 0 times 4759103 (67.06%) aligned exactly 1 time 2031745 (28.63%) aligned >1 times 95.68% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2051803 / 6790848 = 0.3021 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 @ Tue, 16 Jun 2020 08:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:14:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:00: 1000000 INFO @ Tue, 16 Jun 2020 08:15:05: 2000000 INFO @ Tue, 16 Jun 2020 08:15:11: 3000000 INFO @ Tue, 16 Jun 2020 08:15:16: 4000000 INFO @ Tue, 16 Jun 2020 08:15:20: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:15:20: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:15:20: #1 total tags in treatment: 4739045 INFO @ Tue, 16 Jun 2020 08:15:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:15:20: #1 tags after filtering in treatment: 4739045 INFO @ Tue, 16 Jun 2020 08:15:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:21: #2 number of paired peaks: 4058 INFO @ Tue, 16 Jun 2020 08:15:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:21: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:15:21: #2 alternative fragment length(s) may be 0,42,156,252 bps INFO @ Tue, 16 Jun 2020 08:15:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.05_model.r INFO @ Tue, 16 Jun 2020 08:15:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:21: #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 @ Tue, 16 Jun 2020 08:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:15:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:29: 1000000 INFO @ Tue, 16 Jun 2020 08:15:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:35: 2000000 INFO @ Tue, 16 Jun 2020 08:15:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:40: 3000000 INFO @ Tue, 16 Jun 2020 08:15:46: 4000000 INFO @ Tue, 16 Jun 2020 08:15:49: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:15:49: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:15:49: #1 total tags in treatment: 4739045 INFO @ Tue, 16 Jun 2020 08:15:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:15:50: #1 tags after filtering in treatment: 4739045 INFO @ Tue, 16 Jun 2020 08:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:50: #2 number of paired peaks: 4058 INFO @ Tue, 16 Jun 2020 08:15:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:50: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:15:50: #2 alternative fragment length(s) may be 0,42,156,252 bps INFO @ Tue, 16 Jun 2020 08:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.10_model.r INFO @ Tue, 16 Jun 2020 08:15:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:50: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 08:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:15:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:00: 1000000 INFO @ Tue, 16 Jun 2020 08:16:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:05: 2000000 INFO @ Tue, 16 Jun 2020 08:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (245 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:11: 3000000 INFO @ Tue, 16 Jun 2020 08:16:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:20: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:16:20: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:16:20: #1 total tags in treatment: 4739045 INFO @ Tue, 16 Jun 2020 08:16:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:16:20: #1 tags after filtering in treatment: 4739045 INFO @ Tue, 16 Jun 2020 08:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:21: #2 number of paired peaks: 4058 INFO @ Tue, 16 Jun 2020 08:16:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:21: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:16:21: #2 alternative fragment length(s) may be 0,42,156,252 bps INFO @ Tue, 16 Jun 2020 08:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.20_model.r INFO @ Tue, 16 Jun 2020 08:16:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113616/SRX113616.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 0 millis CompletedMACS2peakCalling