Job ID = 6366261 SRX = SRX1007133 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:42:52 prefetch.2.10.7: 1) Downloading 'SRR1993093'... 2020-06-15T22:42:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:36 prefetch.2.10.7: 'SRR1993093' is valid 2020-06-15T22:43:36 prefetch.2.10.7: 1) 'SRR1993093' was downloaded successfully Read 9065402 spots for SRR1993093/SRR1993093.sra Written 9065402 spots for SRR1993093/SRR1993093.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: 00:00:32 9065402 reads; of these: 9065402 (100.00%) were unpaired; of these: 8231466 (90.80%) aligned 0 times 701884 (7.74%) aligned exactly 1 time 132052 (1.46%) aligned >1 times 9.20% overall alignment rate Time searching: 00:00:32 Overall time: 00:00:32 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] 82720 / 833936 = 0.0992 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 07:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.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 07:45:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:20: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:45:20: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:45:20: #1 total tags in treatment: 751216 INFO @ Tue, 16 Jun 2020 07:45:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:20: #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 07:45:20: #1 tags after filtering in treatment: 751216 INFO @ Tue, 16 Jun 2020 07:45:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:20: #2 number of paired peaks: 3113 INFO @ Tue, 16 Jun 2020 07:45:20: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:20: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:20: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:20: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:20: #2 predicted fragment length is 86 bps INFO @ Tue, 16 Jun 2020 07:45:20: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 16 Jun 2020 07:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.05_model.r INFO @ Tue, 16 Jun 2020 07:45:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.05_summits.bed INFO @ Tue, 16 Jun 2020 07:45:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3129 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 @ Tue, 16 Jun 2020 07:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.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 07:45:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:50: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:45:50: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:45:50: #1 total tags in treatment: 751216 INFO @ Tue, 16 Jun 2020 07:45:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:50: #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 07:45:50: #1 tags after filtering in treatment: 751216 INFO @ Tue, 16 Jun 2020 07:45:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:50: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:50: #2 number of paired peaks: 3113 INFO @ Tue, 16 Jun 2020 07:45:50: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:50: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:51: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:51: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:51: #2 predicted fragment length is 86 bps INFO @ Tue, 16 Jun 2020 07:45:51: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 16 Jun 2020 07:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.10_model.r INFO @ Tue, 16 Jun 2020 07:45:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.10_summits.bed INFO @ Tue, 16 Jun 2020 07:45:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1696 records, 4 fields): 4 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 @ Tue, 16 Jun 2020 07:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.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 07:46:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:15: #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 @ Tue, 16 Jun 2020 07:46:20: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:46:20: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:46:20: #1 total tags in treatment: 751216 INFO @ Tue, 16 Jun 2020 07:46:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:20: #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 07:46:20: #1 tags after filtering in treatment: 751216 INFO @ Tue, 16 Jun 2020 07:46:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:21: #2 number of paired peaks: 3113 INFO @ Tue, 16 Jun 2020 07:46:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:21: #2 predicted fragment length is 86 bps INFO @ Tue, 16 Jun 2020 07:46:21: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 16 Jun 2020 07:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.20_model.r INFO @ Tue, 16 Jun 2020 07:46:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:46:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007133/SRX1007133.20_summits.bed INFO @ Tue, 16 Jun 2020 07:46:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (735 records, 4 fields): 2 millis CompletedMACS2peakCalling