Job ID = 6368310 SRX = SRX494993 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:45 prefetch.2.10.7: 1) Downloading 'SRR1198525'... 2020-06-16T00:04:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:09:20 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:09:20 prefetch.2.10.7: 1) 'SRR1198525' was downloaded successfully Read 13396177 spots for SRR1198525/SRR1198525.sra Written 13396177 spots for SRR1198525/SRR1198525.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:03 13396177 reads; of these: 13396177 (100.00%) were unpaired; of these: 885508 (6.61%) aligned 0 times 11084883 (82.75%) aligned exactly 1 time 1425786 (10.64%) aligned >1 times 93.39% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 8766729 / 12510669 = 0.7007 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 09:14:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.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 09:14:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:36: 1000000 INFO @ Tue, 16 Jun 2020 09:14:42: 2000000 INFO @ Tue, 16 Jun 2020 09:14:49: 3000000 INFO @ Tue, 16 Jun 2020 09:14:53: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:53: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:53: #1 total tags in treatment: 3743940 INFO @ Tue, 16 Jun 2020 09:14:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:53: #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 09:14:54: #1 tags after filtering in treatment: 3743940 INFO @ Tue, 16 Jun 2020 09:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:54: #2 number of paired peaks: 4182 INFO @ Tue, 16 Jun 2020 09:14:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:54: #2 predicted fragment length is 355 bps INFO @ Tue, 16 Jun 2020 09:14:54: #2 alternative fragment length(s) may be 355 bps INFO @ Tue, 16 Jun 2020 09:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.05_model.r INFO @ Tue, 16 Jun 2020 09:14:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:54: #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 09:14:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.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 09:14:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:05: 1000000 INFO @ Tue, 16 Jun 2020 09:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.05_summits.bed INFO @ Tue, 16 Jun 2020 09:15:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3844 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:10: 2000000 INFO @ Tue, 16 Jun 2020 09:15:15: 3000000 INFO @ Tue, 16 Jun 2020 09:15:19: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:15:19: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:15:19: #1 total tags in treatment: 3743940 INFO @ Tue, 16 Jun 2020 09:15:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:19: #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 09:15:19: #1 tags after filtering in treatment: 3743940 INFO @ Tue, 16 Jun 2020 09:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:20: #2 number of paired peaks: 4182 INFO @ Tue, 16 Jun 2020 09:15:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:20: #2 predicted fragment length is 355 bps INFO @ Tue, 16 Jun 2020 09:15:20: #2 alternative fragment length(s) may be 355 bps INFO @ Tue, 16 Jun 2020 09:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.10_model.r INFO @ Tue, 16 Jun 2020 09:15:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:20: #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 09:15:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.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 09:15:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:34: 1000000 INFO @ Tue, 16 Jun 2020 09:15:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3160 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:40: 2000000 INFO @ Tue, 16 Jun 2020 09:15:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:49: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:15:49: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:15:49: #1 total tags in treatment: 3743940 INFO @ Tue, 16 Jun 2020 09:15:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:49: #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 09:15:49: #1 tags after filtering in treatment: 3743940 INFO @ Tue, 16 Jun 2020 09:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:50: #2 number of paired peaks: 4182 INFO @ Tue, 16 Jun 2020 09:15:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:50: #2 predicted fragment length is 355 bps INFO @ Tue, 16 Jun 2020 09:15:50: #2 alternative fragment length(s) may be 355 bps INFO @ Tue, 16 Jun 2020 09:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.20_model.r INFO @ Tue, 16 Jun 2020 09:15:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:16:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494993/SRX494993.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2395 records, 4 fields): 3 millis CompletedMACS2peakCalling