Job ID = 6367308 SRX = SRX331070 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:21:16 prefetch.2.10.7: 1) Downloading 'SRR947294'... 2020-06-15T23:21:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:48 prefetch.2.10.7: 'SRR947294' is valid 2020-06-15T23:21:48 prefetch.2.10.7: 1) 'SRR947294' was downloaded successfully Read 7199430 spots for SRR947294/SRR947294.sra Written 7199430 spots for SRR947294/SRR947294.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: 00:01:02 7199430 reads; of these: 7199430 (100.00%) were unpaired; of these: 1004238 (13.95%) aligned 0 times 5317046 (73.85%) aligned exactly 1 time 878146 (12.20%) aligned >1 times 86.05% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 776033 / 6195192 = 0.1253 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 08:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.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 08:24:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:54: 1000000 INFO @ Tue, 16 Jun 2020 08:25:00: 2000000 INFO @ Tue, 16 Jun 2020 08:25:05: 3000000 INFO @ Tue, 16 Jun 2020 08:25:10: 4000000 INFO @ Tue, 16 Jun 2020 08:25:15: 5000000 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 08:25:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:18: #1 total tags in treatment: 5419159 INFO @ Tue, 16 Jun 2020 08:25:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:18: #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 08:25:18: #1 tags after filtering in treatment: 5419159 INFO @ Tue, 16 Jun 2020 08:25:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:18: #2 number of paired peaks: 1113 INFO @ Tue, 16 Jun 2020 08:25:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:18: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:25:18: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.05_model.r INFO @ Tue, 16 Jun 2020 08:25:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.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 08:25:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:25: 1000000 INFO @ Tue, 16 Jun 2020 08:25:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:31: 2000000 INFO @ Tue, 16 Jun 2020 08:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.05_summits.bed INFO @ Tue, 16 Jun 2020 08:25:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5055 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:38: 3000000 INFO @ Tue, 16 Jun 2020 08:25:44: 4000000 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 08:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.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 08:25:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:51: 5000000 INFO @ Tue, 16 Jun 2020 08:25:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:53: #1 total tags in treatment: 5419159 INFO @ Tue, 16 Jun 2020 08:25:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:53: #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 08:25:54: #1 tags after filtering in treatment: 5419159 INFO @ Tue, 16 Jun 2020 08:25:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:54: #2 number of paired peaks: 1113 INFO @ Tue, 16 Jun 2020 08:25:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:54: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:25:54: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:25:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.10_model.r INFO @ Tue, 16 Jun 2020 08:25:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:55: 1000000 INFO @ Tue, 16 Jun 2020 08:26:01: 2000000 INFO @ Tue, 16 Jun 2020 08:26:06: 3000000 INFO @ Tue, 16 Jun 2020 08:26:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:12: 4000000 INFO @ Tue, 16 Jun 2020 08:26:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3270 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:17: 5000000 INFO @ Tue, 16 Jun 2020 08:26:19: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:19: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:19: #1 total tags in treatment: 5419159 INFO @ Tue, 16 Jun 2020 08:26:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:19: #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 08:26:19: #1 tags after filtering in treatment: 5419159 INFO @ Tue, 16 Jun 2020 08:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:20: #2 number of paired peaks: 1113 INFO @ Tue, 16 Jun 2020 08:26:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:20: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:26:20: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.20_model.r INFO @ Tue, 16 Jun 2020 08:26:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331070/SRX331070.20_summits.bed INFO @ Tue, 16 Jun 2020 08:26:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1704 records, 4 fields): 3 millis CompletedMACS2peakCalling