Job ID = 6367751 SRX = SRX4082365 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:20 prefetch.2.10.7: 1) Downloading 'SRR7164183'... 2020-06-15T23:33:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:20 prefetch.2.10.7: 'SRR7164183' is valid 2020-06-15T23:35:20 prefetch.2.10.7: 1) 'SRR7164183' was downloaded successfully 2020-06-15T23:35:20 prefetch.2.10.7: 'SRR7164183' has 0 unresolved dependencies Read 14756742 spots for SRR7164183/SRR7164183.sra Written 14756742 spots for SRR7164183/SRR7164183.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: 00:02:20 14756742 reads; of these: 14756742 (100.00%) were unpaired; of these: 334470 (2.27%) aligned 0 times 13112394 (88.86%) aligned exactly 1 time 1309878 (8.88%) aligned >1 times 97.73% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 2863396 / 14422272 = 0.1985 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 08:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.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 08:41:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:52: 1000000 INFO @ Tue, 16 Jun 2020 08:41:57: 2000000 INFO @ Tue, 16 Jun 2020 08:42:03: 3000000 INFO @ Tue, 16 Jun 2020 08:42:08: 4000000 INFO @ Tue, 16 Jun 2020 08:42:13: 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 08:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.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 08:42:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:19: 6000000 INFO @ Tue, 16 Jun 2020 08:42:23: 1000000 INFO @ Tue, 16 Jun 2020 08:42:25: 7000000 INFO @ Tue, 16 Jun 2020 08:42:29: 2000000 INFO @ Tue, 16 Jun 2020 08:42:30: 8000000 INFO @ Tue, 16 Jun 2020 08:42:34: 3000000 INFO @ Tue, 16 Jun 2020 08:42:36: 9000000 INFO @ Tue, 16 Jun 2020 08:42:40: 4000000 INFO @ Tue, 16 Jun 2020 08:42:42: 10000000 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 08:42:46: 5000000 INFO @ Tue, 16 Jun 2020 08:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.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 08:42:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:48: 11000000 INFO @ Tue, 16 Jun 2020 08:42:51: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:42:51: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:42:51: #1 total tags in treatment: 11558876 INFO @ Tue, 16 Jun 2020 08:42:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:51: #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 08:42:51: #1 tags after filtering in treatment: 11558876 INFO @ Tue, 16 Jun 2020 08:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:52: 1000000 INFO @ Tue, 16 Jun 2020 08:42:52: 6000000 INFO @ Tue, 16 Jun 2020 08:42:52: #2 number of paired peaks: 3875 INFO @ Tue, 16 Jun 2020 08:42:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:53: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:42:53: #2 alternative fragment length(s) may be 2,158 bps INFO @ Tue, 16 Jun 2020 08:42:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.05_model.r INFO @ Tue, 16 Jun 2020 08:42:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:57: 2000000 INFO @ Tue, 16 Jun 2020 08:42:58: 7000000 INFO @ Tue, 16 Jun 2020 08:43:02: 3000000 INFO @ Tue, 16 Jun 2020 08:43:04: 8000000 INFO @ Tue, 16 Jun 2020 08:43:07: 4000000 INFO @ Tue, 16 Jun 2020 08:43:10: 9000000 INFO @ Tue, 16 Jun 2020 08:43:12: 5000000 INFO @ Tue, 16 Jun 2020 08:43:16: 10000000 INFO @ Tue, 16 Jun 2020 08:43:18: 6000000 INFO @ Tue, 16 Jun 2020 08:43:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:22: 11000000 INFO @ Tue, 16 Jun 2020 08:43:23: 7000000 INFO @ Tue, 16 Jun 2020 08:43:25: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:43:25: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:43:25: #1 total tags in treatment: 11558876 INFO @ Tue, 16 Jun 2020 08:43:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:25: #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 08:43:25: #1 tags after filtering in treatment: 11558876 INFO @ Tue, 16 Jun 2020 08:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:27: #2 number of paired peaks: 3875 INFO @ Tue, 16 Jun 2020 08:43:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:27: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:43:27: #2 alternative fragment length(s) may be 2,158 bps INFO @ Tue, 16 Jun 2020 08:43:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.10_model.r INFO @ Tue, 16 Jun 2020 08:43:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:28: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.05_summits.bed INFO @ Tue, 16 Jun 2020 08:43:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9941 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:32: 9000000 INFO @ Tue, 16 Jun 2020 08:43:37: 10000000 INFO @ Tue, 16 Jun 2020 08:43:42: 11000000 INFO @ Tue, 16 Jun 2020 08:43:44: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:43:44: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:43:44: #1 total tags in treatment: 11558876 INFO @ Tue, 16 Jun 2020 08:43:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:44: #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 08:43:44: #1 tags after filtering in treatment: 11558876 INFO @ Tue, 16 Jun 2020 08:43:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:46: #2 number of paired peaks: 3875 INFO @ Tue, 16 Jun 2020 08:43:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:46: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:43:46: #2 alternative fragment length(s) may be 2,158 bps INFO @ Tue, 16 Jun 2020 08:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.20_model.r INFO @ Tue, 16 Jun 2020 08:43:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:43:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.10_summits.bed INFO @ Tue, 16 Jun 2020 08:44:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5760 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082365/SRX4082365.20_summits.bed INFO @ Tue, 16 Jun 2020 08:44:23: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1809 records, 4 fields): 3 millis CompletedMACS2peakCalling