Job ID = 6366887 SRX = SRX2543055 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:23 prefetch.2.10.7: 1) Downloading 'SRR5235991'... 2020-06-15T23:01:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:31 prefetch.2.10.7: 'SRR5235991' is valid 2020-06-15T23:02:31 prefetch.2.10.7: 1) 'SRR5235991' was downloaded successfully 2020-06-15T23:02:31 prefetch.2.10.7: 'SRR5235991' has 0 unresolved dependencies Read 17976698 spots for SRR5235991/SRR5235991.sra Written 17976698 spots for SRR5235991/SRR5235991.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: 00:05:50 17976698 reads; of these: 17976698 (100.00%) were unpaired; of these: 1750169 (9.74%) aligned 0 times 14359663 (79.88%) aligned exactly 1 time 1866866 (10.38%) aligned >1 times 90.26% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3542539 / 16226529 = 0.2183 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 08:13:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.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 08:13:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:40: 1000000 INFO @ Tue, 16 Jun 2020 08:13:46: 2000000 INFO @ Tue, 16 Jun 2020 08:13:52: 3000000 INFO @ Tue, 16 Jun 2020 08:13:58: 4000000 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 08:14:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.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 08:14:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:05: 5000000 INFO @ Tue, 16 Jun 2020 08:14:10: 1000000 INFO @ Tue, 16 Jun 2020 08:14:11: 6000000 INFO @ Tue, 16 Jun 2020 08:14:17: 2000000 INFO @ Tue, 16 Jun 2020 08:14:18: 7000000 INFO @ Tue, 16 Jun 2020 08:14:24: 3000000 INFO @ Tue, 16 Jun 2020 08:14:25: 8000000 INFO @ Tue, 16 Jun 2020 08:14:31: 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 08:14:32: 9000000 INFO @ Tue, 16 Jun 2020 08:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.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 08:14:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:38: 5000000 INFO @ Tue, 16 Jun 2020 08:14:39: 10000000 INFO @ Tue, 16 Jun 2020 08:14:41: 1000000 INFO @ Tue, 16 Jun 2020 08:14:45: 6000000 INFO @ Tue, 16 Jun 2020 08:14:45: 11000000 INFO @ Tue, 16 Jun 2020 08:14:47: 2000000 INFO @ Tue, 16 Jun 2020 08:14:52: 12000000 INFO @ Tue, 16 Jun 2020 08:14:53: 7000000 INFO @ Tue, 16 Jun 2020 08:14:54: 3000000 INFO @ Tue, 16 Jun 2020 08:14:56: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:14:56: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:14:56: #1 total tags in treatment: 12683990 INFO @ Tue, 16 Jun 2020 08:14:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:56: #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 08:14:57: #1 tags after filtering in treatment: 12683990 INFO @ Tue, 16 Jun 2020 08:14:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:58: #2 number of paired peaks: 1662 INFO @ Tue, 16 Jun 2020 08:14:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:58: #2 predicted fragment length is 246 bps INFO @ Tue, 16 Jun 2020 08:14:58: #2 alternative fragment length(s) may be 4,246 bps INFO @ Tue, 16 Jun 2020 08:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.05_model.r INFO @ Tue, 16 Jun 2020 08:14:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:00: 8000000 INFO @ Tue, 16 Jun 2020 08:15:01: 4000000 INFO @ Tue, 16 Jun 2020 08:15:06: 9000000 INFO @ Tue, 16 Jun 2020 08:15:08: 5000000 INFO @ Tue, 16 Jun 2020 08:15:13: 10000000 INFO @ Tue, 16 Jun 2020 08:15:15: 6000000 INFO @ Tue, 16 Jun 2020 08:15:20: 11000000 INFO @ Tue, 16 Jun 2020 08:15:22: 7000000 INFO @ Tue, 16 Jun 2020 08:15:27: 12000000 INFO @ Tue, 16 Jun 2020 08:15:29: 8000000 INFO @ Tue, 16 Jun 2020 08:15:32: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:15:32: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:15:32: #1 total tags in treatment: 12683990 INFO @ Tue, 16 Jun 2020 08:15:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:32: #1 tags after filtering in treatment: 12683990 INFO @ Tue, 16 Jun 2020 08:15:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:33: #2 number of paired peaks: 1662 INFO @ Tue, 16 Jun 2020 08:15:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:33: #2 predicted fragment length is 246 bps INFO @ Tue, 16 Jun 2020 08:15:33: #2 alternative fragment length(s) may be 4,246 bps INFO @ Tue, 16 Jun 2020 08:15:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.10_model.r INFO @ Tue, 16 Jun 2020 08:15:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:35: 9000000 INFO @ Tue, 16 Jun 2020 08:15:42: 10000000 INFO @ Tue, 16 Jun 2020 08:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:48: 11000000 INFO @ Tue, 16 Jun 2020 08:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:48: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6262 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:54: 12000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:59: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:15:59: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:15:59: #1 total tags in treatment: 12683990 INFO @ Tue, 16 Jun 2020 08:15:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:59: #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 08:15:59: #1 tags after filtering in treatment: 12683990 INFO @ Tue, 16 Jun 2020 08:15:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:00: #2 number of paired peaks: 1662 INFO @ Tue, 16 Jun 2020 08:16:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:00: #2 predicted fragment length is 246 bps INFO @ Tue, 16 Jun 2020 08:16:00: #2 alternative fragment length(s) may be 4,246 bps INFO @ Tue, 16 Jun 2020 08:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.20_model.r INFO @ Tue, 16 Jun 2020 08:16:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4012 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543055/SRX2543055.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2027 records, 4 fields): 3 millis CompletedMACS2peakCalling