Job ID = 6368226 SRX = SRX494909 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:10:21 prefetch.2.10.7: 1) Downloading 'SRR1198441'... 2020-06-16T00:10:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:13:21 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:13:21 prefetch.2.10.7: 1) 'SRR1198441' was downloaded successfully Read 24216614 spots for SRR1198441/SRR1198441.sra Written 24216614 spots for SRR1198441/SRR1198441.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: 00:04:59 24216614 reads; of these: 24216614 (100.00%) were unpaired; of these: 5370862 (22.18%) aligned 0 times 13973650 (57.70%) aligned exactly 1 time 4872102 (20.12%) aligned >1 times 77.82% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 9022874 / 18845752 = 0.4788 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 09:23:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.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 09:23:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:40: 1000000 INFO @ Tue, 16 Jun 2020 09:23:45: 2000000 INFO @ Tue, 16 Jun 2020 09:23:51: 3000000 INFO @ Tue, 16 Jun 2020 09:23:56: 4000000 INFO @ Tue, 16 Jun 2020 09:24:01: 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 09:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.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 09:24:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:07: 6000000 INFO @ Tue, 16 Jun 2020 09:24:11: 1000000 INFO @ Tue, 16 Jun 2020 09:24:12: 7000000 INFO @ Tue, 16 Jun 2020 09:24:17: 2000000 INFO @ Tue, 16 Jun 2020 09:24:18: 8000000 INFO @ Tue, 16 Jun 2020 09:24:22: 3000000 INFO @ Tue, 16 Jun 2020 09:24:24: 9000000 INFO @ Tue, 16 Jun 2020 09:24:28: 4000000 INFO @ Tue, 16 Jun 2020 09:24:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:24:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:24:28: #1 total tags in treatment: 9822878 INFO @ Tue, 16 Jun 2020 09:24:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:28: #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 09:24:28: #1 tags after filtering in treatment: 9822878 INFO @ Tue, 16 Jun 2020 09:24:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:29: #2 number of paired peaks: 1054 INFO @ Tue, 16 Jun 2020 09:24:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:29: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:24:29: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:24:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.05_model.r INFO @ Tue, 16 Jun 2020 09:24:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:33: 5000000 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 09:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.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 09:24:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:39: 6000000 INFO @ Tue, 16 Jun 2020 09:24:42: 1000000 INFO @ Tue, 16 Jun 2020 09:24:45: 7000000 INFO @ Tue, 16 Jun 2020 09:24:49: 2000000 INFO @ Tue, 16 Jun 2020 09:24:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:51: 8000000 INFO @ Tue, 16 Jun 2020 09:24:56: 3000000 INFO @ Tue, 16 Jun 2020 09:24:57: 9000000 INFO @ Tue, 16 Jun 2020 09:24:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.05_summits.bed INFO @ Tue, 16 Jun 2020 09:24:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2283 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:02: #1 total tags in treatment: 9822878 INFO @ Tue, 16 Jun 2020 09:25:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:02: #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 09:25:02: #1 tags after filtering in treatment: 9822878 INFO @ Tue, 16 Jun 2020 09:25:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:02: #2 number of paired peaks: 1054 INFO @ Tue, 16 Jun 2020 09:25:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:02: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:25:02: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.10_model.r INFO @ Tue, 16 Jun 2020 09:25:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:03: 4000000 INFO @ Tue, 16 Jun 2020 09:25:09: 5000000 INFO @ Tue, 16 Jun 2020 09:25:16: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:23: 7000000 INFO @ Tue, 16 Jun 2020 09:25:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:29: 8000000 INFO @ Tue, 16 Jun 2020 09:25:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.10_summits.bed INFO @ Tue, 16 Jun 2020 09:25:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1611 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:36: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:25:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:41: #1 total tags in treatment: 9822878 INFO @ Tue, 16 Jun 2020 09:25:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:41: #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 09:25:41: #1 tags after filtering in treatment: 9822878 INFO @ Tue, 16 Jun 2020 09:25:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:42: #2 number of paired peaks: 1054 INFO @ Tue, 16 Jun 2020 09:25:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:42: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:25:42: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:25:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.20_model.r INFO @ Tue, 16 Jun 2020 09:25:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494909/SRX494909.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1047 records, 4 fields): 2 millis CompletedMACS2peakCalling