Job ID = 6366925 SRX = SRX2576628 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:08 prefetch.2.10.7: 1) Downloading 'SRR5272585'... 2020-06-15T23:06:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:57 prefetch.2.10.7: 'SRR5272585' is valid 2020-06-15T23:06:57 prefetch.2.10.7: 1) 'SRR5272585' was downloaded successfully 2020-06-15T23:06:57 prefetch.2.10.7: 'SRR5272585' has 0 unresolved dependencies Read 18751435 spots for SRR5272585/SRR5272585.sra Written 18751435 spots for SRR5272585/SRR5272585.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: 00:03:53 18751435 reads; of these: 18751435 (100.00%) were unpaired; of these: 2652083 (14.14%) aligned 0 times 12988877 (69.27%) aligned exactly 1 time 3110475 (16.59%) aligned >1 times 85.86% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 5332972 / 16099352 = 0.3313 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 08:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.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 08:14:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:02: 1000000 INFO @ Tue, 16 Jun 2020 08:15:07: 2000000 INFO @ Tue, 16 Jun 2020 08:15:12: 3000000 INFO @ Tue, 16 Jun 2020 08:15:17: 4000000 INFO @ Tue, 16 Jun 2020 08:15:22: 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 08:15:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.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 08:15:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:27: 6000000 INFO @ Tue, 16 Jun 2020 08:15:33: 7000000 INFO @ Tue, 16 Jun 2020 08:15:33: 1000000 INFO @ Tue, 16 Jun 2020 08:15:38: 8000000 INFO @ Tue, 16 Jun 2020 08:15:39: 2000000 INFO @ Tue, 16 Jun 2020 08:15:43: 9000000 INFO @ Tue, 16 Jun 2020 08:15:46: 3000000 INFO @ Tue, 16 Jun 2020 08:15:49: 10000000 INFO @ Tue, 16 Jun 2020 08:15:52: 4000000 INFO @ Tue, 16 Jun 2020 08:15:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:53: #1 total tags in treatment: 10766380 INFO @ Tue, 16 Jun 2020 08:15:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:53: #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 08:15:53: #1 tags after filtering in treatment: 10766380 INFO @ Tue, 16 Jun 2020 08:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:54: #2 number of paired peaks: 1288 INFO @ Tue, 16 Jun 2020 08:15:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:54: #2 predicted fragment length is 254 bps INFO @ Tue, 16 Jun 2020 08:15:54: #2 alternative fragment length(s) may be 254 bps INFO @ Tue, 16 Jun 2020 08:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.05_model.r INFO @ Tue, 16 Jun 2020 08:15:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:54: #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 08:15:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.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 08:15:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:58: 5000000 INFO @ Tue, 16 Jun 2020 08:16:03: 1000000 INFO @ Tue, 16 Jun 2020 08:16:04: 6000000 INFO @ Tue, 16 Jun 2020 08:16:08: 2000000 INFO @ Tue, 16 Jun 2020 08:16:10: 7000000 INFO @ Tue, 16 Jun 2020 08:16:14: 3000000 INFO @ Tue, 16 Jun 2020 08:16:16: 8000000 INFO @ Tue, 16 Jun 2020 08:16:19: 4000000 INFO @ Tue, 16 Jun 2020 08:16:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:23: 9000000 INFO @ Tue, 16 Jun 2020 08:16:25: 5000000 INFO @ Tue, 16 Jun 2020 08:16:29: 10000000 INFO @ Tue, 16 Jun 2020 08:16:30: 6000000 INFO @ Tue, 16 Jun 2020 08:16:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:16:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:16:34: #1 total tags in treatment: 10766380 INFO @ Tue, 16 Jun 2020 08:16:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:34: #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 08:16:34: #1 tags after filtering in treatment: 10766380 INFO @ Tue, 16 Jun 2020 08:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.05_summits.bed INFO @ Tue, 16 Jun 2020 08:16:34: Done! INFO @ Tue, 16 Jun 2020 08:16:35: #2 number of paired peaks: 1288 INFO @ Tue, 16 Jun 2020 08:16:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:35: #2 predicted fragment length is 254 bps INFO @ Tue, 16 Jun 2020 08:16:35: #2 alternative fragment length(s) may be 254 bps INFO @ Tue, 16 Jun 2020 08:16:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.10_model.r INFO @ Tue, 16 Jun 2020 08:16:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:36: 7000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2990 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:41: 8000000 INFO @ Tue, 16 Jun 2020 08:16:45: 9000000 INFO @ Tue, 16 Jun 2020 08:16:50: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:16:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:16:54: #1 total tags in treatment: 10766380 INFO @ Tue, 16 Jun 2020 08:16:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:54: #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 08:16:54: #1 tags after filtering in treatment: 10766380 INFO @ Tue, 16 Jun 2020 08:16:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:55: #2 number of paired peaks: 1288 INFO @ Tue, 16 Jun 2020 08:16:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:55: #2 predicted fragment length is 254 bps INFO @ Tue, 16 Jun 2020 08:16:55: #2 alternative fragment length(s) may be 254 bps INFO @ Tue, 16 Jun 2020 08:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.20_model.r INFO @ Tue, 16 Jun 2020 08:16:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.10_summits.bed INFO @ Tue, 16 Jun 2020 08:17:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2300 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576628/SRX2576628.20_summits.bed INFO @ Tue, 16 Jun 2020 08:17:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1738 records, 4 fields): 3 millis CompletedMACS2peakCalling