Job ID = 6368706 SRX = SRX5402730 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:19 prefetch.2.10.7: 1) Downloading 'SRR8602964'... 2020-06-16T00:29:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:12 prefetch.2.10.7: 1) 'SRR8602964' was downloaded successfully Read 24353821 spots for SRR8602964/SRR8602964.sra Written 24353821 spots for SRR8602964/SRR8602964.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: 00:05:09 24353821 reads; of these: 24353821 (100.00%) were unpaired; of these: 3665307 (15.05%) aligned 0 times 18499183 (75.96%) aligned exactly 1 time 2189331 (8.99%) aligned >1 times 84.95% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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 12 files... [bam_rmdupse_core] 11637458 / 20688514 = 0.5625 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 09:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.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 09:43:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:10: 1000000 INFO @ Tue, 16 Jun 2020 09:43:16: 2000000 INFO @ Tue, 16 Jun 2020 09:43:22: 3000000 INFO @ Tue, 16 Jun 2020 09:43:29: 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 09:43:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.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 09:43:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:35: 5000000 INFO @ Tue, 16 Jun 2020 09:43:41: 1000000 INFO @ Tue, 16 Jun 2020 09:43:42: 6000000 INFO @ Tue, 16 Jun 2020 09:43:48: 2000000 INFO @ Tue, 16 Jun 2020 09:43:49: 7000000 INFO @ Tue, 16 Jun 2020 09:43:55: 3000000 INFO @ Tue, 16 Jun 2020 09:43:55: 8000000 INFO @ Tue, 16 Jun 2020 09:44:02: 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 09:44:02: 9000000 INFO @ Tue, 16 Jun 2020 09:44:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:02: #1 total tags in treatment: 9051056 INFO @ Tue, 16 Jun 2020 09:44:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:02: #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 09:44:03: #1 tags after filtering in treatment: 9051056 INFO @ Tue, 16 Jun 2020 09:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:04: #2 number of paired peaks: 4890 INFO @ Tue, 16 Jun 2020 09:44:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:04: #2 predicted fragment length is 189 bps INFO @ Tue, 16 Jun 2020 09:44:04: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 16 Jun 2020 09:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.05_model.r INFO @ Tue, 16 Jun 2020 09:44:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.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 09:44:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:09: 5000000 INFO @ Tue, 16 Jun 2020 09:44:12: 1000000 INFO @ Tue, 16 Jun 2020 09:44:16: 6000000 INFO @ Tue, 16 Jun 2020 09:44:20: 2000000 INFO @ Tue, 16 Jun 2020 09:44:23: 7000000 INFO @ Tue, 16 Jun 2020 09:44:28: 3000000 INFO @ Tue, 16 Jun 2020 09:44:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:30: 8000000 INFO @ Tue, 16 Jun 2020 09:44:36: 4000000 INFO @ Tue, 16 Jun 2020 09:44:37: 9000000 INFO @ Tue, 16 Jun 2020 09:44:38: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:38: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:38: #1 total tags in treatment: 9051056 INFO @ Tue, 16 Jun 2020 09:44:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:38: #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 09:44:38: #1 tags after filtering in treatment: 9051056 INFO @ Tue, 16 Jun 2020 09:44:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:39: #2 number of paired peaks: 4890 INFO @ Tue, 16 Jun 2020 09:44:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:39: #2 predicted fragment length is 189 bps INFO @ Tue, 16 Jun 2020 09:44:39: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 16 Jun 2020 09:44:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.10_model.r INFO @ Tue, 16 Jun 2020 09:44:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.05_summits.bed INFO @ Tue, 16 Jun 2020 09:44:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6607 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:44: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:44:51: 6000000 INFO @ Tue, 16 Jun 2020 09:44:59: 7000000 INFO @ Tue, 16 Jun 2020 09:45:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:06: 8000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:45:13: 9000000 INFO @ Tue, 16 Jun 2020 09:45:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:13: #1 total tags in treatment: 9051056 INFO @ Tue, 16 Jun 2020 09:45:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:13: #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 09:45:13: #1 tags after filtering in treatment: 9051056 INFO @ Tue, 16 Jun 2020 09:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:14: #2 number of paired peaks: 4890 INFO @ Tue, 16 Jun 2020 09:45:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:15: #2 predicted fragment length is 189 bps INFO @ Tue, 16 Jun 2020 09:45:15: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 16 Jun 2020 09:45:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.20_model.r INFO @ Tue, 16 Jun 2020 09:45:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.10_summits.bed INFO @ Tue, 16 Jun 2020 09:45:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5339 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402730/SRX5402730.20_summits.bed INFO @ Tue, 16 Jun 2020 09:45:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4299 records, 4 fields): 6 millis CompletedMACS2peakCalling