Job ID = 6368704 SRX = SRX5402728 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:32:45 prefetch.2.10.7: 1) Downloading 'SRR8602962'... 2020-06-16T00:32:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:15 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:15 prefetch.2.10.7: 1) 'SRR8602962' was downloaded successfully Read 23847839 spots for SRR8602962/SRR8602962.sra Written 23847839 spots for SRR8602962/SRR8602962.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: 00:04:56 23847839 reads; of these: 23847839 (100.00%) were unpaired; of these: 2876300 (12.06%) aligned 0 times 18799871 (78.83%) aligned exactly 1 time 2171668 (9.11%) aligned >1 times 87.94% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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] 9003904 / 20971539 = 0.4293 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 09:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.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 09:46:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:12: 1000000 INFO @ Tue, 16 Jun 2020 09:46:18: 2000000 INFO @ Tue, 16 Jun 2020 09:46:23: 3000000 INFO @ Tue, 16 Jun 2020 09:46:28: 4000000 INFO @ Tue, 16 Jun 2020 09:46:33: 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 09:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.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 09:46:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:38: 6000000 INFO @ Tue, 16 Jun 2020 09:46:43: 1000000 INFO @ Tue, 16 Jun 2020 09:46:43: 7000000 INFO @ Tue, 16 Jun 2020 09:46:49: 2000000 INFO @ Tue, 16 Jun 2020 09:46:49: 8000000 INFO @ Tue, 16 Jun 2020 09:46:54: 3000000 INFO @ Tue, 16 Jun 2020 09:46:54: 9000000 INFO @ Tue, 16 Jun 2020 09:47:00: 4000000 INFO @ Tue, 16 Jun 2020 09:47:00: 10000000 INFO @ Tue, 16 Jun 2020 09:47:05: 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 09:47:06: 11000000 INFO @ Tue, 16 Jun 2020 09:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.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 09:47:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:11: 6000000 INFO @ Tue, 16 Jun 2020 09:47:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:11: #1 total tags in treatment: 11967635 INFO @ Tue, 16 Jun 2020 09:47:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:11: #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 09:47:11: #1 tags after filtering in treatment: 11967635 INFO @ Tue, 16 Jun 2020 09:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:13: #2 number of paired peaks: 5026 INFO @ Tue, 16 Jun 2020 09:47:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:13: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 09:47:13: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 09:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.05_model.r INFO @ Tue, 16 Jun 2020 09:47:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:13: 1000000 INFO @ Tue, 16 Jun 2020 09:47:16: 7000000 INFO @ Tue, 16 Jun 2020 09:47:18: 2000000 INFO @ Tue, 16 Jun 2020 09:47:22: 8000000 INFO @ Tue, 16 Jun 2020 09:47:24: 3000000 INFO @ Tue, 16 Jun 2020 09:47:28: 9000000 INFO @ Tue, 16 Jun 2020 09:47:29: 4000000 INFO @ Tue, 16 Jun 2020 09:47:33: 10000000 INFO @ Tue, 16 Jun 2020 09:47:35: 5000000 INFO @ Tue, 16 Jun 2020 09:47:39: 11000000 INFO @ Tue, 16 Jun 2020 09:47:40: 6000000 INFO @ Tue, 16 Jun 2020 09:47:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:44: #1 total tags in treatment: 11967635 INFO @ Tue, 16 Jun 2020 09:47:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:44: #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 09:47:44: #1 tags after filtering in treatment: 11967635 INFO @ Tue, 16 Jun 2020 09:47:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:46: #2 number of paired peaks: 5026 INFO @ Tue, 16 Jun 2020 09:47:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:46: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 09:47:46: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 09:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.10_model.r INFO @ Tue, 16 Jun 2020 09:47:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:46: 7000000 INFO @ Tue, 16 Jun 2020 09:47:51: 8000000 INFO @ Tue, 16 Jun 2020 09:47:57: 9000000 INFO @ Tue, 16 Jun 2020 09:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.05_summits.bed INFO @ Tue, 16 Jun 2020 09:47:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7970 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:02: 10000000 INFO @ Tue, 16 Jun 2020 09:48:08: 11000000 INFO @ Tue, 16 Jun 2020 09:48:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:48:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:48:13: #1 total tags in treatment: 11967635 INFO @ Tue, 16 Jun 2020 09:48:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:13: #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 09:48:14: #1 tags after filtering in treatment: 11967635 INFO @ Tue, 16 Jun 2020 09:48:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:15: #2 number of paired peaks: 5026 INFO @ Tue, 16 Jun 2020 09:48:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:15: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 09:48:15: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 09:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.20_model.r INFO @ Tue, 16 Jun 2020 09:48:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:48:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.10_summits.bed INFO @ Tue, 16 Jun 2020 09:48:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6425 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402728/SRX5402728.20_summits.bed INFO @ Tue, 16 Jun 2020 09:49:00: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5031 records, 4 fields): 6 millis CompletedMACS2peakCalling