Job ID = 6368910 SRX = SRX6720177 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:48 prefetch.2.10.7: 1) Downloading 'SRR9972853'... 2020-06-16T00:28:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:31:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:31:52 prefetch.2.10.7: 1) 'SRR9972853' was downloaded successfully Read 22682876 spots for SRR9972853/SRR9972853.sra Written 22682876 spots for SRR9972853/SRR9972853.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: 00:04:49 22682876 reads; of these: 22682876 (100.00%) were unpaired; of these: 1053303 (4.64%) aligned 0 times 18405258 (81.14%) aligned exactly 1 time 3224315 (14.21%) aligned >1 times 95.36% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 10156516 / 21629573 = 0.4696 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 09:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.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 09:43:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:56: 1000000 INFO @ Tue, 16 Jun 2020 09:44:01: 2000000 INFO @ Tue, 16 Jun 2020 09:44:06: 3000000 INFO @ Tue, 16 Jun 2020 09:44:10: 4000000 INFO @ Tue, 16 Jun 2020 09:44:15: 5000000 INFO @ Tue, 16 Jun 2020 09:44:19: 6000000 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 09:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.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 09:44:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:24: 7000000 INFO @ Tue, 16 Jun 2020 09:44:27: 1000000 INFO @ Tue, 16 Jun 2020 09:44:29: 8000000 INFO @ Tue, 16 Jun 2020 09:44:33: 2000000 INFO @ Tue, 16 Jun 2020 09:44:33: 9000000 INFO @ Tue, 16 Jun 2020 09:44:38: 10000000 INFO @ Tue, 16 Jun 2020 09:44:38: 3000000 INFO @ Tue, 16 Jun 2020 09:44:43: 11000000 INFO @ Tue, 16 Jun 2020 09:44:43: 4000000 INFO @ Tue, 16 Jun 2020 09:44:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:45: #1 total tags in treatment: 11473057 INFO @ Tue, 16 Jun 2020 09:44:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:45: #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 09:44:45: #1 tags after filtering in treatment: 11473057 INFO @ Tue, 16 Jun 2020 09:44:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:46: #2 number of paired peaks: 1701 INFO @ Tue, 16 Jun 2020 09:44:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:46: #2 predicted fragment length is 166 bps INFO @ Tue, 16 Jun 2020 09:44:46: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 16 Jun 2020 09:44:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.05_model.r INFO @ Tue, 16 Jun 2020 09:44:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:49: 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 09:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.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 09:44:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:54: 6000000 INFO @ Tue, 16 Jun 2020 09:44:56: 1000000 INFO @ Tue, 16 Jun 2020 09:44:59: 7000000 INFO @ Tue, 16 Jun 2020 09:45:01: 2000000 INFO @ Tue, 16 Jun 2020 09:45:05: 8000000 INFO @ Tue, 16 Jun 2020 09:45:06: 3000000 INFO @ Tue, 16 Jun 2020 09:45:10: 9000000 INFO @ Tue, 16 Jun 2020 09:45:10: 4000000 INFO @ Tue, 16 Jun 2020 09:45:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:15: 5000000 INFO @ Tue, 16 Jun 2020 09:45:16: 10000000 INFO @ Tue, 16 Jun 2020 09:45:20: 6000000 INFO @ Tue, 16 Jun 2020 09:45:21: 11000000 INFO @ Tue, 16 Jun 2020 09:45:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:24: #1 total tags in treatment: 11473057 INFO @ Tue, 16 Jun 2020 09:45:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:24: #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 09:45:25: 7000000 INFO @ Tue, 16 Jun 2020 09:45:25: #1 tags after filtering in treatment: 11473057 INFO @ Tue, 16 Jun 2020 09:45:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:26: #2 number of paired peaks: 1701 INFO @ Tue, 16 Jun 2020 09:45:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:26: #2 predicted fragment length is 166 bps INFO @ Tue, 16 Jun 2020 09:45:26: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 16 Jun 2020 09:45:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.10_model.r INFO @ Tue, 16 Jun 2020 09:45:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.05_summits.bed INFO @ Tue, 16 Jun 2020 09:45:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5417 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:29: 8000000 INFO @ Tue, 16 Jun 2020 09:45:34: 9000000 INFO @ Tue, 16 Jun 2020 09:45:39: 10000000 INFO @ Tue, 16 Jun 2020 09:45:44: 11000000 INFO @ Tue, 16 Jun 2020 09:45:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:46: #1 total tags in treatment: 11473057 INFO @ Tue, 16 Jun 2020 09:45:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:46: #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 09:45:46: #1 tags after filtering in treatment: 11473057 INFO @ Tue, 16 Jun 2020 09:45:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:47: #2 number of paired peaks: 1701 INFO @ Tue, 16 Jun 2020 09:45:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:47: #2 predicted fragment length is 166 bps INFO @ Tue, 16 Jun 2020 09:45:47: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 16 Jun 2020 09:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.20_model.r INFO @ Tue, 16 Jun 2020 09:45:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:47: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.10_summits.bed INFO @ Tue, 16 Jun 2020 09:46:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3461 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720177/SRX6720177.20_summits.bed INFO @ Tue, 16 Jun 2020 09:46:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1804 records, 4 fields): 3 millis CompletedMACS2peakCalling