Job ID = 6367389 SRX = SRX331148 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:51 prefetch.2.10.7: 1) Downloading 'SRR947379'... 2020-06-15T23:27:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:02 prefetch.2.10.7: 'SRR947379' is valid 2020-06-15T23:29:02 prefetch.2.10.7: 1) 'SRR947379' was downloaded successfully Read 5485338 spots for SRR947379/SRR947379.sra Written 5485338 spots for SRR947379/SRR947379.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: 00:00:46 5485338 reads; of these: 5485338 (100.00%) were unpaired; of these: 1581867 (28.84%) aligned 0 times 3412122 (62.20%) aligned exactly 1 time 491349 (8.96%) aligned >1 times 71.16% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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_rmdupse_core] 811302 / 3903471 = 0.2078 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 08:31:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.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 08:31:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:21: 1000000 INFO @ Tue, 16 Jun 2020 08:31:26: 2000000 INFO @ Tue, 16 Jun 2020 08:31:30: 3000000 INFO @ Tue, 16 Jun 2020 08:31:30: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:30: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:30: #1 total tags in treatment: 3092169 INFO @ Tue, 16 Jun 2020 08:31:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:30: #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 08:31:30: #1 tags after filtering in treatment: 3092169 INFO @ Tue, 16 Jun 2020 08:31:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:31: #2 number of paired peaks: 1876 INFO @ Tue, 16 Jun 2020 08:31:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:31: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:31:31: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 08:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.05_model.r INFO @ Tue, 16 Jun 2020 08:31:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4491 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 08:31:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.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 08:31:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:51: 1000000 INFO @ Tue, 16 Jun 2020 08:31:55: 2000000 INFO @ Tue, 16 Jun 2020 08:32:00: 3000000 INFO @ Tue, 16 Jun 2020 08:32:00: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:00: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:00: #1 total tags in treatment: 3092169 INFO @ Tue, 16 Jun 2020 08:32:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:00: #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 08:32:00: #1 tags after filtering in treatment: 3092169 INFO @ Tue, 16 Jun 2020 08:32:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:00: #2 number of paired peaks: 1876 INFO @ Tue, 16 Jun 2020 08:32:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:01: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:32:01: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 08:32:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.10_model.r INFO @ Tue, 16 Jun 2020 08:32:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2412 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 08:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.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 08:32:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:21: 1000000 INFO @ Tue, 16 Jun 2020 08:32:26: 2000000 INFO @ Tue, 16 Jun 2020 08:32:30: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:31: #1 total tags in treatment: 3092169 INFO @ Tue, 16 Jun 2020 08:32:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:31: #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 08:32:31: #1 tags after filtering in treatment: 3092169 INFO @ Tue, 16 Jun 2020 08:32:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:31: #2 number of paired peaks: 1876 INFO @ Tue, 16 Jun 2020 08:32:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:31: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:32:31: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 08:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.20_model.r INFO @ Tue, 16 Jun 2020 08:32:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331148/SRX331148.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1019 records, 4 fields): 2 millis CompletedMACS2peakCalling