Job ID = 6366255 SRX = SRX094475 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:52:56 prefetch.2.10.7: 1) Downloading 'SRR340087'... 2020-06-15T22:52:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:53 prefetch.2.10.7: 'SRR340087' is valid 2020-06-15T22:53:53 prefetch.2.10.7: 1) 'SRR340087' was downloaded successfully Read 12796605 spots for SRR340087/SRR340087.sra Written 12796605 spots for SRR340087/SRR340087.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: 00:01:53 12796605 reads; of these: 12796605 (100.00%) were unpaired; of these: 2949296 (23.05%) aligned 0 times 8729340 (68.22%) aligned exactly 1 time 1117969 (8.74%) aligned >1 times 76.95% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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_rmdupse_core] 1039170 / 9847309 = 0.1055 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 07:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.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 07:59:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:11: 1000000 INFO @ Tue, 16 Jun 2020 07:59:16: 2000000 INFO @ Tue, 16 Jun 2020 07:59:21: 3000000 INFO @ Tue, 16 Jun 2020 07:59:26: 4000000 INFO @ Tue, 16 Jun 2020 07:59:31: 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 07:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.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 07:59:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:36: 6000000 INFO @ Tue, 16 Jun 2020 07:59:41: 1000000 INFO @ Tue, 16 Jun 2020 07:59:41: 7000000 INFO @ Tue, 16 Jun 2020 07:59:46: 2000000 INFO @ Tue, 16 Jun 2020 07:59:46: 8000000 INFO @ Tue, 16 Jun 2020 07:59:51: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:59:51: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:59:51: #1 total tags in treatment: 8808139 INFO @ Tue, 16 Jun 2020 07:59:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:51: #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 07:59:51: #1 tags after filtering in treatment: 8808139 INFO @ Tue, 16 Jun 2020 07:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:52: 3000000 INFO @ Tue, 16 Jun 2020 07:59:52: #2 number of paired peaks: 2842 INFO @ Tue, 16 Jun 2020 07:59:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:52: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 07:59:52: #2 alternative fragment length(s) may be 4,117,125 bps INFO @ Tue, 16 Jun 2020 07:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.05_model.r INFO @ Tue, 16 Jun 2020 07:59:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:57: 4000000 INFO @ Tue, 16 Jun 2020 08:00:02: 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 08:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.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 08:00:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:07: 6000000 INFO @ Tue, 16 Jun 2020 08:00:11: 1000000 INFO @ Tue, 16 Jun 2020 08:00:12: 7000000 INFO @ Tue, 16 Jun 2020 08:00:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:16: 2000000 INFO @ Tue, 16 Jun 2020 08:00:18: 8000000 INFO @ Tue, 16 Jun 2020 08:00:21: 3000000 INFO @ Tue, 16 Jun 2020 08:00:22: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:00:22: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:00:22: #1 total tags in treatment: 8808139 INFO @ Tue, 16 Jun 2020 08:00:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:22: #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 08:00:22: #1 tags after filtering in treatment: 8808139 INFO @ Tue, 16 Jun 2020 08:00:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:23: #2 number of paired peaks: 2842 INFO @ Tue, 16 Jun 2020 08:00:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:23: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:00:23: #2 alternative fragment length(s) may be 4,117,125 bps INFO @ Tue, 16 Jun 2020 08:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.10_model.r INFO @ Tue, 16 Jun 2020 08:00:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.05_summits.bed INFO @ Tue, 16 Jun 2020 08:00:25: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (12266 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:00:27: 4000000 INFO @ Tue, 16 Jun 2020 08:00:32: 5000000 INFO @ Tue, 16 Jun 2020 08:00:37: 6000000 INFO @ Tue, 16 Jun 2020 08:00:42: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:00:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:47: 8000000 INFO @ Tue, 16 Jun 2020 08:00:51: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:00:51: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:00:51: #1 total tags in treatment: 8808139 INFO @ Tue, 16 Jun 2020 08:00:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:51: #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 08:00:52: #1 tags after filtering in treatment: 8808139 INFO @ Tue, 16 Jun 2020 08:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:53: #2 number of paired peaks: 2842 INFO @ Tue, 16 Jun 2020 08:00:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:53: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:00:53: #2 alternative fragment length(s) may be 4,117,125 bps INFO @ Tue, 16 Jun 2020 08:00:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.20_model.r INFO @ Tue, 16 Jun 2020 08:00:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.10_summits.bed INFO @ Tue, 16 Jun 2020 08:00:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6515 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:01:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094475/SRX094475.20_summits.bed INFO @ Tue, 16 Jun 2020 08:01:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1602 records, 4 fields): 2 millis CompletedMACS2peakCalling