Job ID = 6365913 SRX = SRX043846 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:40:51 prefetch.2.10.7: 1) Downloading 'SRR107301'... 2020-06-15T22:40:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:41:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:41:16 prefetch.2.10.7: 'SRR107301' is valid 2020-06-15T22:41:16 prefetch.2.10.7: 1) 'SRR107301' was downloaded successfully Read 4359117 spots for SRR107301/SRR107301.sra Written 4359117 spots for SRR107301/SRR107301.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:30 4359117 reads; of these: 4359117 (100.00%) were unpaired; of these: 1505873 (34.55%) aligned 0 times 2537245 (58.21%) aligned exactly 1 time 315999 (7.25%) aligned >1 times 65.45% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 247249 / 2853244 = 0.0867 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 07:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.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 07:43:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:16: 1000000 INFO @ Tue, 16 Jun 2020 07:43:22: 2000000 INFO @ Tue, 16 Jun 2020 07:43:25: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:43:25: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:43:25: #1 total tags in treatment: 2605995 INFO @ Tue, 16 Jun 2020 07:43:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:25: #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 07:43:25: #1 tags after filtering in treatment: 2605995 INFO @ Tue, 16 Jun 2020 07:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:25: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:25: #2 number of paired peaks: 2326 INFO @ Tue, 16 Jun 2020 07:43:25: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:25: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:25: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:25: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:25: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 07:43:25: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 16 Jun 2020 07:43:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.05_model.r INFO @ Tue, 16 Jun 2020 07:43:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.05_summits.bed INFO @ Tue, 16 Jun 2020 07:43:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2077 records, 4 fields): 4 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 07:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.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 07:43:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:45: 1000000 INFO @ Tue, 16 Jun 2020 07:43:50: 2000000 INFO @ Tue, 16 Jun 2020 07:43:53: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:43:53: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:43:53: #1 total tags in treatment: 2605995 INFO @ Tue, 16 Jun 2020 07:43:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:53: #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 07:43:53: #1 tags after filtering in treatment: 2605995 INFO @ Tue, 16 Jun 2020 07:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:54: #2 number of paired peaks: 2326 INFO @ Tue, 16 Jun 2020 07:43:54: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:54: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:54: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 07:43:54: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 16 Jun 2020 07:43:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.10_model.r INFO @ Tue, 16 Jun 2020 07:43:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.10_summits.bed INFO @ Tue, 16 Jun 2020 07:44:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (817 records, 4 fields): 3 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 07:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.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 07:44:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:15: 1000000 INFO @ Tue, 16 Jun 2020 07:44:20: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:44:23: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:44:23: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:44:23: #1 total tags in treatment: 2605995 INFO @ Tue, 16 Jun 2020 07:44:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:23: #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 07:44:23: #1 tags after filtering in treatment: 2605995 INFO @ Tue, 16 Jun 2020 07:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:24: #2 number of paired peaks: 2326 INFO @ Tue, 16 Jun 2020 07:44:24: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:24: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:24: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:24: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:24: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 07:44:24: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 16 Jun 2020 07:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.20_model.r INFO @ Tue, 16 Jun 2020 07:44:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:44:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043846/SRX043846.20_summits.bed INFO @ Tue, 16 Jun 2020 07:44:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 1 millis CompletedMACS2peakCalling