Job ID = 6365944 SRX = SRX043876 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:32:51 prefetch.2.10.7: 1) Downloading 'SRR107348'... 2020-06-15T22:32:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:27 prefetch.2.10.7: 'SRR107348' is valid 2020-06-15T22:33:27 prefetch.2.10.7: 1) 'SRR107348' was downloaded successfully Read 3599715 spots for SRR107348/SRR107348.sra Written 3599715 spots for SRR107348/SRR107348.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: 00:00:32 3599715 reads; of these: 3599715 (100.00%) were unpaired; of these: 977812 (27.16%) aligned 0 times 2338307 (64.96%) aligned exactly 1 time 283596 (7.88%) aligned >1 times 72.84% overall alignment rate Time searching: 00:00:32 Overall time: 00:00:32 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] 341706 / 2621903 = 0.1303 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 07:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.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 07:35:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:29: 1000000 INFO @ Tue, 16 Jun 2020 07:35:35: 2000000 INFO @ Tue, 16 Jun 2020 07:35:36: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:35:36: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:35:36: #1 total tags in treatment: 2280197 INFO @ Tue, 16 Jun 2020 07:35:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:36: #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 07:35:36: #1 tags after filtering in treatment: 2280197 INFO @ Tue, 16 Jun 2020 07:35:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:36: #2 number of paired peaks: 3350 INFO @ Tue, 16 Jun 2020 07:35:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:37: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 07:35:37: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 07:35:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.05_model.r INFO @ Tue, 16 Jun 2020 07:35:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:35:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.05_summits.bed INFO @ Tue, 16 Jun 2020 07:35:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3199 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 07:35:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.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 07:35:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:59: 1000000 INFO @ Tue, 16 Jun 2020 07:36:05: 2000000 INFO @ Tue, 16 Jun 2020 07:36:06: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:36:06: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:36:06: #1 total tags in treatment: 2280197 INFO @ Tue, 16 Jun 2020 07:36:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:06: #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 07:36:06: #1 tags after filtering in treatment: 2280197 INFO @ Tue, 16 Jun 2020 07:36:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:07: #2 number of paired peaks: 3350 INFO @ Tue, 16 Jun 2020 07:36:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:07: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 07:36:07: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 07:36:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.10_model.r INFO @ Tue, 16 Jun 2020 07:36:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.10_summits.bed INFO @ Tue, 16 Jun 2020 07:36:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1308 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 07:36:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.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 07:36:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:36:34: 2000000 INFO @ Tue, 16 Jun 2020 07:36:36: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:36:36: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:36:36: #1 total tags in treatment: 2280197 INFO @ Tue, 16 Jun 2020 07:36:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:36: #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 07:36:36: #1 tags after filtering in treatment: 2280197 INFO @ Tue, 16 Jun 2020 07:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:36: #2 number of paired peaks: 3350 INFO @ Tue, 16 Jun 2020 07:36:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:36: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 07:36:36: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 07:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.20_model.r INFO @ Tue, 16 Jun 2020 07:36:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:36:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043876/SRX043876.20_summits.bed INFO @ Tue, 16 Jun 2020 07:36:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (330 records, 4 fields): 2 millis CompletedMACS2peakCalling