Job ID = 6368404 SRX = SRX495083 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:51 prefetch.2.10.7: 1) Downloading 'SRR1198615'... 2020-06-16T00:21:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:40 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:40 prefetch.2.10.7: 'SRR1198615' is valid 2020-06-16T00:22:40 prefetch.2.10.7: 1) 'SRR1198615' was downloaded successfully Read 7257325 spots for SRR1198615/SRR1198615.sra Written 7257325 spots for SRR1198615/SRR1198615.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: 00:01:32 7257325 reads; of these: 7257325 (100.00%) were unpaired; of these: 462752 (6.38%) aligned 0 times 5282248 (72.79%) aligned exactly 1 time 1512325 (20.84%) aligned >1 times 93.62% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 5013597 / 6794573 = 0.7379 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 09:26:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.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 09:26:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:19: 1000000 INFO @ Tue, 16 Jun 2020 09:26:25: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:25: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:25: #1 total tags in treatment: 1780976 INFO @ Tue, 16 Jun 2020 09:26:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:25: #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 09:26:25: #1 tags after filtering in treatment: 1780976 INFO @ Tue, 16 Jun 2020 09:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:25: #2 number of paired peaks: 1271 INFO @ Tue, 16 Jun 2020 09:26:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:25: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:26:25: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.05_model.r INFO @ Tue, 16 Jun 2020 09:26:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1614 records, 4 fields): 3 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 09:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.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 09:26:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:49: 1000000 INFO @ Tue, 16 Jun 2020 09:26:55: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:55: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:55: #1 total tags in treatment: 1780976 INFO @ Tue, 16 Jun 2020 09:26:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:55: #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 09:26:55: #1 tags after filtering in treatment: 1780976 INFO @ Tue, 16 Jun 2020 09:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:55: #2 number of paired peaks: 1271 INFO @ Tue, 16 Jun 2020 09:26:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:55: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:26:55: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.10_model.r INFO @ Tue, 16 Jun 2020 09:26:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (714 records, 4 fields): 2 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 09:27:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.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 09:27:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:19: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:25: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:27:25: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:27:25: #1 total tags in treatment: 1780976 INFO @ Tue, 16 Jun 2020 09:27:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:25: #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 09:27:25: #1 tags after filtering in treatment: 1780976 INFO @ Tue, 16 Jun 2020 09:27:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:25: #2 number of paired peaks: 1271 INFO @ Tue, 16 Jun 2020 09:27:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:25: #2 predicted fragment length is 151 bps INFO @ Tue, 16 Jun 2020 09:27:25: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 16 Jun 2020 09:27:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.20_model.r INFO @ Tue, 16 Jun 2020 09:27:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495083/SRX495083.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (297 records, 4 fields): 2 millis CompletedMACS2peakCalling