Job ID = 6368320 SRX = SRX495003 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:09:39 prefetch.2.10.7: 1) Downloading 'SRR1198535'... 2020-06-16T00:09:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:10:29 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:10:30 prefetch.2.10.7: 'SRR1198535' is valid 2020-06-16T00:10:30 prefetch.2.10.7: 1) 'SRR1198535' was downloaded successfully Read 6972845 spots for SRR1198535/SRR1198535.sra Written 6972845 spots for SRR1198535/SRR1198535.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: 00:01:08 6972845 reads; of these: 6972845 (100.00%) were unpaired; of these: 196858 (2.82%) aligned 0 times 5677685 (81.43%) aligned exactly 1 time 1098302 (15.75%) aligned >1 times 97.18% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 1899300 / 6775987 = 0.2803 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 09:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.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 09:13:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:55: 1000000 INFO @ Tue, 16 Jun 2020 09:14:00: 2000000 INFO @ Tue, 16 Jun 2020 09:14:05: 3000000 INFO @ Tue, 16 Jun 2020 09:14:10: 4000000 INFO @ Tue, 16 Jun 2020 09:14:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:15: #1 total tags in treatment: 4876687 INFO @ Tue, 16 Jun 2020 09:14:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:15: #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 09:14:15: #1 tags after filtering in treatment: 4876687 INFO @ Tue, 16 Jun 2020 09:14:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:15: #2 number of paired peaks: 3891 INFO @ Tue, 16 Jun 2020 09:14:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:16: #2 predicted fragment length is 284 bps INFO @ Tue, 16 Jun 2020 09:14:16: #2 alternative fragment length(s) may be 284 bps INFO @ Tue, 16 Jun 2020 09:14:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.05_model.r INFO @ Tue, 16 Jun 2020 09:14:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:16: #3 Pre-compute pvalue-qvalue table... 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 09:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.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 09:14:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:25: 1000000 INFO @ Tue, 16 Jun 2020 09:14:30: 2000000 INFO @ Tue, 16 Jun 2020 09:14:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:35: 3000000 INFO @ Tue, 16 Jun 2020 09:14:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.05_summits.bed INFO @ Tue, 16 Jun 2020 09:14:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6209 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:40: 4000000 INFO @ Tue, 16 Jun 2020 09:14:45: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:45: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:45: #1 total tags in treatment: 4876687 INFO @ Tue, 16 Jun 2020 09:14:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:45: #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 09:14:45: #1 tags after filtering in treatment: 4876687 INFO @ Tue, 16 Jun 2020 09:14:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:45: #2 number of paired peaks: 3891 INFO @ Tue, 16 Jun 2020 09:14:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:45: #2 predicted fragment length is 284 bps INFO @ Tue, 16 Jun 2020 09:14:45: #2 alternative fragment length(s) may be 284 bps INFO @ Tue, 16 Jun 2020 09:14:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.10_model.r INFO @ Tue, 16 Jun 2020 09:14:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:45: #3 Pre-compute pvalue-qvalue table... 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 09:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.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 09:14:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:55: 1000000 INFO @ Tue, 16 Jun 2020 09:15:00: 2000000 INFO @ Tue, 16 Jun 2020 09:15:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:05: 3000000 INFO @ Tue, 16 Jun 2020 09:15:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3403 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:10: 4000000 INFO @ Tue, 16 Jun 2020 09:15:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:15:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:15:15: #1 total tags in treatment: 4876687 INFO @ Tue, 16 Jun 2020 09:15:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:15: #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 09:15:15: #1 tags after filtering in treatment: 4876687 INFO @ Tue, 16 Jun 2020 09:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:15: #2 number of paired peaks: 3891 INFO @ Tue, 16 Jun 2020 09:15:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:15: #2 predicted fragment length is 284 bps INFO @ Tue, 16 Jun 2020 09:15:15: #2 alternative fragment length(s) may be 284 bps INFO @ Tue, 16 Jun 2020 09:15:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.20_model.r INFO @ Tue, 16 Jun 2020 09:15:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:15:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495003/SRX495003.20_summits.bed INFO @ Tue, 16 Jun 2020 09:15:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1436 records, 4 fields): 4 millis CompletedMACS2peakCalling