Job ID = 6507801 SRX = SRX466517 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:30:47 prefetch.2.10.7: 1) Downloading 'SRR1163583'... 2020-06-26T13:30:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:31:43 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:31:44 prefetch.2.10.7: 'SRR1163583' is valid 2020-06-26T13:31:44 prefetch.2.10.7: 1) 'SRR1163583' was downloaded successfully Read 6078767 spots for SRR1163583/SRR1163583.sra Written 6078767 spots for SRR1163583/SRR1163583.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: 00:01:10 6078767 reads; of these: 6078767 (100.00%) were unpaired; of these: 318901 (5.25%) aligned 0 times 5061662 (83.27%) aligned exactly 1 time 698204 (11.49%) aligned >1 times 94.75% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 1457267 / 5759866 = 0.2530 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 @ Fri, 26 Jun 2020 22:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.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 @ Fri, 26 Jun 2020 22:35:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:35:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:35:06: 1000000 INFO @ Fri, 26 Jun 2020 22:35:11: 2000000 INFO @ Fri, 26 Jun 2020 22:35:17: 3000000 INFO @ Fri, 26 Jun 2020 22:35:22: 4000000 INFO @ Fri, 26 Jun 2020 22:35:24: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:35:24: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:35:24: #1 total tags in treatment: 4302599 INFO @ Fri, 26 Jun 2020 22:35:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:35:24: #1 tags after filtering in treatment: 4302599 INFO @ Fri, 26 Jun 2020 22:35:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:35:24: #1 finished! INFO @ Fri, 26 Jun 2020 22:35:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:35:25: #2 number of paired peaks: 3393 INFO @ Fri, 26 Jun 2020 22:35:25: start model_add_line... INFO @ Fri, 26 Jun 2020 22:35:25: start X-correlation... INFO @ Fri, 26 Jun 2020 22:35:25: end of X-cor INFO @ Fri, 26 Jun 2020 22:35:25: #2 finished! INFO @ Fri, 26 Jun 2020 22:35:25: #2 predicted fragment length is 260 bps INFO @ Fri, 26 Jun 2020 22:35:25: #2 alternative fragment length(s) may be 260 bps INFO @ Fri, 26 Jun 2020 22:35:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.05_model.r INFO @ Fri, 26 Jun 2020 22:35:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:35:25: #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 @ Fri, 26 Jun 2020 22:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.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 @ Fri, 26 Jun 2020 22:35:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:35:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:35:36: 1000000 INFO @ Fri, 26 Jun 2020 22:35:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:35:42: 2000000 INFO @ Fri, 26 Jun 2020 22:35:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.05_summits.bed INFO @ Fri, 26 Jun 2020 22:35:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6330 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:35:48: 3000000 INFO @ Fri, 26 Jun 2020 22:35:54: 4000000 INFO @ Fri, 26 Jun 2020 22:35:56: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:35:56: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:35:56: #1 total tags in treatment: 4302599 INFO @ Fri, 26 Jun 2020 22:35:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:35:56: #1 tags after filtering in treatment: 4302599 INFO @ Fri, 26 Jun 2020 22:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:35:56: #1 finished! INFO @ Fri, 26 Jun 2020 22:35:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:35:57: #2 number of paired peaks: 3393 INFO @ Fri, 26 Jun 2020 22:35:57: start model_add_line... INFO @ Fri, 26 Jun 2020 22:35:57: start X-correlation... INFO @ Fri, 26 Jun 2020 22:35:57: end of X-cor INFO @ Fri, 26 Jun 2020 22:35:57: #2 finished! INFO @ Fri, 26 Jun 2020 22:35:57: #2 predicted fragment length is 260 bps INFO @ Fri, 26 Jun 2020 22:35:57: #2 alternative fragment length(s) may be 260 bps INFO @ Fri, 26 Jun 2020 22:35:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.10_model.r INFO @ Fri, 26 Jun 2020 22:35:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:35:57: #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 @ Fri, 26 Jun 2020 22:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.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 @ Fri, 26 Jun 2020 22:36:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:05: 1000000 INFO @ Fri, 26 Jun 2020 22:36:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:36:11: 2000000 INFO @ Fri, 26 Jun 2020 22:36:16: 3000000 INFO @ Fri, 26 Jun 2020 22:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.10_summits.bed INFO @ Fri, 26 Jun 2020 22:36:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3391 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:36:22: 4000000 INFO @ Fri, 26 Jun 2020 22:36:23: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:36:23: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:36:23: #1 total tags in treatment: 4302599 INFO @ Fri, 26 Jun 2020 22:36:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:36:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:36:23: #1 tags after filtering in treatment: 4302599 INFO @ Fri, 26 Jun 2020 22:36:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:36:23: #1 finished! INFO @ Fri, 26 Jun 2020 22:36:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:36:24: #2 number of paired peaks: 3393 INFO @ Fri, 26 Jun 2020 22:36:24: start model_add_line... INFO @ Fri, 26 Jun 2020 22:36:24: start X-correlation... INFO @ Fri, 26 Jun 2020 22:36:24: end of X-cor INFO @ Fri, 26 Jun 2020 22:36:24: #2 finished! INFO @ Fri, 26 Jun 2020 22:36:24: #2 predicted fragment length is 260 bps INFO @ Fri, 26 Jun 2020 22:36:24: #2 alternative fragment length(s) may be 260 bps INFO @ Fri, 26 Jun 2020 22:36:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.20_model.r INFO @ Fri, 26 Jun 2020 22:36:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:36:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:36:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466517/SRX466517.20_summits.bed INFO @ Fri, 26 Jun 2020 22:36:45: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1007 records, 4 fields): 3 millis CompletedMACS2peakCalling