Job ID = 6507992 SRX = SRX743642 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:58:30 prefetch.2.10.7: 1) Downloading 'SRR1630857'... 2020-06-26T13:58:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:59:51 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:59:52 prefetch.2.10.7: 'SRR1630857' is valid 2020-06-26T13:59:52 prefetch.2.10.7: 1) 'SRR1630857' was downloaded successfully Read 8858052 spots for SRR1630857/SRR1630857.sra Written 8858052 spots for SRR1630857/SRR1630857.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: 00:02:32 8858052 reads; of these: 8858052 (100.00%) were unpaired; of these: 117959 (1.33%) aligned 0 times 8064158 (91.04%) aligned exactly 1 time 675935 (7.63%) aligned >1 times 98.67% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 1043916 / 8740093 = 0.1194 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 23:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.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 23:05:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:05:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:06:00: 1000000 INFO @ Fri, 26 Jun 2020 23:06:07: 2000000 INFO @ Fri, 26 Jun 2020 23:06:14: 3000000 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 23:06:22: 4000000 INFO @ Fri, 26 Jun 2020 23:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.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 23:06:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:06:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:06:29: 5000000 INFO @ Fri, 26 Jun 2020 23:06:30: 1000000 INFO @ Fri, 26 Jun 2020 23:06:37: 6000000 INFO @ Fri, 26 Jun 2020 23:06:38: 2000000 INFO @ Fri, 26 Jun 2020 23:06:45: 7000000 INFO @ Fri, 26 Jun 2020 23:06:45: 3000000 INFO @ Fri, 26 Jun 2020 23:06:50: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 23:06:50: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 23:06:50: #1 total tags in treatment: 7696177 INFO @ Fri, 26 Jun 2020 23:06:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:06:50: #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 23:06:50: #1 tags after filtering in treatment: 7696177 INFO @ Fri, 26 Jun 2020 23:06:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:06:50: #1 finished! INFO @ Fri, 26 Jun 2020 23:06:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:06:50: #2 looking for paired plus/minus strand peaks... 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 23:06:51: #2 number of paired peaks: 1929 INFO @ Fri, 26 Jun 2020 23:06:51: start model_add_line... INFO @ Fri, 26 Jun 2020 23:06:51: start X-correlation... INFO @ Fri, 26 Jun 2020 23:06:51: end of X-cor INFO @ Fri, 26 Jun 2020 23:06:51: #2 finished! INFO @ Fri, 26 Jun 2020 23:06:51: #2 predicted fragment length is 206 bps INFO @ Fri, 26 Jun 2020 23:06:51: #2 alternative fragment length(s) may be 3,206,223 bps INFO @ Fri, 26 Jun 2020 23:06:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.05_model.r INFO @ Fri, 26 Jun 2020 23:06:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:06:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:06:53: 4000000 INFO @ Fri, 26 Jun 2020 23:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.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 23:06:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:06:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:07:01: 5000000 INFO @ Fri, 26 Jun 2020 23:07:01: 1000000 INFO @ Fri, 26 Jun 2020 23:07:09: 6000000 INFO @ Fri, 26 Jun 2020 23:07:09: 2000000 INFO @ Fri, 26 Jun 2020 23:07:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:07:16: 7000000 INFO @ Fri, 26 Jun 2020 23:07:16: 3000000 INFO @ Fri, 26 Jun 2020 23:07:22: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 23:07:22: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 23:07:22: #1 total tags in treatment: 7696177 INFO @ Fri, 26 Jun 2020 23:07:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:07:22: #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 23:07:22: #1 tags after filtering in treatment: 7696177 INFO @ Fri, 26 Jun 2020 23:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:07:22: #1 finished! INFO @ Fri, 26 Jun 2020 23:07:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:07:23: #2 number of paired peaks: 1929 INFO @ Fri, 26 Jun 2020 23:07:23: start model_add_line... INFO @ Fri, 26 Jun 2020 23:07:23: start X-correlation... INFO @ Fri, 26 Jun 2020 23:07:23: end of X-cor INFO @ Fri, 26 Jun 2020 23:07:23: #2 finished! INFO @ Fri, 26 Jun 2020 23:07:23: #2 predicted fragment length is 206 bps INFO @ Fri, 26 Jun 2020 23:07:23: #2 alternative fragment length(s) may be 3,206,223 bps INFO @ Fri, 26 Jun 2020 23:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.10_model.r INFO @ Fri, 26 Jun 2020 23:07:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:07:24: 4000000 INFO @ Fri, 26 Jun 2020 23:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.05_summits.bed INFO @ Fri, 26 Jun 2020 23:07:27: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7968 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:07:31: 5000000 INFO @ Fri, 26 Jun 2020 23:07:38: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:07:46: 7000000 INFO @ Fri, 26 Jun 2020 23:07:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:07:50: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 23:07:50: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 23:07:50: #1 total tags in treatment: 7696177 INFO @ Fri, 26 Jun 2020 23:07:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:07:50: #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 23:07:51: #1 tags after filtering in treatment: 7696177 INFO @ Fri, 26 Jun 2020 23:07:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:07:51: #1 finished! INFO @ Fri, 26 Jun 2020 23:07:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:07:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:07:51: #2 number of paired peaks: 1929 INFO @ Fri, 26 Jun 2020 23:07:51: start model_add_line... INFO @ Fri, 26 Jun 2020 23:07:51: start X-correlation... INFO @ Fri, 26 Jun 2020 23:07:51: end of X-cor INFO @ Fri, 26 Jun 2020 23:07:51: #2 finished! INFO @ Fri, 26 Jun 2020 23:07:51: #2 predicted fragment length is 206 bps INFO @ Fri, 26 Jun 2020 23:07:51: #2 alternative fragment length(s) may be 3,206,223 bps INFO @ Fri, 26 Jun 2020 23:07:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.20_model.r INFO @ Fri, 26 Jun 2020 23:07:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:07:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.10_summits.bed INFO @ Fri, 26 Jun 2020 23:07:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3438 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:08:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743642/SRX743642.20_summits.bed INFO @ Fri, 26 Jun 2020 23:08:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (504 records, 4 fields): 2 millis CompletedMACS2peakCalling