Job ID = 6507961 SRX = SRX495120 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:56:11 prefetch.2.10.7: 1) Downloading 'SRR1198652'... 2020-06-26T12:56:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:58:38 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:58:38 prefetch.2.10.7: 1) 'SRR1198652' was downloaded successfully Read 19824579 spots for SRR1198652/SRR1198652.sra Written 19824579 spots for SRR1198652/SRR1198652.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: 00:04:08 19824579 reads; of these: 19824579 (100.00%) were unpaired; of these: 637178 (3.21%) aligned 0 times 16350418 (82.48%) aligned exactly 1 time 2836983 (14.31%) aligned >1 times 96.79% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12434765 / 19187401 = 0.6481 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 22:07:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.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 22:07:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:07:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:07:27: 1000000 INFO @ Fri, 26 Jun 2020 22:07:33: 2000000 INFO @ Fri, 26 Jun 2020 22:07:39: 3000000 INFO @ Fri, 26 Jun 2020 22:07:45: 4000000 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 22:07:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.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 22:07:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:07:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:07:51: 5000000 INFO @ Fri, 26 Jun 2020 22:07:58: 1000000 INFO @ Fri, 26 Jun 2020 22:07:58: 6000000 INFO @ Fri, 26 Jun 2020 22:08:03: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:08:03: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:08:03: #1 total tags in treatment: 6752636 INFO @ Fri, 26 Jun 2020 22:08:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:08:03: #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 22:08:03: #1 tags after filtering in treatment: 6752636 INFO @ Fri, 26 Jun 2020 22:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:08:03: #1 finished! INFO @ Fri, 26 Jun 2020 22:08:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:08:03: #2 number of paired peaks: 2044 INFO @ Fri, 26 Jun 2020 22:08:03: start model_add_line... INFO @ Fri, 26 Jun 2020 22:08:03: start X-correlation... INFO @ Fri, 26 Jun 2020 22:08:03: end of X-cor INFO @ Fri, 26 Jun 2020 22:08:03: #2 finished! INFO @ Fri, 26 Jun 2020 22:08:03: #2 predicted fragment length is 196 bps INFO @ Fri, 26 Jun 2020 22:08:03: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 26 Jun 2020 22:08:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.05_model.r INFO @ Fri, 26 Jun 2020 22:08:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:08:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:08:04: 2000000 INFO @ Fri, 26 Jun 2020 22:08:10: 3000000 INFO @ Fri, 26 Jun 2020 22:08:16: 4000000 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 22:08:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.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 22:08:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:08:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:08:22: 5000000 INFO @ Fri, 26 Jun 2020 22:08:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:08:27: 1000000 INFO @ Fri, 26 Jun 2020 22:08:28: 6000000 INFO @ Fri, 26 Jun 2020 22:08:33: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:08:33: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:08:33: #1 total tags in treatment: 6752636 INFO @ Fri, 26 Jun 2020 22:08:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:08:33: #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 22:08:33: #1 tags after filtering in treatment: 6752636 INFO @ Fri, 26 Jun 2020 22:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:08:33: #1 finished! INFO @ Fri, 26 Jun 2020 22:08:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.05_summits.bed INFO @ Fri, 26 Jun 2020 22:08:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4064 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:08:33: #2 number of paired peaks: 2044 INFO @ Fri, 26 Jun 2020 22:08:33: start model_add_line... INFO @ Fri, 26 Jun 2020 22:08:33: start X-correlation... INFO @ Fri, 26 Jun 2020 22:08:33: end of X-cor INFO @ Fri, 26 Jun 2020 22:08:33: #2 finished! INFO @ Fri, 26 Jun 2020 22:08:33: #2 predicted fragment length is 196 bps INFO @ Fri, 26 Jun 2020 22:08:33: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 26 Jun 2020 22:08:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.10_model.r INFO @ Fri, 26 Jun 2020 22:08:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:08:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:08:34: 2000000 INFO @ Fri, 26 Jun 2020 22:08:40: 3000000 INFO @ Fri, 26 Jun 2020 22:08:47: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:08:53: 5000000 INFO @ Fri, 26 Jun 2020 22:08:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:08:59: 6000000 INFO @ Fri, 26 Jun 2020 22:09:04: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:09:04: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:09:04: #1 total tags in treatment: 6752636 INFO @ Fri, 26 Jun 2020 22:09:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:09:04: #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 22:09:04: #1 tags after filtering in treatment: 6752636 INFO @ Fri, 26 Jun 2020 22:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:09:04: #1 finished! INFO @ Fri, 26 Jun 2020 22:09:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:09:04: #2 number of paired peaks: 2044 INFO @ Fri, 26 Jun 2020 22:09:04: start model_add_line... INFO @ Fri, 26 Jun 2020 22:09:05: start X-correlation... INFO @ Fri, 26 Jun 2020 22:09:05: end of X-cor INFO @ Fri, 26 Jun 2020 22:09:05: #2 finished! INFO @ Fri, 26 Jun 2020 22:09:05: #2 predicted fragment length is 196 bps INFO @ Fri, 26 Jun 2020 22:09:05: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 26 Jun 2020 22:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.20_model.r INFO @ Fri, 26 Jun 2020 22:09:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:09:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.10_summits.bed INFO @ Fri, 26 Jun 2020 22:09:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2051 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:09:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:09:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:09:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:09:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495120/SRX495120.20_summits.bed INFO @ Fri, 26 Jun 2020 22:09:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (753 records, 4 fields): 3 millis CompletedMACS2peakCalling