Job ID = 6366633 SRX = SRX2144180 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:23 prefetch.2.10.7: 1) Downloading 'SRR4188784'... 2020-06-15T22:57:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:53 prefetch.2.10.7: 'SRR4188784' is valid 2020-06-15T22:57:53 prefetch.2.10.7: 1) 'SRR4188784' was downloaded successfully Read 6729731 spots for SRR4188784/SRR4188784.sra Written 6729731 spots for SRR4188784/SRR4188784.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: 00:01:22 6729731 reads; of these: 6729731 (100.00%) were unpaired; of these: 1635568 (24.30%) aligned 0 times 4477996 (66.54%) aligned exactly 1 time 616167 (9.16%) aligned >1 times 75.70% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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] 340575 / 5094163 = 0.0669 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 08:01:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.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 08:01:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:27: 1000000 INFO @ Tue, 16 Jun 2020 08:01:32: 2000000 INFO @ Tue, 16 Jun 2020 08:01:38: 3000000 INFO @ Tue, 16 Jun 2020 08:01:44: 4000000 INFO @ Tue, 16 Jun 2020 08:01:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:01:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:01:48: #1 total tags in treatment: 4753588 INFO @ Tue, 16 Jun 2020 08:01:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:48: #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 08:01:48: #1 tags after filtering in treatment: 4753588 INFO @ Tue, 16 Jun 2020 08:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:48: #2 looking for paired plus/minus strand peaks... 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 08:01:49: #2 number of paired peaks: 2584 INFO @ Tue, 16 Jun 2020 08:01:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:49: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:01:49: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:01:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.05_model.r INFO @ Tue, 16 Jun 2020 08:01:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.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 08:01:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:56: 1000000 INFO @ Tue, 16 Jun 2020 08:02:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:02: 2000000 INFO @ Tue, 16 Jun 2020 08:02:08: 3000000 INFO @ Tue, 16 Jun 2020 08:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3079 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:13: 4000000 INFO @ Tue, 16 Jun 2020 08:02:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:18: #1 total tags in treatment: 4753588 INFO @ Tue, 16 Jun 2020 08:02:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:18: #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 08:02:18: #1 tags after filtering in treatment: 4753588 INFO @ Tue, 16 Jun 2020 08:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:18: #2 number of paired peaks: 2584 INFO @ Tue, 16 Jun 2020 08:02:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:18: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:02:18: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.10_model.r INFO @ Tue, 16 Jun 2020 08:02:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:18: #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 08:02:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.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 08:02:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:27: 1000000 INFO @ Tue, 16 Jun 2020 08:02:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:33: 2000000 INFO @ Tue, 16 Jun 2020 08:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.10_summits.bed INFO @ Tue, 16 Jun 2020 08:02:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1543 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:39: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:02:45: 4000000 INFO @ Tue, 16 Jun 2020 08:02:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:49: #1 total tags in treatment: 4753588 INFO @ Tue, 16 Jun 2020 08:02:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:49: #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 08:02:49: #1 tags after filtering in treatment: 4753588 INFO @ Tue, 16 Jun 2020 08:02:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:50: #2 number of paired peaks: 2584 INFO @ Tue, 16 Jun 2020 08:02:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:50: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:02:50: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:02:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.20_model.r INFO @ Tue, 16 Jun 2020 08:02:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144180/SRX2144180.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (589 records, 4 fields): 1 millis CompletedMACS2peakCalling