Job ID = 6366624 SRX = SRX2144171 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:53 prefetch.2.10.7: 1) Downloading 'SRR4188775'... 2020-06-15T23:00:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:24 prefetch.2.10.7: 'SRR4188775' is valid 2020-06-15T23:01:24 prefetch.2.10.7: 1) 'SRR4188775' was downloaded successfully Read 9709567 spots for SRR4188775/SRR4188775.sra Written 9709567 spots for SRR4188775/SRR4188775.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: 00:01:45 9709567 reads; of these: 9709567 (100.00%) were unpaired; of these: 3748021 (38.60%) aligned 0 times 5180922 (53.36%) aligned exactly 1 time 780624 (8.04%) aligned >1 times 61.40% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 1616219 / 5961546 = 0.2711 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 08:06:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.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 08:06:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:14: 1000000 INFO @ Tue, 16 Jun 2020 08:06:20: 2000000 INFO @ Tue, 16 Jun 2020 08:06:26: 3000000 INFO @ Tue, 16 Jun 2020 08:06:32: 4000000 INFO @ Tue, 16 Jun 2020 08:06:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:06:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:06:34: #1 total tags in treatment: 4345327 INFO @ Tue, 16 Jun 2020 08:06:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:34: #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 08:06:34: #1 tags after filtering in treatment: 4345327 INFO @ Tue, 16 Jun 2020 08:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:34: #2 number of paired peaks: 2971 INFO @ Tue, 16 Jun 2020 08:06:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:35: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:06:35: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.05_model.r INFO @ Tue, 16 Jun 2020 08:06:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:35: #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 08:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.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 08:06:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:45: 1000000 INFO @ Tue, 16 Jun 2020 08:06:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:51: 2000000 INFO @ Tue, 16 Jun 2020 08:06:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3718 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:57: 3000000 INFO @ Tue, 16 Jun 2020 08:07:03: 4000000 INFO @ Tue, 16 Jun 2020 08:07:04: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:07:04: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:07:04: #1 total tags in treatment: 4345327 INFO @ Tue, 16 Jun 2020 08:07:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:04: #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 08:07:05: #1 tags after filtering in treatment: 4345327 INFO @ Tue, 16 Jun 2020 08:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:05: #2 number of paired peaks: 2971 INFO @ Tue, 16 Jun 2020 08:07:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:05: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:07:05: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.10_model.r INFO @ Tue, 16 Jun 2020 08:07:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:05: #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 08:07:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.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 08:07:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:15: 1000000 INFO @ Tue, 16 Jun 2020 08:07:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:21: 2000000 INFO @ Tue, 16 Jun 2020 08:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1813 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:27: 3000000 INFO @ Tue, 16 Jun 2020 08:07:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:07:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:07:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:07:34: #1 total tags in treatment: 4345327 INFO @ Tue, 16 Jun 2020 08:07:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:34: #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 08:07:34: #1 tags after filtering in treatment: 4345327 INFO @ Tue, 16 Jun 2020 08:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:35: #2 number of paired peaks: 2971 INFO @ Tue, 16 Jun 2020 08:07:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:35: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:07:35: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:07:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.20_model.r INFO @ Tue, 16 Jun 2020 08:07:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144171/SRX2144171.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 2 millis CompletedMACS2peakCalling