Job ID = 6368132 SRX = SRX467179 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:05:46 prefetch.2.10.7: 1) Downloading 'SRR1164603'... 2020-06-16T00:05:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:06:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:06:50 prefetch.2.10.7: 'SRR1164603' is valid 2020-06-16T00:06:50 prefetch.2.10.7: 1) 'SRR1164603' was downloaded successfully Read 7588464 spots for SRR1164603/SRR1164603.sra Written 7588464 spots for SRR1164603/SRR1164603.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: 00:00:59 7588464 reads; of these: 7588464 (100.00%) were unpaired; of these: 2777985 (36.61%) aligned 0 times 4042276 (53.27%) aligned exactly 1 time 768203 (10.12%) aligned >1 times 63.39% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 539576 / 4810479 = 0.1122 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 09:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.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 09:09:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:44: 1000000 INFO @ Tue, 16 Jun 2020 09:09:49: 2000000 INFO @ Tue, 16 Jun 2020 09:09:54: 3000000 INFO @ Tue, 16 Jun 2020 09:09:58: 4000000 INFO @ Tue, 16 Jun 2020 09:10:00: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:10:00: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:10:00: #1 total tags in treatment: 4270903 INFO @ Tue, 16 Jun 2020 09:10:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:00: #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 09:10:00: #1 tags after filtering in treatment: 4270903 INFO @ Tue, 16 Jun 2020 09:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:00: #2 number of paired peaks: 1516 INFO @ Tue, 16 Jun 2020 09:10:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:00: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:10:00: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 09:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.05_model.r INFO @ Tue, 16 Jun 2020 09:10:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:00: #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 09:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.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 09:10:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:14: 1000000 INFO @ Tue, 16 Jun 2020 09:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4192 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:18: 2000000 INFO @ Tue, 16 Jun 2020 09:10:23: 3000000 INFO @ Tue, 16 Jun 2020 09:10:28: 4000000 INFO @ Tue, 16 Jun 2020 09:10:29: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:10:29: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:10:29: #1 total tags in treatment: 4270903 INFO @ Tue, 16 Jun 2020 09:10:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:29: #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 09:10:29: #1 tags after filtering in treatment: 4270903 INFO @ Tue, 16 Jun 2020 09:10:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:29: #2 number of paired peaks: 1516 INFO @ Tue, 16 Jun 2020 09:10:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:29: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:10:29: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 09:10:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.10_model.r INFO @ Tue, 16 Jun 2020 09:10:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:29: #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 09:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.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 09:10:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:44: 1000000 INFO @ Tue, 16 Jun 2020 09:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.10_summits.bed INFO @ Tue, 16 Jun 2020 09:10:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2958 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:49: 2000000 INFO @ Tue, 16 Jun 2020 09:10:54: 3000000 INFO @ Tue, 16 Jun 2020 09:10:59: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:00: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:11:00: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:11:00: #1 total tags in treatment: 4270903 INFO @ Tue, 16 Jun 2020 09:11:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:00: #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 09:11:00: #1 tags after filtering in treatment: 4270903 INFO @ Tue, 16 Jun 2020 09:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:01: #2 number of paired peaks: 1516 INFO @ Tue, 16 Jun 2020 09:11:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:01: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:11:01: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 09:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.20_model.r INFO @ Tue, 16 Jun 2020 09:11:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467179/SRX467179.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1805 records, 4 fields): 3 millis CompletedMACS2peakCalling