Job ID = 6366691 SRX = SRX2228847 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:08 prefetch.2.10.7: 1) Downloading 'SRR4380303'... 2020-06-15T23:04:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:54 prefetch.2.10.7: 'SRR4380303' is valid 2020-06-15T23:04:54 prefetch.2.10.7: 1) 'SRR4380303' was downloaded successfully Read 20144069 spots for SRR4380303/SRR4380303.sra Written 20144069 spots for SRR4380303/SRR4380303.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: 00:03:20 20144069 reads; of these: 20144069 (100.00%) were unpaired; of these: 1900209 (9.43%) aligned 0 times 15069214 (74.81%) aligned exactly 1 time 3174646 (15.76%) aligned >1 times 90.57% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 14103235 / 18243860 = 0.7730 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 08:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.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 08:11:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:59: 1000000 INFO @ Tue, 16 Jun 2020 08:12:05: 2000000 INFO @ Tue, 16 Jun 2020 08:12:11: 3000000 INFO @ Tue, 16 Jun 2020 08:12:17: 4000000 INFO @ Tue, 16 Jun 2020 08:12:17: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:12:17: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:12:17: #1 total tags in treatment: 4140625 INFO @ Tue, 16 Jun 2020 08:12:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:17: #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 08:12:18: #1 tags after filtering in treatment: 4140625 INFO @ Tue, 16 Jun 2020 08:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:18: #2 number of paired peaks: 1015 INFO @ Tue, 16 Jun 2020 08:12:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:18: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:12:18: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 16 Jun 2020 08:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.05_model.r INFO @ Tue, 16 Jun 2020 08:12:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:18: #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 08:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.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 08:12:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:29: 1000000 INFO @ Tue, 16 Jun 2020 08:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.05_summits.bed INFO @ Tue, 16 Jun 2020 08:12:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1037 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:35: 2000000 INFO @ Tue, 16 Jun 2020 08:12:40: 3000000 INFO @ Tue, 16 Jun 2020 08:12:46: 4000000 INFO @ Tue, 16 Jun 2020 08:12:47: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:12:47: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:12:47: #1 total tags in treatment: 4140625 INFO @ Tue, 16 Jun 2020 08:12:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:47: #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 08:12:47: #1 tags after filtering in treatment: 4140625 INFO @ Tue, 16 Jun 2020 08:12:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:47: #2 number of paired peaks: 1015 INFO @ Tue, 16 Jun 2020 08:12:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:47: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:12:47: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 16 Jun 2020 08:12:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.10_model.r INFO @ Tue, 16 Jun 2020 08:12:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:47: #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 08:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.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 08:12:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:59: 1000000 INFO @ Tue, 16 Jun 2020 08:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.10_summits.bed INFO @ Tue, 16 Jun 2020 08:13:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:05: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:13:11: 3000000 INFO @ Tue, 16 Jun 2020 08:13:16: 4000000 INFO @ Tue, 16 Jun 2020 08:13:17: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:13:17: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:13:17: #1 total tags in treatment: 4140625 INFO @ Tue, 16 Jun 2020 08:13:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:17: #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 08:13:17: #1 tags after filtering in treatment: 4140625 INFO @ Tue, 16 Jun 2020 08:13:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:17: #2 number of paired peaks: 1015 INFO @ Tue, 16 Jun 2020 08:13:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:18: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:13:18: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 16 Jun 2020 08:13:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.20_model.r INFO @ Tue, 16 Jun 2020 08:13:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:13:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228847/SRX2228847.20_summits.bed INFO @ Tue, 16 Jun 2020 08:13:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (353 records, 4 fields): 1 millis CompletedMACS2peakCalling