Job ID = 6367576 SRX = SRX331332 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:37 prefetch.2.10.7: 1) Downloading 'SRR947569'... 2020-06-15T23:28:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:17 prefetch.2.10.7: 'SRR947569' is valid 2020-06-15T23:29:17 prefetch.2.10.7: 1) 'SRR947569' was downloaded successfully Read 4833160 spots for SRR947569/SRR947569.sra Written 4833160 spots for SRR947569/SRR947569.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: 00:00:26 4833160 reads; of these: 4833160 (100.00%) were unpaired; of these: 3089927 (63.93%) aligned 0 times 1531224 (31.68%) aligned exactly 1 time 212009 (4.39%) aligned >1 times 36.07% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 162416 / 1743233 = 0.0932 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 08:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.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 08:30:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:51: 1000000 INFO @ Tue, 16 Jun 2020 08:30:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:54: #1 total tags in treatment: 1580817 INFO @ Tue, 16 Jun 2020 08:30:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:54: #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 08:30:54: #1 tags after filtering in treatment: 1580817 INFO @ Tue, 16 Jun 2020 08:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:54: #2 number of paired peaks: 2325 INFO @ Tue, 16 Jun 2020 08:30:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:54: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:30:54: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 16 Jun 2020 08:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.05_model.r INFO @ Tue, 16 Jun 2020 08:30:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3394 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 08:31:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.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 08:31:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:22: 1000000 INFO @ Tue, 16 Jun 2020 08:31:26: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:26: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:26: #1 total tags in treatment: 1580817 INFO @ Tue, 16 Jun 2020 08:31:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:26: #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 08:31:26: #1 tags after filtering in treatment: 1580817 INFO @ Tue, 16 Jun 2020 08:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:26: #2 number of paired peaks: 2325 INFO @ Tue, 16 Jun 2020 08:31:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:26: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:31:26: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 16 Jun 2020 08:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.10_model.r INFO @ Tue, 16 Jun 2020 08:31:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1794 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.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 08:31:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:51: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:54: #1 total tags in treatment: 1580817 INFO @ Tue, 16 Jun 2020 08:31:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:54: #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 08:31:54: #1 tags after filtering in treatment: 1580817 INFO @ Tue, 16 Jun 2020 08:31:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:54: #2 number of paired peaks: 2325 INFO @ Tue, 16 Jun 2020 08:31:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:54: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:31:54: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 16 Jun 2020 08:31:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.20_model.r INFO @ Tue, 16 Jun 2020 08:31:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:31:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331332/SRX331332.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (745 records, 4 fields): 2 millis CompletedMACS2peakCalling