Job ID = 6507715 SRX = SRX1010106 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:28:02 prefetch.2.10.7: 1) Downloading 'SRR1998062'... 2020-06-26T13:28:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:28:36 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:28:36 prefetch.2.10.7: 'SRR1998062' is valid 2020-06-26T13:28:36 prefetch.2.10.7: 1) 'SRR1998062' was downloaded successfully Read 1846797 spots for SRR1998062/SRR1998062.sra Written 1846797 spots for SRR1998062/SRR1998062.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: 00:02:53 1846797 reads; of these: 1846797 (100.00%) were paired; of these: 1012119 (54.80%) aligned concordantly 0 times 576823 (31.23%) aligned concordantly exactly 1 time 257855 (13.96%) aligned concordantly >1 times ---- 1012119 pairs aligned concordantly 0 times; of these: 137150 (13.55%) aligned discordantly 1 time ---- 874969 pairs aligned 0 times concordantly or discordantly; of these: 1749938 mates make up the pairs; of these: 1047447 (59.86%) aligned 0 times 274572 (15.69%) aligned exactly 1 time 427919 (24.45%) aligned >1 times 71.64% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 329961 / 880636 = 0.3747 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 @ Fri, 26 Jun 2020 22:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.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 @ Fri, 26 Jun 2020 22:32:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:32:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:01: 1000000 INFO @ Fri, 26 Jun 2020 22:33:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:33:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:33:06: #1 total tags in treatment: 521322 INFO @ Fri, 26 Jun 2020 22:33:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:33:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:33:06: #1 tags after filtering in treatment: 458550 INFO @ Fri, 26 Jun 2020 22:33:06: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 22:33:06: #1 finished! INFO @ Fri, 26 Jun 2020 22:33:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:33:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:33:06: #2 number of paired peaks: 1826 INFO @ Fri, 26 Jun 2020 22:33:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:33:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:33:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:33:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:33:06: #2 predicted fragment length is 237 bps INFO @ Fri, 26 Jun 2020 22:33:06: #2 alternative fragment length(s) may be 237 bps INFO @ Fri, 26 Jun 2020 22:33:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.05_model.r INFO @ Fri, 26 Jun 2020 22:33:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:33:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:33:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:33:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:33:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:33:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.05_summits.bed INFO @ Fri, 26 Jun 2020 22:33:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1274 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 @ Fri, 26 Jun 2020 22:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.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 @ Fri, 26 Jun 2020 22:33:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:31: 1000000 INFO @ Fri, 26 Jun 2020 22:33:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:33:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:33:36: #1 total tags in treatment: 521322 INFO @ Fri, 26 Jun 2020 22:33:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:33:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:33:36: #1 tags after filtering in treatment: 458550 INFO @ Fri, 26 Jun 2020 22:33:36: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 22:33:36: #1 finished! INFO @ Fri, 26 Jun 2020 22:33:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:33:36: #2 number of paired peaks: 1826 INFO @ Fri, 26 Jun 2020 22:33:36: start model_add_line... INFO @ Fri, 26 Jun 2020 22:33:36: start X-correlation... INFO @ Fri, 26 Jun 2020 22:33:36: end of X-cor INFO @ Fri, 26 Jun 2020 22:33:36: #2 finished! INFO @ Fri, 26 Jun 2020 22:33:36: #2 predicted fragment length is 237 bps INFO @ Fri, 26 Jun 2020 22:33:36: #2 alternative fragment length(s) may be 237 bps INFO @ Fri, 26 Jun 2020 22:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.10_model.r INFO @ Fri, 26 Jun 2020 22:33:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:33:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:33:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:33:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:33:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.10_summits.bed INFO @ Fri, 26 Jun 2020 22:33:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (988 records, 4 fields): 5 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 @ Fri, 26 Jun 2020 22:33:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.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 @ Fri, 26 Jun 2020 22:33:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:34:01: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:34:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:34:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:34:06: #1 total tags in treatment: 521322 INFO @ Fri, 26 Jun 2020 22:34:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:34:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:34:06: #1 tags after filtering in treatment: 458550 INFO @ Fri, 26 Jun 2020 22:34:06: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 22:34:06: #1 finished! INFO @ Fri, 26 Jun 2020 22:34:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:34:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:34:06: #2 number of paired peaks: 1826 INFO @ Fri, 26 Jun 2020 22:34:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:34:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:34:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:34:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:34:06: #2 predicted fragment length is 237 bps INFO @ Fri, 26 Jun 2020 22:34:06: #2 alternative fragment length(s) may be 237 bps INFO @ Fri, 26 Jun 2020 22:34:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.20_model.r INFO @ Fri, 26 Jun 2020 22:34:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:34:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:34:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:34:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:34:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:34:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1010106/SRX1010106.20_summits.bed INFO @ Fri, 26 Jun 2020 22:34:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (655 records, 4 fields): 2 millis CompletedMACS2peakCalling