Job ID = 6366577 SRX = SRX1995069 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:50:41 prefetch.2.10.7: 1) Downloading 'SRR3994001'... 2020-06-15T22:50:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:45 prefetch.2.10.7: 1) 'SRR3994001' was downloaded successfully Read 23762585 spots for SRR3994001/SRR3994001.sra Written 23762585 spots for SRR3994001/SRR3994001.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: 00:04:59 23762585 reads; of these: 23762585 (100.00%) were paired; of these: 21211499 (89.26%) aligned concordantly 0 times 1901431 (8.00%) aligned concordantly exactly 1 time 649655 (2.73%) aligned concordantly >1 times ---- 21211499 pairs aligned concordantly 0 times; of these: 28657 (0.14%) aligned discordantly 1 time ---- 21182842 pairs aligned 0 times concordantly or discordantly; of these: 42365684 mates make up the pairs; of these: 42296692 (99.84%) aligned 0 times 35740 (0.08%) aligned exactly 1 time 33252 (0.08%) aligned >1 times 11.00% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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_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] 1684249 / 2578202 = 0.6533 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 08:02:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.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 08:02:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:27: 1000000 INFO @ Tue, 16 Jun 2020 08:02:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:31: #1 total tags in treatment: 880682 INFO @ Tue, 16 Jun 2020 08:02:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:31: #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 08:02:31: #1 tags after filtering in treatment: 773207 INFO @ Tue, 16 Jun 2020 08:02:31: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 08:02:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:31: #2 number of paired peaks: 3045 INFO @ Tue, 16 Jun 2020 08:02:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:31: #2 predicted fragment length is 224 bps INFO @ Tue, 16 Jun 2020 08:02:31: #2 alternative fragment length(s) may be 4,188,206,224 bps INFO @ Tue, 16 Jun 2020 08:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.05_model.r INFO @ Tue, 16 Jun 2020 08:02:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 1 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 08:02:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.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 08:02:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:56: 1000000 INFO @ Tue, 16 Jun 2020 08:03:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:03:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:03:00: #1 total tags in treatment: 880682 INFO @ Tue, 16 Jun 2020 08:03:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:00: #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 08:03:00: #1 tags after filtering in treatment: 773207 INFO @ Tue, 16 Jun 2020 08:03:00: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 08:03:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:00: #2 number of paired peaks: 3045 INFO @ Tue, 16 Jun 2020 08:03:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:00: #2 predicted fragment length is 224 bps INFO @ Tue, 16 Jun 2020 08:03:00: #2 alternative fragment length(s) may be 4,188,206,224 bps INFO @ Tue, 16 Jun 2020 08:03:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.10_model.r INFO @ Tue, 16 Jun 2020 08:03:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.10_summits.bed INFO @ Tue, 16 Jun 2020 08:03:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (165 records, 4 fields): 1 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 08:03:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.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 08:03:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:26: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:03:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:03:29: #1 total tags in treatment: 880682 INFO @ Tue, 16 Jun 2020 08:03:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:29: #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 08:03:30: #1 tags after filtering in treatment: 773207 INFO @ Tue, 16 Jun 2020 08:03:30: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 08:03:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:30: #2 number of paired peaks: 3045 INFO @ Tue, 16 Jun 2020 08:03:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:30: #2 predicted fragment length is 224 bps INFO @ Tue, 16 Jun 2020 08:03:30: #2 alternative fragment length(s) may be 4,188,206,224 bps INFO @ Tue, 16 Jun 2020 08:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.20_model.r INFO @ Tue, 16 Jun 2020 08:03:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995069/SRX1995069.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 1 millis CompletedMACS2peakCalling