Job ID = 6497330 SRX = SRX1010108 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:00:27 prefetch.2.10.7: 1) Downloading 'SRR1998064'... 2020-06-25T22:00:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:02:42 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:02:42 prefetch.2.10.7: 1) 'SRR1998064' was downloaded successfully Read 4692533 spots for SRR1998064/SRR1998064.sra Written 4692533 spots for SRR1998064/SRR1998064.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: 00:12:05 4692533 reads; of these: 4692533 (100.00%) were paired; of these: 2003930 (42.70%) aligned concordantly 0 times 1442912 (30.75%) aligned concordantly exactly 1 time 1245691 (26.55%) aligned concordantly >1 times ---- 2003930 pairs aligned concordantly 0 times; of these: 317938 (15.87%) aligned discordantly 1 time ---- 1685992 pairs aligned 0 times concordantly or discordantly; of these: 3371984 mates make up the pairs; of these: 2252280 (66.79%) aligned 0 times 515855 (15.30%) aligned exactly 1 time 603849 (17.91%) aligned >1 times 76.00% overall alignment rate Time searching: 00:12:05 Overall time: 00:12:05 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] 358261 / 2774130 = 0.1291 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 07:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.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 07:18:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:18:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:18:47: 1000000 INFO @ Fri, 26 Jun 2020 07:18:53: 2000000 INFO @ Fri, 26 Jun 2020 07:18:59: 3000000 INFO @ Fri, 26 Jun 2020 07:19:05: 4000000 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 07:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.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 07:19:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:19:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:19:12: 5000000 INFO @ Fri, 26 Jun 2020 07:19:19: 1000000 INFO @ Fri, 26 Jun 2020 07:19:19: 6000000 INFO @ Fri, 26 Jun 2020 07:19:22: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 07:19:22: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 07:19:22: #1 total tags in treatment: 2342560 INFO @ Fri, 26 Jun 2020 07:19:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:19:22: #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 07:19:22: #1 tags after filtering in treatment: 1665372 INFO @ Fri, 26 Jun 2020 07:19:22: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 26 Jun 2020 07:19:22: #1 finished! INFO @ Fri, 26 Jun 2020 07:19:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:19:23: #2 number of paired peaks: 2163 INFO @ Fri, 26 Jun 2020 07:19:23: start model_add_line... INFO @ Fri, 26 Jun 2020 07:19:23: start X-correlation... INFO @ Fri, 26 Jun 2020 07:19:23: end of X-cor INFO @ Fri, 26 Jun 2020 07:19:23: #2 finished! INFO @ Fri, 26 Jun 2020 07:19:23: #2 predicted fragment length is 229 bps INFO @ Fri, 26 Jun 2020 07:19:23: #2 alternative fragment length(s) may be 229 bps INFO @ Fri, 26 Jun 2020 07:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.05_model.r INFO @ Fri, 26 Jun 2020 07:19:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:19:27: 2000000 INFO @ Fri, 26 Jun 2020 07:19:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.05_summits.bed INFO @ Fri, 26 Jun 2020 07:19:30: Done! pass1 - making usageList (6 chroms): 7 millis pass2 - checking and writing primary data (2813 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:19:34: 3000000 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 07:19:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.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 07:19:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:19:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:19:42: 4000000 INFO @ Fri, 26 Jun 2020 07:19:49: 1000000 INFO @ Fri, 26 Jun 2020 07:19:50: 5000000 INFO @ Fri, 26 Jun 2020 07:19:57: 2000000 INFO @ Fri, 26 Jun 2020 07:19:58: 6000000 INFO @ Fri, 26 Jun 2020 07:20:01: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 07:20:01: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 07:20:01: #1 total tags in treatment: 2342560 INFO @ Fri, 26 Jun 2020 07:20:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:01: #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 07:20:01: #1 tags after filtering in treatment: 1665372 INFO @ Fri, 26 Jun 2020 07:20:01: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 26 Jun 2020 07:20:01: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:01: #2 number of paired peaks: 2163 INFO @ Fri, 26 Jun 2020 07:20:01: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:01: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:01: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:01: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:01: #2 predicted fragment length is 229 bps INFO @ Fri, 26 Jun 2020 07:20:01: #2 alternative fragment length(s) may be 229 bps INFO @ Fri, 26 Jun 2020 07:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.10_model.r INFO @ Fri, 26 Jun 2020 07:20:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:05: 3000000 INFO @ Fri, 26 Jun 2020 07:20:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.10_summits.bed INFO @ Fri, 26 Jun 2020 07:20:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1628 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:12: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:20:20: 5000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:20:28: 6000000 INFO @ Fri, 26 Jun 2020 07:20:31: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 07:20:31: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 07:20:31: #1 total tags in treatment: 2342560 INFO @ Fri, 26 Jun 2020 07:20:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:31: #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 07:20:31: #1 tags after filtering in treatment: 1665372 INFO @ Fri, 26 Jun 2020 07:20:31: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 26 Jun 2020 07:20:31: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:31: #2 number of paired peaks: 2163 INFO @ Fri, 26 Jun 2020 07:20:31: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:31: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:31: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:31: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:31: #2 predicted fragment length is 229 bps INFO @ Fri, 26 Jun 2020 07:20:31: #2 alternative fragment length(s) may be 229 bps INFO @ Fri, 26 Jun 2020 07:20:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.20_model.r INFO @ Fri, 26 Jun 2020 07:20:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010108/SRX1010108.20_summits.bed INFO @ Fri, 26 Jun 2020 07:20:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (956 records, 4 fields): 3 millis CompletedMACS2peakCalling