Job ID = 6366576 SRX = SRX1995068 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:54:15 prefetch.2.10.7: 1) Downloading 'SRR3994000'... 2020-06-15T22:54:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:22 prefetch.2.10.7: 1) 'SRR3994000' was downloaded successfully 2020-06-15T22:56:22 prefetch.2.10.7: 'SRR3994000' has 0 unresolved dependencies Read 15852792 spots for SRR3994000/SRR3994000.sra Written 15852792 spots for SRR3994000/SRR3994000.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: 00:16:10 15852792 reads; of these: 15852792 (100.00%) were paired; of these: 4338263 (27.37%) aligned concordantly 0 times 7731759 (48.77%) aligned concordantly exactly 1 time 3782770 (23.86%) aligned concordantly >1 times ---- 4338263 pairs aligned concordantly 0 times; of these: 1598164 (36.84%) aligned discordantly 1 time ---- 2740099 pairs aligned 0 times concordantly or discordantly; of these: 5480198 mates make up the pairs; of these: 2574842 (46.98%) aligned 0 times 1090670 (19.90%) aligned exactly 1 time 1814686 (33.11%) aligned >1 times 91.88% overall alignment rate Time searching: 00:16:10 Overall time: 00:16:10 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 12 files... [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] 5026542 / 13102700 = 0.3836 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 08:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.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 08:20:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:49: 1000000 INFO @ Tue, 16 Jun 2020 08:20:55: 2000000 INFO @ Tue, 16 Jun 2020 08:21:01: 3000000 INFO @ Tue, 16 Jun 2020 08:21:06: 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 @ Tue, 16 Jun 2020 08:21:12: 5000000 INFO @ Tue, 16 Jun 2020 08:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.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 08:21:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:19: 6000000 INFO @ Tue, 16 Jun 2020 08:21:21: 1000000 INFO @ Tue, 16 Jun 2020 08:21:25: 7000000 INFO @ Tue, 16 Jun 2020 08:21:28: 2000000 INFO @ Tue, 16 Jun 2020 08:21:32: 8000000 INFO @ Tue, 16 Jun 2020 08:21:35: 3000000 INFO @ Tue, 16 Jun 2020 08:21:39: 9000000 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 08:21:41: 4000000 INFO @ Tue, 16 Jun 2020 08:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.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 08:21:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:46: 10000000 INFO @ Tue, 16 Jun 2020 08:21:48: 5000000 INFO @ Tue, 16 Jun 2020 08:21:50: 1000000 INFO @ Tue, 16 Jun 2020 08:21:52: 11000000 INFO @ Tue, 16 Jun 2020 08:21:55: 6000000 INFO @ Tue, 16 Jun 2020 08:21:57: 2000000 INFO @ Tue, 16 Jun 2020 08:21:59: 12000000 INFO @ Tue, 16 Jun 2020 08:22:01: 7000000 INFO @ Tue, 16 Jun 2020 08:22:04: 3000000 INFO @ Tue, 16 Jun 2020 08:22:05: 13000000 INFO @ Tue, 16 Jun 2020 08:22:08: 8000000 INFO @ Tue, 16 Jun 2020 08:22:11: 4000000 INFO @ Tue, 16 Jun 2020 08:22:12: 14000000 INFO @ Tue, 16 Jun 2020 08:22:15: 9000000 INFO @ Tue, 16 Jun 2020 08:22:18: 5000000 INFO @ Tue, 16 Jun 2020 08:22:19: 15000000 INFO @ Tue, 16 Jun 2020 08:22:22: 10000000 INFO @ Tue, 16 Jun 2020 08:22:25: 6000000 INFO @ Tue, 16 Jun 2020 08:22:26: 16000000 INFO @ Tue, 16 Jun 2020 08:22:29: 11000000 INFO @ Tue, 16 Jun 2020 08:22:32: 7000000 INFO @ Tue, 16 Jun 2020 08:22:33: 17000000 INFO @ Tue, 16 Jun 2020 08:22:37: 12000000 INFO @ Tue, 16 Jun 2020 08:22:39: 8000000 INFO @ Tue, 16 Jun 2020 08:22:40: 18000000 INFO @ Tue, 16 Jun 2020 08:22:44: 13000000 INFO @ Tue, 16 Jun 2020 08:22:46: 9000000 INFO @ Tue, 16 Jun 2020 08:22:47: 19000000 INFO @ Tue, 16 Jun 2020 08:22:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:22:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:22:48: #1 total tags in treatment: 6916558 INFO @ Tue, 16 Jun 2020 08:22:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:48: #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 08:22:48: #1 tags after filtering in treatment: 4492420 INFO @ Tue, 16 Jun 2020 08:22:48: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 16 Jun 2020 08:22:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:48: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:48: #2 number of paired peaks: 7443 INFO @ Tue, 16 Jun 2020 08:22:48: start model_add_line... BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:49: #2 predicted fragment length is 267 bps INFO @ Tue, 16 Jun 2020 08:22:49: #2 alternative fragment length(s) may be 267 bps INFO @ Tue, 16 Jun 2020 08:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.05_model.r INFO @ Tue, 16 Jun 2020 08:22:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:51: 14000000 INFO @ Tue, 16 Jun 2020 08:22:53: 10000000 INFO @ Tue, 16 Jun 2020 08:22:57: 15000000 INFO @ Tue, 16 Jun 2020 08:23:00: 11000000 INFO @ Tue, 16 Jun 2020 08:23:04: 16000000 INFO @ Tue, 16 Jun 2020 08:23:06: 12000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:10: 17000000 INFO @ Tue, 16 Jun 2020 08:23:13: 13000000 INFO @ Tue, 16 Jun 2020 08:23:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:16: 18000000 INFO @ Tue, 16 Jun 2020 08:23:19: 14000000 INFO @ Tue, 16 Jun 2020 08:23:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.05_summits.bed INFO @ Tue, 16 Jun 2020 08:23:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4150 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:23: 19000000 INFO @ Tue, 16 Jun 2020 08:23:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:23:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:23:23: #1 total tags in treatment: 6916558 INFO @ Tue, 16 Jun 2020 08:23:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:23: #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 08:23:23: #1 tags after filtering in treatment: 4492420 INFO @ Tue, 16 Jun 2020 08:23:23: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 16 Jun 2020 08:23:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:24: #2 number of paired peaks: 7443 INFO @ Tue, 16 Jun 2020 08:23:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:24: #2 predicted fragment length is 267 bps INFO @ Tue, 16 Jun 2020 08:23:24: #2 alternative fragment length(s) may be 267 bps INFO @ Tue, 16 Jun 2020 08:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.10_model.r INFO @ Tue, 16 Jun 2020 08:23:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:25: 15000000 INFO @ Tue, 16 Jun 2020 08:23:31: 16000000 INFO @ Tue, 16 Jun 2020 08:23:37: 17000000 INFO @ Tue, 16 Jun 2020 08:23:43: 18000000 INFO @ Tue, 16 Jun 2020 08:23:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:48: 19000000 INFO @ Tue, 16 Jun 2020 08:23:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:23:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:23:49: #1 total tags in treatment: 6916558 INFO @ Tue, 16 Jun 2020 08:23:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:49: #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 08:23:49: #1 tags after filtering in treatment: 4492420 INFO @ Tue, 16 Jun 2020 08:23:49: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 16 Jun 2020 08:23:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:50: #2 number of paired peaks: 7443 INFO @ Tue, 16 Jun 2020 08:23:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:50: #2 predicted fragment length is 267 bps INFO @ Tue, 16 Jun 2020 08:23:50: #2 alternative fragment length(s) may be 267 bps INFO @ Tue, 16 Jun 2020 08:23:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.20_model.r INFO @ Tue, 16 Jun 2020 08:23:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2836 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995068/SRX1995068.20_summits.bed INFO @ Tue, 16 Jun 2020 08:24:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1652 records, 4 fields): 3 millis CompletedMACS2peakCalling