Job ID = 6366587 SRX = SRX2035134 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:53:11 prefetch.2.10.7: 1) Downloading 'SRR4044258'... 2020-06-15T22:53:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:26 prefetch.2.10.7: 1) 'SRR4044258' was downloaded successfully Read 6829144 spots for SRR4044258/SRR4044258.sra Written 6829144 spots for SRR4044258/SRR4044258.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: 00:08:47 6829144 reads; of these: 6829144 (100.00%) were paired; of these: 1034900 (15.15%) aligned concordantly 0 times 5272483 (77.21%) aligned concordantly exactly 1 time 521761 (7.64%) aligned concordantly >1 times ---- 1034900 pairs aligned concordantly 0 times; of these: 487329 (47.09%) aligned discordantly 1 time ---- 547571 pairs aligned 0 times concordantly or discordantly; of these: 1095142 mates make up the pairs; of these: 927381 (84.68%) aligned 0 times 76608 (7.00%) aligned exactly 1 time 91153 (8.32%) aligned >1 times 93.21% overall alignment rate Time searching: 00:08:47 Overall time: 00:08:47 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 8 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] 193403 / 6268861 = 0.0309 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 08:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.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 08:12:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:22: 1000000 INFO @ Tue, 16 Jun 2020 08:12:29: 2000000 INFO @ Tue, 16 Jun 2020 08:12:36: 3000000 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 08:12:43: 4000000 INFO @ Tue, 16 Jun 2020 08:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.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 08:12:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:51: 5000000 INFO @ Tue, 16 Jun 2020 08:12:53: 1000000 INFO @ Tue, 16 Jun 2020 08:12:59: 6000000 INFO @ Tue, 16 Jun 2020 08:13:00: 2000000 INFO @ Tue, 16 Jun 2020 08:13:07: 7000000 INFO @ Tue, 16 Jun 2020 08:13:08: 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 @ Tue, 16 Jun 2020 08:13:14: 8000000 INFO @ Tue, 16 Jun 2020 08:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.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 08:13:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:16: 4000000 INFO @ Tue, 16 Jun 2020 08:13:22: 9000000 INFO @ Tue, 16 Jun 2020 08:13:22: 1000000 INFO @ Tue, 16 Jun 2020 08:13:24: 5000000 INFO @ Tue, 16 Jun 2020 08:13:30: 10000000 INFO @ Tue, 16 Jun 2020 08:13:31: 2000000 INFO @ Tue, 16 Jun 2020 08:13:32: 6000000 INFO @ Tue, 16 Jun 2020 08:13:38: 11000000 INFO @ Tue, 16 Jun 2020 08:13:39: 3000000 INFO @ Tue, 16 Jun 2020 08:13:39: 7000000 INFO @ Tue, 16 Jun 2020 08:13:46: 12000000 INFO @ Tue, 16 Jun 2020 08:13:46: 4000000 INFO @ Tue, 16 Jun 2020 08:13:47: 8000000 INFO @ Tue, 16 Jun 2020 08:13:49: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:13:49: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:13:49: #1 total tags in treatment: 5605769 INFO @ Tue, 16 Jun 2020 08:13:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:49: #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 08:13:49: #1 tags after filtering in treatment: 5025673 INFO @ Tue, 16 Jun 2020 08:13:49: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:13:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:50: #2 number of paired peaks: 4812 INFO @ Tue, 16 Jun 2020 08:13:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:50: #2 predicted fragment length is 272 bps INFO @ Tue, 16 Jun 2020 08:13:50: #2 alternative fragment length(s) may be 272 bps INFO @ Tue, 16 Jun 2020 08:13:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.05_model.r INFO @ Tue, 16 Jun 2020 08:13:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:54: 5000000 INFO @ Tue, 16 Jun 2020 08:13:55: 9000000 INFO @ Tue, 16 Jun 2020 08:14:02: 6000000 INFO @ Tue, 16 Jun 2020 08:14:03: 10000000 INFO @ Tue, 16 Jun 2020 08:14:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:10: 7000000 INFO @ Tue, 16 Jun 2020 08:14:10: 11000000 INFO @ Tue, 16 Jun 2020 08:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4358 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:17: 8000000 INFO @ Tue, 16 Jun 2020 08:14:18: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:21: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:14:21: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:14:21: #1 total tags in treatment: 5605769 INFO @ Tue, 16 Jun 2020 08:14:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:21: #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 08:14:21: #1 tags after filtering in treatment: 5025673 INFO @ Tue, 16 Jun 2020 08:14:21: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:14:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:22: #2 number of paired peaks: 4812 INFO @ Tue, 16 Jun 2020 08:14:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:22: #2 predicted fragment length is 272 bps INFO @ Tue, 16 Jun 2020 08:14:22: #2 alternative fragment length(s) may be 272 bps INFO @ Tue, 16 Jun 2020 08:14:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.10_model.r INFO @ Tue, 16 Jun 2020 08:14:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:25: 9000000 INFO @ Tue, 16 Jun 2020 08:14:32: 10000000 INFO @ Tue, 16 Jun 2020 08:14:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:40: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3430 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:47: 12000000 INFO @ Tue, 16 Jun 2020 08:14:50: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:14:50: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:14:50: #1 total tags in treatment: 5605769 INFO @ Tue, 16 Jun 2020 08:14:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:50: #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 08:14:50: #1 tags after filtering in treatment: 5025673 INFO @ Tue, 16 Jun 2020 08:14:50: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:14:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:50: #2 number of paired peaks: 4812 INFO @ Tue, 16 Jun 2020 08:14:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:51: #2 predicted fragment length is 272 bps INFO @ Tue, 16 Jun 2020 08:14:51: #2 alternative fragment length(s) may be 272 bps INFO @ Tue, 16 Jun 2020 08:14:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.20_model.r INFO @ Tue, 16 Jun 2020 08:14:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035134/SRX2035134.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2664 records, 4 fields): 4 millis CompletedMACS2peakCalling