Job ID = 7112018 SRX = SRX8357678 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:17:33 prefetch.2.10.7: 1) Downloading 'SRR11806266'... 2020-07-22T05:17:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:18:41 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:18:41 prefetch.2.10.7: 'SRR11806266' is valid 2020-07-22T05:18:41 prefetch.2.10.7: 1) 'SRR11806266' was downloaded successfully 2020-07-22T05:18:41 prefetch.2.10.7: 'SRR11806266' has 0 unresolved dependencies Read 3154633 spots for SRR11806266/SRR11806266.sra Written 3154633 spots for SRR11806266/SRR11806266.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: 00:01:21 3154633 reads; of these: 3154633 (100.00%) were paired; of these: 1472147 (46.67%) aligned concordantly 0 times 1301891 (41.27%) aligned concordantly exactly 1 time 380595 (12.06%) aligned concordantly >1 times ---- 1472147 pairs aligned concordantly 0 times; of these: 8614 (0.59%) aligned discordantly 1 time ---- 1463533 pairs aligned 0 times concordantly or discordantly; of these: 2927066 mates make up the pairs; of these: 2873216 (98.16%) aligned 0 times 22478 (0.77%) aligned exactly 1 time 31372 (1.07%) aligned >1 times 54.46% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 254349 / 1689128 = 0.1506 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 @ Wed, 22 Jul 2020 14:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 14:21:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:21:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:21:42: 1000000 INFO @ Wed, 22 Jul 2020 14:21:47: 2000000 INFO @ Wed, 22 Jul 2020 14:21:52: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:21:52: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:21:52: #1 total tags in treatment: 1428797 INFO @ Wed, 22 Jul 2020 14:21:52: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:21:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:21:52: #1 tags after filtering in treatment: 1130994 INFO @ Wed, 22 Jul 2020 14:21:52: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 14:21:52: #1 finished! INFO @ Wed, 22 Jul 2020 14:21:52: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:21:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:21:53: #2 number of paired peaks: 154 WARNING @ Wed, 22 Jul 2020 14:21:53: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 22 Jul 2020 14:21:53: start model_add_line... INFO @ Wed, 22 Jul 2020 14:21:53: start X-correlation... INFO @ Wed, 22 Jul 2020 14:21:53: end of X-cor INFO @ Wed, 22 Jul 2020 14:21:53: #2 finished! INFO @ Wed, 22 Jul 2020 14:21:53: #2 predicted fragment length is 123 bps INFO @ Wed, 22 Jul 2020 14:21:53: #2 alternative fragment length(s) may be 51,97,123,131,153,182,208,243,369,528,566,587 bps INFO @ Wed, 22 Jul 2020 14:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.05_model.r INFO @ Wed, 22 Jul 2020 14:21:53: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:21:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.05_peaks.xls INFO @ Wed, 22 Jul 2020 14:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.05_summits.bed INFO @ Wed, 22 Jul 2020 14:21:56: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (109 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 @ Wed, 22 Jul 2020 14:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 14:22:06: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:22:06: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:22:12: 1000000 INFO @ Wed, 22 Jul 2020 14:22:18: 2000000 INFO @ Wed, 22 Jul 2020 14:22:23: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:22:23: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:22:23: #1 total tags in treatment: 1428797 INFO @ Wed, 22 Jul 2020 14:22:23: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:22:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:22:23: #1 tags after filtering in treatment: 1130994 INFO @ Wed, 22 Jul 2020 14:22:23: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 14:22:23: #1 finished! INFO @ Wed, 22 Jul 2020 14:22:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:22:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:22:23: #2 number of paired peaks: 154 WARNING @ Wed, 22 Jul 2020 14:22:23: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 22 Jul 2020 14:22:23: start model_add_line... INFO @ Wed, 22 Jul 2020 14:22:23: start X-correlation... INFO @ Wed, 22 Jul 2020 14:22:23: end of X-cor INFO @ Wed, 22 Jul 2020 14:22:23: #2 finished! INFO @ Wed, 22 Jul 2020 14:22:23: #2 predicted fragment length is 123 bps INFO @ Wed, 22 Jul 2020 14:22:23: #2 alternative fragment length(s) may be 51,97,123,131,153,182,208,243,369,528,566,587 bps INFO @ Wed, 22 Jul 2020 14:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.10_model.r INFO @ Wed, 22 Jul 2020 14:22:23: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:22:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:22:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.10_peaks.xls INFO @ Wed, 22 Jul 2020 14:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.10_summits.bed INFO @ Wed, 22 Jul 2020 14:22:26: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (60 records, 4 fields): 2 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 @ Wed, 22 Jul 2020 14:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 14:22:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:22:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:22:42: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:22:47: 2000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:22:53: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:22:53: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:22:53: #1 total tags in treatment: 1428797 INFO @ Wed, 22 Jul 2020 14:22:53: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:22:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:22:53: #1 tags after filtering in treatment: 1130994 INFO @ Wed, 22 Jul 2020 14:22:53: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 14:22:53: #1 finished! INFO @ Wed, 22 Jul 2020 14:22:53: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:22:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:22:53: #2 number of paired peaks: 154 WARNING @ Wed, 22 Jul 2020 14:22:53: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 22 Jul 2020 14:22:53: start model_add_line... INFO @ Wed, 22 Jul 2020 14:22:53: start X-correlation... INFO @ Wed, 22 Jul 2020 14:22:53: end of X-cor INFO @ Wed, 22 Jul 2020 14:22:53: #2 finished! INFO @ Wed, 22 Jul 2020 14:22:53: #2 predicted fragment length is 123 bps INFO @ Wed, 22 Jul 2020 14:22:53: #2 alternative fragment length(s) may be 51,97,123,131,153,182,208,243,369,528,566,587 bps INFO @ Wed, 22 Jul 2020 14:22:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.20_model.r INFO @ Wed, 22 Jul 2020 14:22:53: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:22:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:22:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.20_peaks.xls INFO @ Wed, 22 Jul 2020 14:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8357678/SRX8357678.20_summits.bed INFO @ Wed, 22 Jul 2020 14:22:57: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling