Job ID = 7111959 SRX = SRX8357674 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:16:40 prefetch.2.10.7: 1) Downloading 'SRR11806262'... 2020-07-22T05:16:40 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:18:07 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:18:07 prefetch.2.10.7: 'SRR11806262' is valid 2020-07-22T05:18:07 prefetch.2.10.7: 1) 'SRR11806262' was downloaded successfully 2020-07-22T05:18:07 prefetch.2.10.7: 'SRR11806262' has 0 unresolved dependencies Read 6125074 spots for SRR11806262/SRR11806262.sra Written 6125074 spots for SRR11806262/SRR11806262.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: 00:02:25 6125074 reads; of these: 6125074 (100.00%) were paired; of these: 2655537 (43.36%) aligned concordantly 0 times 2465609 (40.25%) aligned concordantly exactly 1 time 1003928 (16.39%) aligned concordantly >1 times ---- 2655537 pairs aligned concordantly 0 times; of these: 4754 (0.18%) aligned discordantly 1 time ---- 2650783 pairs aligned 0 times concordantly or discordantly; of these: 5301566 mates make up the pairs; of these: 5244931 (98.93%) aligned 0 times 27576 (0.52%) aligned exactly 1 time 29059 (0.55%) aligned >1 times 57.18% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 738738 / 3472449 = 0.2127 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 14:22:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.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 14:22:41: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:22:41: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:22:46: 1000000 INFO @ Wed, 22 Jul 2020 14:22:50: 2000000 INFO @ Wed, 22 Jul 2020 14:22:55: 3000000 INFO @ Wed, 22 Jul 2020 14:23:00: 4000000 INFO @ Wed, 22 Jul 2020 14:23:05: 5000000 INFO @ Wed, 22 Jul 2020 14:23:07: #1 tag size is determined as 38 bps INFO @ Wed, 22 Jul 2020 14:23:07: #1 tag size = 38 INFO @ Wed, 22 Jul 2020 14:23:07: #1 total tags in treatment: 2731549 INFO @ Wed, 22 Jul 2020 14:23:07: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:23:07: #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 14:23:07: #1 tags after filtering in treatment: 1839679 INFO @ Wed, 22 Jul 2020 14:23:07: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 14:23:07: #1 finished! INFO @ Wed, 22 Jul 2020 14:23:07: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:23:07: #2 number of paired peaks: 168 WARNING @ Wed, 22 Jul 2020 14:23:07: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Wed, 22 Jul 2020 14:23:07: start model_add_line... INFO @ Wed, 22 Jul 2020 14:23:07: start X-correlation... INFO @ Wed, 22 Jul 2020 14:23:07: end of X-cor INFO @ Wed, 22 Jul 2020 14:23:07: #2 finished! INFO @ Wed, 22 Jul 2020 14:23:07: #2 predicted fragment length is 152 bps INFO @ Wed, 22 Jul 2020 14:23:07: #2 alternative fragment length(s) may be 30,82,119,136,140,152,173,190,232,275,301,385,414,426,458,518,547,571,587 bps INFO @ Wed, 22 Jul 2020 14:23:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.05_model.r INFO @ Wed, 22 Jul 2020 14:23:07: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:23:07: #3 Pre-compute pvalue-qvalue table... 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 14:23:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.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 14:23:11: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:23:11: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:23:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:23:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.05_peaks.xls INFO @ Wed, 22 Jul 2020 14:23:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:23:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.05_summits.bed INFO @ Wed, 22 Jul 2020 14:23:13: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (122 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:23:16: 1000000 INFO @ Wed, 22 Jul 2020 14:23:20: 2000000 INFO @ Wed, 22 Jul 2020 14:23:25: 3000000 INFO @ Wed, 22 Jul 2020 14:23:30: 4000000 INFO @ Wed, 22 Jul 2020 14:23:35: 5000000 INFO @ Wed, 22 Jul 2020 14:23:37: #1 tag size is determined as 38 bps INFO @ Wed, 22 Jul 2020 14:23:37: #1 tag size = 38 INFO @ Wed, 22 Jul 2020 14:23:37: #1 total tags in treatment: 2731549 INFO @ Wed, 22 Jul 2020 14:23:37: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:23:37: #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 14:23:37: #1 tags after filtering in treatment: 1839679 INFO @ Wed, 22 Jul 2020 14:23:37: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 14:23:37: #1 finished! INFO @ Wed, 22 Jul 2020 14:23:37: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:23:37: #2 number of paired peaks: 168 WARNING @ Wed, 22 Jul 2020 14:23:37: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Wed, 22 Jul 2020 14:23:37: start model_add_line... INFO @ Wed, 22 Jul 2020 14:23:37: start X-correlation... INFO @ Wed, 22 Jul 2020 14:23:37: end of X-cor INFO @ Wed, 22 Jul 2020 14:23:37: #2 finished! INFO @ Wed, 22 Jul 2020 14:23:37: #2 predicted fragment length is 152 bps INFO @ Wed, 22 Jul 2020 14:23:37: #2 alternative fragment length(s) may be 30,82,119,136,140,152,173,190,232,275,301,385,414,426,458,518,547,571,587 bps INFO @ Wed, 22 Jul 2020 14:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.10_model.r INFO @ Wed, 22 Jul 2020 14:23:37: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:23:37: #3 Pre-compute pvalue-qvalue table... 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 14:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.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 14:23:41: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:23:41: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:23:42: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:23:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.10_peaks.xls INFO @ Wed, 22 Jul 2020 14:23:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:23:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.10_summits.bed INFO @ Wed, 22 Jul 2020 14:23:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:23:46: 1000000 INFO @ Wed, 22 Jul 2020 14:23:51: 2000000 INFO @ Wed, 22 Jul 2020 14:23:56: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:24:01: 4000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:24:06: 5000000 INFO @ Wed, 22 Jul 2020 14:24:09: #1 tag size is determined as 38 bps INFO @ Wed, 22 Jul 2020 14:24:09: #1 tag size = 38 INFO @ Wed, 22 Jul 2020 14:24:09: #1 total tags in treatment: 2731549 INFO @ Wed, 22 Jul 2020 14:24:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:24:09: #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 14:24:09: #1 tags after filtering in treatment: 1839679 INFO @ Wed, 22 Jul 2020 14:24:09: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 14:24:09: #1 finished! INFO @ Wed, 22 Jul 2020 14:24:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:24:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:24:09: #2 number of paired peaks: 168 WARNING @ Wed, 22 Jul 2020 14:24:09: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Wed, 22 Jul 2020 14:24:09: start model_add_line... INFO @ Wed, 22 Jul 2020 14:24:09: start X-correlation... INFO @ Wed, 22 Jul 2020 14:24:09: end of X-cor INFO @ Wed, 22 Jul 2020 14:24:09: #2 finished! INFO @ Wed, 22 Jul 2020 14:24:09: #2 predicted fragment length is 152 bps INFO @ Wed, 22 Jul 2020 14:24:09: #2 alternative fragment length(s) may be 30,82,119,136,140,152,173,190,232,275,301,385,414,426,458,518,547,571,587 bps INFO @ Wed, 22 Jul 2020 14:24:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.20_model.r INFO @ Wed, 22 Jul 2020 14:24:09: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:24:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:24:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:24:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.20_peaks.xls INFO @ Wed, 22 Jul 2020 14:24:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:24:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8357674/SRX8357674.20_summits.bed INFO @ Wed, 22 Jul 2020 14:24:15: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (26 records, 4 fields): 1 millis CompletedMACS2peakCalling