Job ID = 14520496 SRX = SRX11781169 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:14:08 prefetch.2.10.7: 1) Downloading 'SRR15481112'... 2022-01-15T10:14:08 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:14:22 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:14:22 prefetch.2.10.7: 'SRR15481112' is valid 2022-01-15T10:14:22 prefetch.2.10.7: 1) 'SRR15481112' was downloaded successfully 2022-01-15T10:14:22 prefetch.2.10.7: 'SRR15481112' has 0 unresolved dependencies Read 6375781 spots for SRR15481112/SRR15481112.sra Written 6375781 spots for SRR15481112/SRR15481112.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: 00:02:48 6375781 reads; of these: 6375781 (100.00%) were paired; of these: 4006754 (62.84%) aligned concordantly 0 times 2066457 (32.41%) aligned concordantly exactly 1 time 302570 (4.75%) aligned concordantly >1 times ---- 4006754 pairs aligned concordantly 0 times; of these: 42701 (1.07%) aligned discordantly 1 time ---- 3964053 pairs aligned 0 times concordantly or discordantly; of these: 7928106 mates make up the pairs; of these: 4355842 (54.94%) aligned 0 times 3096927 (39.06%) aligned exactly 1 time 475337 (6.00%) aligned >1 times 65.84% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 259157 / 2410939 = 0.1075 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:20:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.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 @ Sat, 15 Jan 2022 19:20:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:10: 1000000 INFO @ Sat, 15 Jan 2022 19:20:14: 2000000 INFO @ Sat, 15 Jan 2022 19:20:18: 3000000 INFO @ Sat, 15 Jan 2022 19:20:23: 4000000 INFO @ Sat, 15 Jan 2022 19:20:27: 5000000 INFO @ Sat, 15 Jan 2022 19:20:31: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:20:35: 7000000 INFO @ Sat, 15 Jan 2022 19:20:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.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 @ Sat, 15 Jan 2022 19:20:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:39: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:20:39: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:20:39: #1 total tags in treatment: 2112154 INFO @ Sat, 15 Jan 2022 19:20:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:20:39: #1 tags after filtering in treatment: 1517518 INFO @ Sat, 15 Jan 2022 19:20:39: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:20:39: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:39: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:20:39: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:20:39: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:39: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:39: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:39: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:39: #2 predicted fragment length is 287 bps INFO @ Sat, 15 Jan 2022 19:20:39: #2 alternative fragment length(s) may be 1,199,234,255,271,287 bps INFO @ Sat, 15 Jan 2022 19:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.05_model.r INFO @ Sat, 15 Jan 2022 19:20:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:40: 1000000 INFO @ Sat, 15 Jan 2022 19:20:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:20:44: 2000000 INFO @ Sat, 15 Jan 2022 19:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.05_summits.bed INFO @ Sat, 15 Jan 2022 19:20:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:20:47: 3000000 INFO @ Sat, 15 Jan 2022 19:20:51: 4000000 INFO @ Sat, 15 Jan 2022 19:20:55: 5000000 INFO @ Sat, 15 Jan 2022 19:20:59: 6000000 INFO @ Sat, 15 Jan 2022 19:21:03: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.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 @ Sat, 15 Jan 2022 19:21:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:21:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:21:07: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:21:07: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:21:07: #1 total tags in treatment: 2112154 INFO @ Sat, 15 Jan 2022 19:21:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:21:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:21:07: #1 tags after filtering in treatment: 1517518 INFO @ Sat, 15 Jan 2022 19:21:07: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:21:07: #1 finished! INFO @ Sat, 15 Jan 2022 19:21:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:21:07: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:21:07: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:21:07: start model_add_line... INFO @ Sat, 15 Jan 2022 19:21:07: start X-correlation... INFO @ Sat, 15 Jan 2022 19:21:07: end of X-cor INFO @ Sat, 15 Jan 2022 19:21:07: #2 finished! INFO @ Sat, 15 Jan 2022 19:21:07: #2 predicted fragment length is 287 bps INFO @ Sat, 15 Jan 2022 19:21:07: #2 alternative fragment length(s) may be 1,199,234,255,271,287 bps INFO @ Sat, 15 Jan 2022 19:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.10_model.r INFO @ Sat, 15 Jan 2022 19:21:07: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:21:11: 1000000 INFO @ Sat, 15 Jan 2022 19:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.10_summits.bed INFO @ Sat, 15 Jan 2022 19:21:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:21:16: 2000000 INFO @ Sat, 15 Jan 2022 19:21:21: 3000000 INFO @ Sat, 15 Jan 2022 19:21:26: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:21:31: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:21:37: 6000000 INFO @ Sat, 15 Jan 2022 19:21:42: 7000000 INFO @ Sat, 15 Jan 2022 19:21:46: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:21:46: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:21:46: #1 total tags in treatment: 2112154 INFO @ Sat, 15 Jan 2022 19:21:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:21:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:21:46: #1 tags after filtering in treatment: 1517518 INFO @ Sat, 15 Jan 2022 19:21:46: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:21:46: #1 finished! INFO @ Sat, 15 Jan 2022 19:21:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:21:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:21:47: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:21:47: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:21:47: start model_add_line... INFO @ Sat, 15 Jan 2022 19:21:47: start X-correlation... INFO @ Sat, 15 Jan 2022 19:21:47: end of X-cor INFO @ Sat, 15 Jan 2022 19:21:47: #2 finished! INFO @ Sat, 15 Jan 2022 19:21:47: #2 predicted fragment length is 287 bps INFO @ Sat, 15 Jan 2022 19:21:47: #2 alternative fragment length(s) may be 1,199,234,255,271,287 bps INFO @ Sat, 15 Jan 2022 19:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.20_model.r INFO @ Sat, 15 Jan 2022 19:21:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:21:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781169/SRX11781169.20_summits.bed INFO @ Sat, 15 Jan 2022 19:21:52: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling