Job ID = 7107412 SRX = SRX6911550 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17777328 spots for SRR10191177/SRR10191177.sra Written 17777328 spots for SRR10191177/SRR10191177.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: 00:05:02 17777328 reads; of these: 17777328 (100.00%) were paired; of these: 15227548 (85.66%) aligned concordantly 0 times 1999773 (11.25%) aligned concordantly exactly 1 time 550007 (3.09%) aligned concordantly >1 times ---- 15227548 pairs aligned concordantly 0 times; of these: 168763 (1.11%) aligned discordantly 1 time ---- 15058785 pairs aligned 0 times concordantly or discordantly; of these: 30117570 mates make up the pairs; of these: 29829250 (99.04%) aligned 0 times 134952 (0.45%) aligned exactly 1 time 153368 (0.51%) aligned >1 times 16.10% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 1026750 / 2717578 = 0.3778 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 13:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.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 13:12:31: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:12:31: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:12:39: 1000000 INFO @ Wed, 22 Jul 2020 13:12:47: 2000000 INFO @ Wed, 22 Jul 2020 13:12:54: 3000000 INFO @ Wed, 22 Jul 2020 13:12:59: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:12:59: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:12:59: #1 total tags in treatment: 1567747 INFO @ Wed, 22 Jul 2020 13:12:59: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:12:59: #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 13:12:59: #1 tags after filtering in treatment: 1144572 INFO @ Wed, 22 Jul 2020 13:12:59: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Jul 2020 13:12:59: #1 finished! INFO @ Wed, 22 Jul 2020 13:12:59: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:12:59: #2 number of paired peaks: 111 WARNING @ Wed, 22 Jul 2020 13:12:59: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 22 Jul 2020 13:12:59: start model_add_line... INFO @ Wed, 22 Jul 2020 13:12:59: start X-correlation... INFO @ Wed, 22 Jul 2020 13:12:59: end of X-cor INFO @ Wed, 22 Jul 2020 13:12:59: #2 finished! INFO @ Wed, 22 Jul 2020 13:12:59: #2 predicted fragment length is 231 bps INFO @ Wed, 22 Jul 2020 13:12:59: #2 alternative fragment length(s) may be 3,231,254,270 bps INFO @ Wed, 22 Jul 2020 13:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.05_model.r INFO @ Wed, 22 Jul 2020 13:12:59: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:12:59: #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 13:13:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.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 13:13:01: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:13:01: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:13:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.05_summits.bed INFO @ Wed, 22 Jul 2020 13:13:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:13:09: 1000000 INFO @ Wed, 22 Jul 2020 13:13:17: 2000000 INFO @ Wed, 22 Jul 2020 13:13:25: 3000000 INFO @ Wed, 22 Jul 2020 13:13:29: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:13:29: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:13:29: #1 total tags in treatment: 1567747 INFO @ Wed, 22 Jul 2020 13:13:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:13:29: #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 13:13:29: #1 tags after filtering in treatment: 1144572 INFO @ Wed, 22 Jul 2020 13:13:29: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Jul 2020 13:13:29: #1 finished! INFO @ Wed, 22 Jul 2020 13:13:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:13:30: #2 number of paired peaks: 111 WARNING @ Wed, 22 Jul 2020 13:13:30: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 22 Jul 2020 13:13:30: start model_add_line... BedGraph に変換中... INFO @ Wed, 22 Jul 2020 13:13:30: start X-correlation... INFO @ Wed, 22 Jul 2020 13:13:30: end of X-cor INFO @ Wed, 22 Jul 2020 13:13:30: #2 finished! INFO @ Wed, 22 Jul 2020 13:13:30: #2 predicted fragment length is 231 bps INFO @ Wed, 22 Jul 2020 13:13:30: #2 alternative fragment length(s) may be 3,231,254,270 bps INFO @ Wed, 22 Jul 2020 13:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.10_model.r 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 13:13:30: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.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 13:13:31: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:13:31: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:13:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.10_summits.bed INFO @ Wed, 22 Jul 2020 13:13:34: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (72 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:13:39: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:13:46: 2000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:13:54: 3000000 INFO @ Wed, 22 Jul 2020 13:13:59: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:13:59: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:13:59: #1 total tags in treatment: 1567747 INFO @ Wed, 22 Jul 2020 13:13:59: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:13:59: #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 13:13:59: #1 tags after filtering in treatment: 1144572 INFO @ Wed, 22 Jul 2020 13:13:59: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Jul 2020 13:13:59: #1 finished! INFO @ Wed, 22 Jul 2020 13:13:59: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:13:59: #2 number of paired peaks: 111 WARNING @ Wed, 22 Jul 2020 13:13:59: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 22 Jul 2020 13:13:59: start model_add_line... INFO @ Wed, 22 Jul 2020 13:13:59: start X-correlation... INFO @ Wed, 22 Jul 2020 13:13:59: end of X-cor INFO @ Wed, 22 Jul 2020 13:13:59: #2 finished! INFO @ Wed, 22 Jul 2020 13:13:59: #2 predicted fragment length is 231 bps INFO @ Wed, 22 Jul 2020 13:13:59: #2 alternative fragment length(s) may be 3,231,254,270 bps INFO @ Wed, 22 Jul 2020 13:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.20_model.r INFO @ Wed, 22 Jul 2020 13:13:59: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:14:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911550/SRX6911550.20_summits.bed INFO @ Wed, 22 Jul 2020 13:14:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 26 millis CompletedMACS2peakCalling