Job ID = 7099090 SRX = SRX6911496 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17150849 spots for SRR10191123/SRR10191123.sra Written 17150849 spots for SRR10191123/SRR10191123.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: 00:14:27 17150849 reads; of these: 17150849 (100.00%) were paired; of these: 6804220 (39.67%) aligned concordantly 0 times 8960135 (52.24%) aligned concordantly exactly 1 time 1386494 (8.08%) aligned concordantly >1 times ---- 6804220 pairs aligned concordantly 0 times; of these: 203289 (2.99%) aligned discordantly 1 time ---- 6600931 pairs aligned 0 times concordantly or discordantly; of these: 13201862 mates make up the pairs; of these: 12403893 (93.96%) aligned 0 times 610059 (4.62%) aligned exactly 1 time 187910 (1.42%) aligned >1 times 63.84% overall alignment rate Time searching: 00:14:27 Overall time: 00:14:27 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_sort_core] merging from 12 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 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] 2851153 / 10548988 = 0.2703 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 12:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.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 12:25:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:25:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:25:30: 1000000 INFO @ Wed, 22 Jul 2020 12:25:37: 2000000 INFO @ Wed, 22 Jul 2020 12:25:43: 3000000 INFO @ Wed, 22 Jul 2020 12:25:49: 4000000 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 12:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.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 12:25:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:25:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:25:55: 5000000 INFO @ Wed, 22 Jul 2020 12:26:01: 6000000 INFO @ Wed, 22 Jul 2020 12:26:02: 1000000 INFO @ Wed, 22 Jul 2020 12:26:08: 7000000 INFO @ Wed, 22 Jul 2020 12:26:09: 2000000 INFO @ Wed, 22 Jul 2020 12:26:15: 8000000 INFO @ Wed, 22 Jul 2020 12:26:17: 3000000 INFO @ Wed, 22 Jul 2020 12:26:22: 9000000 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 12:26:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.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 12:26:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:26:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:26:25: 4000000 INFO @ Wed, 22 Jul 2020 12:26:29: 10000000 INFO @ Wed, 22 Jul 2020 12:26:31: 1000000 INFO @ Wed, 22 Jul 2020 12:26:33: 5000000 INFO @ Wed, 22 Jul 2020 12:26:35: 11000000 INFO @ Wed, 22 Jul 2020 12:26:38: 2000000 INFO @ Wed, 22 Jul 2020 12:26:40: 6000000 INFO @ Wed, 22 Jul 2020 12:26:43: 12000000 INFO @ Wed, 22 Jul 2020 12:26:45: 3000000 INFO @ Wed, 22 Jul 2020 12:26:48: 7000000 INFO @ Wed, 22 Jul 2020 12:26:50: 13000000 INFO @ Wed, 22 Jul 2020 12:26:52: 4000000 INFO @ Wed, 22 Jul 2020 12:26:56: 8000000 INFO @ Wed, 22 Jul 2020 12:26:57: 14000000 INFO @ Wed, 22 Jul 2020 12:26:59: 5000000 INFO @ Wed, 22 Jul 2020 12:27:04: 9000000 INFO @ Wed, 22 Jul 2020 12:27:04: 15000000 INFO @ Wed, 22 Jul 2020 12:27:06: 6000000 INFO @ Wed, 22 Jul 2020 12:27:12: 16000000 INFO @ Wed, 22 Jul 2020 12:27:12: 10000000 INFO @ Wed, 22 Jul 2020 12:27:13: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:27:13: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:27:13: #1 total tags in treatment: 7518582 INFO @ Wed, 22 Jul 2020 12:27:13: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:27:13: #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 12:27:13: 7000000 INFO @ Wed, 22 Jul 2020 12:27:13: #1 tags after filtering in treatment: 2470943 INFO @ Wed, 22 Jul 2020 12:27:13: #1 Redundant rate of treatment: 0.67 INFO @ Wed, 22 Jul 2020 12:27:13: #1 finished! INFO @ Wed, 22 Jul 2020 12:27:13: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:27:14: #2 number of paired peaks: 940 WARNING @ Wed, 22 Jul 2020 12:27:14: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Wed, 22 Jul 2020 12:27:14: start model_add_line... INFO @ Wed, 22 Jul 2020 12:27:14: start X-correlation... INFO @ Wed, 22 Jul 2020 12:27:14: end of X-cor INFO @ Wed, 22 Jul 2020 12:27:14: #2 finished! INFO @ Wed, 22 Jul 2020 12:27:14: #2 predicted fragment length is 274 bps INFO @ Wed, 22 Jul 2020 12:27:14: #2 alternative fragment length(s) may be 0,157,198,216,242,260,274,302 bps INFO @ Wed, 22 Jul 2020 12:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.05_model.r INFO @ Wed, 22 Jul 2020 12:27:14: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:27:20: 11000000 INFO @ Wed, 22 Jul 2020 12:27:20: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:27:27: 9000000 INFO @ Wed, 22 Jul 2020 12:27:27: 12000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:27:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.05_summits.bed INFO @ Wed, 22 Jul 2020 12:27:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:27:34: 10000000 INFO @ Wed, 22 Jul 2020 12:27:35: 13000000 INFO @ Wed, 22 Jul 2020 12:27:40: 11000000 INFO @ Wed, 22 Jul 2020 12:27:42: 14000000 INFO @ Wed, 22 Jul 2020 12:27:47: 12000000 INFO @ Wed, 22 Jul 2020 12:27:50: 15000000 INFO @ Wed, 22 Jul 2020 12:27:54: 13000000 INFO @ Wed, 22 Jul 2020 12:27:58: 16000000 INFO @ Wed, 22 Jul 2020 12:27:59: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:27:59: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:27:59: #1 total tags in treatment: 7518582 INFO @ Wed, 22 Jul 2020 12:27:59: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:27:59: #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 12:27:59: #1 tags after filtering in treatment: 2470943 INFO @ Wed, 22 Jul 2020 12:27:59: #1 Redundant rate of treatment: 0.67 INFO @ Wed, 22 Jul 2020 12:27:59: #1 finished! INFO @ Wed, 22 Jul 2020 12:27:59: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:28:00: #2 number of paired peaks: 940 WARNING @ Wed, 22 Jul 2020 12:28:00: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Wed, 22 Jul 2020 12:28:00: start model_add_line... INFO @ Wed, 22 Jul 2020 12:28:00: start X-correlation... INFO @ Wed, 22 Jul 2020 12:28:00: end of X-cor INFO @ Wed, 22 Jul 2020 12:28:00: #2 finished! INFO @ Wed, 22 Jul 2020 12:28:00: #2 predicted fragment length is 274 bps INFO @ Wed, 22 Jul 2020 12:28:00: #2 alternative fragment length(s) may be 0,157,198,216,242,260,274,302 bps INFO @ Wed, 22 Jul 2020 12:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.10_model.r INFO @ Wed, 22 Jul 2020 12:28:00: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:28:01: 14000000 INFO @ Wed, 22 Jul 2020 12:28:08: 15000000 INFO @ Wed, 22 Jul 2020 12:28:14: 16000000 INFO @ Wed, 22 Jul 2020 12:28:15: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:28:15: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:28:15: #1 total tags in treatment: 7518582 INFO @ Wed, 22 Jul 2020 12:28:15: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:28:15: #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 12:28:15: #1 tags after filtering in treatment: 2470943 INFO @ Wed, 22 Jul 2020 12:28:15: #1 Redundant rate of treatment: 0.67 INFO @ Wed, 22 Jul 2020 12:28:15: #1 finished! INFO @ Wed, 22 Jul 2020 12:28:15: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:28:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:28:16: #2 number of paired peaks: 940 WARNING @ Wed, 22 Jul 2020 12:28:16: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Wed, 22 Jul 2020 12:28:16: start model_add_line... INFO @ Wed, 22 Jul 2020 12:28:16: start X-correlation... INFO @ Wed, 22 Jul 2020 12:28:16: end of X-cor INFO @ Wed, 22 Jul 2020 12:28:16: #2 finished! INFO @ Wed, 22 Jul 2020 12:28:16: #2 predicted fragment length is 274 bps INFO @ Wed, 22 Jul 2020 12:28:16: #2 alternative fragment length(s) may be 0,157,198,216,242,260,274,302 bps INFO @ Wed, 22 Jul 2020 12:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.20_model.r INFO @ Wed, 22 Jul 2020 12:28:16: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:28:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:28:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:28:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:28:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.10_summits.bed INFO @ Wed, 22 Jul 2020 12:28:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:28:32: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911496/SRX6911496.20_summits.bed INFO @ Wed, 22 Jul 2020 12:28:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 2 millis CompletedMACS2peakCalling