Job ID = 14520902 SRX = SRX8245438 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13694986 spots for SRR11684649/SRR11684649.sra Written 13694986 spots for SRR11684649/SRR11684649.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: 00:26:34 13694986 reads; of these: 13694986 (100.00%) were paired; of these: 7582607 (55.37%) aligned concordantly 0 times 2700707 (19.72%) aligned concordantly exactly 1 time 3411672 (24.91%) aligned concordantly >1 times ---- 7582607 pairs aligned concordantly 0 times; of these: 57315 (0.76%) aligned discordantly 1 time ---- 7525292 pairs aligned 0 times concordantly or discordantly; of these: 15050584 mates make up the pairs; of these: 8543045 (56.76%) aligned 0 times 2839809 (18.87%) aligned exactly 1 time 3667730 (24.37%) aligned >1 times 68.81% overall alignment rate Time searching: 00:26:34 Overall time: 00:26:34 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 8 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] 584505 / 6168858 = 0.0948 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 20:39:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.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 20:39:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:39:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:39:57: 1000000 INFO @ Sat, 15 Jan 2022 20:40:02: 2000000 INFO @ Sat, 15 Jan 2022 20:40:08: 3000000 INFO @ Sat, 15 Jan 2022 20:40:13: 4000000 INFO @ Sat, 15 Jan 2022 20:40:18: 5000000 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 20:40:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.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 20:40:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:40:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:40:23: 6000000 INFO @ Sat, 15 Jan 2022 20:40:29: 1000000 INFO @ Sat, 15 Jan 2022 20:40:29: 7000000 INFO @ Sat, 15 Jan 2022 20:40:35: 8000000 INFO @ Sat, 15 Jan 2022 20:40:36: 2000000 INFO @ Sat, 15 Jan 2022 20:40:42: 9000000 INFO @ Sat, 15 Jan 2022 20:40:43: 3000000 INFO @ Sat, 15 Jan 2022 20:40:48: 10000000 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 20:40:50: 4000000 INFO @ Sat, 15 Jan 2022 20:40:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.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 20:40:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:40:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:40:54: 11000000 INFO @ Sat, 15 Jan 2022 20:40:57: 5000000 INFO @ Sat, 15 Jan 2022 20:40:58: 1000000 INFO @ Sat, 15 Jan 2022 20:41:00: 12000000 INFO @ Sat, 15 Jan 2022 20:41:04: 6000000 INFO @ Sat, 15 Jan 2022 20:41:04: 2000000 INFO @ Sat, 15 Jan 2022 20:41:06: 13000000 INFO @ Sat, 15 Jan 2022 20:41:10: 3000000 INFO @ Sat, 15 Jan 2022 20:41:11: 7000000 INFO @ Sat, 15 Jan 2022 20:41:12: 14000000 INFO @ Sat, 15 Jan 2022 20:41:17: 4000000 INFO @ Sat, 15 Jan 2022 20:41:17: 8000000 INFO @ Sat, 15 Jan 2022 20:41:19: 15000000 INFO @ Sat, 15 Jan 2022 20:41:23: 5000000 INFO @ Sat, 15 Jan 2022 20:41:25: 9000000 INFO @ Sat, 15 Jan 2022 20:41:25: 16000000 INFO @ Sat, 15 Jan 2022 20:41:29: 6000000 INFO @ Sat, 15 Jan 2022 20:41:31: 17000000 INFO @ Sat, 15 Jan 2022 20:41:32: 10000000 INFO @ Sat, 15 Jan 2022 20:41:35: 7000000 INFO @ Sat, 15 Jan 2022 20:41:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:41:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:41:35: #1 total tags in treatment: 5543436 INFO @ Sat, 15 Jan 2022 20:41:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:41:35: #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 20:41:35: #1 tags after filtering in treatment: 1487304 INFO @ Sat, 15 Jan 2022 20:41:35: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 15 Jan 2022 20:41:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:41:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:41:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:41:35: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 20:41:35: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 20:41:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:41:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:41:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:41:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:41:35: #2 predicted fragment length is 346 bps INFO @ Sat, 15 Jan 2022 20:41:35: #2 alternative fragment length(s) may be 4,320,346,366 bps INFO @ Sat, 15 Jan 2022 20:41:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.05_model.r INFO @ Sat, 15 Jan 2022 20:41:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:41:39: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:41:41: 8000000 INFO @ Sat, 15 Jan 2022 20:41:46: 12000000 INFO @ Sat, 15 Jan 2022 20:41:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:41:47: 9000000 INFO @ Sat, 15 Jan 2022 20:41:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:41:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:41:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.05_summits.bed INFO @ Sat, 15 Jan 2022 20:41:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:41:53: 13000000 INFO @ Sat, 15 Jan 2022 20:41:53: 10000000 INFO @ Sat, 15 Jan 2022 20:41:59: 11000000 INFO @ Sat, 15 Jan 2022 20:41:59: 14000000 INFO @ Sat, 15 Jan 2022 20:42:06: 12000000 INFO @ Sat, 15 Jan 2022 20:42:06: 15000000 INFO @ Sat, 15 Jan 2022 20:42:12: 13000000 INFO @ Sat, 15 Jan 2022 20:42:13: 16000000 INFO @ Sat, 15 Jan 2022 20:42:18: 14000000 INFO @ Sat, 15 Jan 2022 20:42:20: 17000000 INFO @ Sat, 15 Jan 2022 20:42:24: 15000000 INFO @ Sat, 15 Jan 2022 20:42:25: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:42:25: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:42:25: #1 total tags in treatment: 5543436 INFO @ Sat, 15 Jan 2022 20:42:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:42:25: #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 20:42:25: #1 tags after filtering in treatment: 1487304 INFO @ Sat, 15 Jan 2022 20:42:25: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 15 Jan 2022 20:42:25: #1 finished! INFO @ Sat, 15 Jan 2022 20:42:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:42:25: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 20:42:25: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 20:42:25: start model_add_line... INFO @ Sat, 15 Jan 2022 20:42:25: start X-correlation... INFO @ Sat, 15 Jan 2022 20:42:25: end of X-cor INFO @ Sat, 15 Jan 2022 20:42:25: #2 finished! INFO @ Sat, 15 Jan 2022 20:42:25: #2 predicted fragment length is 346 bps INFO @ Sat, 15 Jan 2022 20:42:25: #2 alternative fragment length(s) may be 4,320,346,366 bps INFO @ Sat, 15 Jan 2022 20:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.10_model.r INFO @ Sat, 15 Jan 2022 20:42:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:42:30: 16000000 INFO @ Sat, 15 Jan 2022 20:42:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:42:35: 17000000 INFO @ Sat, 15 Jan 2022 20:42:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:42:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:42:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.10_summits.bed INFO @ Sat, 15 Jan 2022 20:42:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:42:39: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:42:39: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:42:39: #1 total tags in treatment: 5543436 INFO @ Sat, 15 Jan 2022 20:42:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:42:39: #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 20:42:39: #1 tags after filtering in treatment: 1487304 INFO @ Sat, 15 Jan 2022 20:42:39: #1 Redundant rate of treatment: 0.73 INFO @ Sat, 15 Jan 2022 20:42:39: #1 finished! INFO @ Sat, 15 Jan 2022 20:42:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:42:39: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 20:42:39: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 20:42:39: start model_add_line... INFO @ Sat, 15 Jan 2022 20:42:39: start X-correlation... INFO @ Sat, 15 Jan 2022 20:42:39: end of X-cor INFO @ Sat, 15 Jan 2022 20:42:39: #2 finished! INFO @ Sat, 15 Jan 2022 20:42:39: #2 predicted fragment length is 346 bps INFO @ Sat, 15 Jan 2022 20:42:39: #2 alternative fragment length(s) may be 4,320,346,366 bps INFO @ Sat, 15 Jan 2022 20:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.20_model.r INFO @ Sat, 15 Jan 2022 20:42:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:42:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245438/SRX8245438.20_summits.bed INFO @ Sat, 15 Jan 2022 20:42:51: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (105 records, 4 fields): 2 millis CompletedMACS2peakCalling