Job ID = 14520744 SRX = SRX8245505 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10482161 spots for SRR11684716/SRR11684716.sra Written 10482161 spots for SRR11684716/SRR11684716.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: 00:16:44 10482161 reads; of these: 10482161 (100.00%) were paired; of these: 5746424 (54.82%) aligned concordantly 0 times 2225478 (21.23%) aligned concordantly exactly 1 time 2510259 (23.95%) aligned concordantly >1 times ---- 5746424 pairs aligned concordantly 0 times; of these: 113790 (1.98%) aligned discordantly 1 time ---- 5632634 pairs aligned 0 times concordantly or discordantly; of these: 11265268 mates make up the pairs; of these: 7510776 (66.67%) aligned 0 times 1821742 (16.17%) aligned exactly 1 time 1932750 (17.16%) aligned >1 times 64.17% overall alignment rate Time searching: 00:16:44 Overall time: 00:16:44 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] 488761 / 4842040 = 0.1009 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 20:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.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 20:06:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:06:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:06:33: 1000000 INFO @ Sat, 15 Jan 2022 20:06:38: 2000000 INFO @ Sat, 15 Jan 2022 20:06:42: 3000000 INFO @ Sat, 15 Jan 2022 20:06:46: 4000000 INFO @ Sat, 15 Jan 2022 20:06:50: 5000000 INFO @ Sat, 15 Jan 2022 20:06:55: 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 20:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.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 20:06:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:06:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:06:59: 7000000 INFO @ Sat, 15 Jan 2022 20:07:03: 8000000 INFO @ Sat, 15 Jan 2022 20:07:04: 1000000 INFO @ Sat, 15 Jan 2022 20:07:08: 9000000 INFO @ Sat, 15 Jan 2022 20:07:09: 2000000 INFO @ Sat, 15 Jan 2022 20:07:12: 10000000 INFO @ Sat, 15 Jan 2022 20:07:14: 3000000 INFO @ Sat, 15 Jan 2022 20:07:16: 11000000 INFO @ Sat, 15 Jan 2022 20:07:18: 4000000 INFO @ Sat, 15 Jan 2022 20:07:20: 12000000 INFO @ Sat, 15 Jan 2022 20:07:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:07:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:07:22: #1 total tags in treatment: 4252951 INFO @ Sat, 15 Jan 2022 20:07:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:07:22: #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 20:07:22: #1 tags after filtering in treatment: 1973952 INFO @ Sat, 15 Jan 2022 20:07:22: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 15 Jan 2022 20:07:22: #1 finished! INFO @ Sat, 15 Jan 2022 20:07:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:07:23: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 20:07:23: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 20:07:23: start model_add_line... INFO @ Sat, 15 Jan 2022 20:07:23: start X-correlation... INFO @ Sat, 15 Jan 2022 20:07:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:07:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:07:23: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Jan 2022 20:07:23: #2 alternative fragment length(s) may be 2,224,227,243,260 bps INFO @ Sat, 15 Jan 2022 20:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.05_model.r INFO @ Sat, 15 Jan 2022 20:07:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:07:23: 5000000 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 20:07:27: 6000000 INFO @ Sat, 15 Jan 2022 20:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.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 20:07:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:07:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:07:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.05_summits.bed INFO @ Sat, 15 Jan 2022 20:07:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:07:32: 7000000 INFO @ Sat, 15 Jan 2022 20:07:33: 1000000 INFO @ Sat, 15 Jan 2022 20:07:37: 8000000 INFO @ Sat, 15 Jan 2022 20:07:38: 2000000 INFO @ Sat, 15 Jan 2022 20:07:42: 9000000 INFO @ Sat, 15 Jan 2022 20:07:42: 3000000 INFO @ Sat, 15 Jan 2022 20:07:46: 4000000 INFO @ Sat, 15 Jan 2022 20:07:47: 10000000 INFO @ Sat, 15 Jan 2022 20:07:51: 5000000 INFO @ Sat, 15 Jan 2022 20:07:52: 11000000 INFO @ Sat, 15 Jan 2022 20:07:56: 6000000 INFO @ Sat, 15 Jan 2022 20:07:57: 12000000 INFO @ Sat, 15 Jan 2022 20:08:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:08:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:08:00: #1 total tags in treatment: 4252951 INFO @ Sat, 15 Jan 2022 20:08:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:08:00: #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 20:08:00: #1 tags after filtering in treatment: 1973952 INFO @ Sat, 15 Jan 2022 20:08:00: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 15 Jan 2022 20:08:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:08:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:08:00: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 20:08:00: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 20:08:00: start model_add_line... INFO @ Sat, 15 Jan 2022 20:08:00: start X-correlation... INFO @ Sat, 15 Jan 2022 20:08:00: 7000000 INFO @ Sat, 15 Jan 2022 20:08:00: end of X-cor INFO @ Sat, 15 Jan 2022 20:08:00: #2 finished! INFO @ Sat, 15 Jan 2022 20:08:00: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Jan 2022 20:08:00: #2 alternative fragment length(s) may be 2,224,227,243,260 bps INFO @ Sat, 15 Jan 2022 20:08:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.10_model.r INFO @ Sat, 15 Jan 2022 20:08:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:08:04: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:08:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:08:08: 9000000 INFO @ Sat, 15 Jan 2022 20:08:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.10_summits.bed INFO @ Sat, 15 Jan 2022 20:08:09: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (299 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:08:13: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:08:17: 11000000 INFO @ Sat, 15 Jan 2022 20:08:21: 12000000 INFO @ Sat, 15 Jan 2022 20:08:23: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:08:23: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:08:23: #1 total tags in treatment: 4252951 INFO @ Sat, 15 Jan 2022 20:08:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:08:23: #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 20:08:23: #1 tags after filtering in treatment: 1973952 INFO @ Sat, 15 Jan 2022 20:08:23: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 15 Jan 2022 20:08:23: #1 finished! INFO @ Sat, 15 Jan 2022 20:08:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:08:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:08:23: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 20:08:23: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 20:08:23: start model_add_line... INFO @ Sat, 15 Jan 2022 20:08:23: start X-correlation... INFO @ Sat, 15 Jan 2022 20:08:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:08:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:08:23: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Jan 2022 20:08:23: #2 alternative fragment length(s) may be 2,224,227,243,260 bps INFO @ Sat, 15 Jan 2022 20:08:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.20_model.r INFO @ Sat, 15 Jan 2022 20:08:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:08:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245505/SRX8245505.20_summits.bed INFO @ Sat, 15 Jan 2022 20:08:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 1 millis CompletedMACS2peakCalling