Job ID = 14520896 SRX = SRX8245432 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9695276 spots for SRR11684643/SRR11684643.sra Written 9695276 spots for SRR11684643/SRR11684643.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: 00:14:06 9695276 reads; of these: 9695276 (100.00%) were paired; of these: 4927014 (50.82%) aligned concordantly 0 times 2413054 (24.89%) aligned concordantly exactly 1 time 2355208 (24.29%) aligned concordantly >1 times ---- 4927014 pairs aligned concordantly 0 times; of these: 76850 (1.56%) aligned discordantly 1 time ---- 4850164 pairs aligned 0 times concordantly or discordantly; of these: 9700328 mates make up the pairs; of these: 6771624 (69.81%) aligned 0 times 1534395 (15.82%) aligned exactly 1 time 1394309 (14.37%) aligned >1 times 65.08% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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] 381343 / 4829679 = 0.0790 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 20:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.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 20:25:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:25:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:25:18: 1000000 INFO @ Sat, 15 Jan 2022 20:25:23: 2000000 INFO @ Sat, 15 Jan 2022 20:25:28: 3000000 INFO @ Sat, 15 Jan 2022 20:25:32: 4000000 INFO @ Sat, 15 Jan 2022 20:25:37: 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 20:25:42: 6000000 INFO @ Sat, 15 Jan 2022 20:25:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.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 20:25:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:25:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:25:47: 7000000 INFO @ Sat, 15 Jan 2022 20:25:48: 1000000 INFO @ Sat, 15 Jan 2022 20:25:52: 8000000 INFO @ Sat, 15 Jan 2022 20:25:53: 2000000 INFO @ Sat, 15 Jan 2022 20:25:57: 9000000 INFO @ Sat, 15 Jan 2022 20:25:58: 3000000 INFO @ Sat, 15 Jan 2022 20:26:02: 4000000 INFO @ Sat, 15 Jan 2022 20:26:03: 10000000 INFO @ Sat, 15 Jan 2022 20:26:07: 5000000 INFO @ Sat, 15 Jan 2022 20:26:09: 11000000 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 20:26:12: 6000000 INFO @ Sat, 15 Jan 2022 20:26:13: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:26:13: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:26:13: #1 total tags in treatment: 4388153 INFO @ Sat, 15 Jan 2022 20:26:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:26:13: #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 20:26:13: #1 tags after filtering in treatment: 2179256 INFO @ Sat, 15 Jan 2022 20:26:13: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 20:26:13: #1 finished! INFO @ Sat, 15 Jan 2022 20:26:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:26:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:26:13: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:26:13: 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 20:26:13: start model_add_line... INFO @ Sat, 15 Jan 2022 20:26:13: start X-correlation... INFO @ Sat, 15 Jan 2022 20:26:13: end of X-cor INFO @ Sat, 15 Jan 2022 20:26:13: #2 finished! INFO @ Sat, 15 Jan 2022 20:26:13: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Jan 2022 20:26:13: #2 alternative fragment length(s) may be 0,178,182,202,223,574,596 bps INFO @ Sat, 15 Jan 2022 20:26:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.05_model.r INFO @ Sat, 15 Jan 2022 20:26:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:26:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.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 20:26:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:26:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:26:17: 7000000 INFO @ Sat, 15 Jan 2022 20:26:19: 1000000 INFO @ Sat, 15 Jan 2022 20:26:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:26:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:26:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:26:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.05_summits.bed INFO @ Sat, 15 Jan 2022 20:26:21: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (359 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:26:22: 8000000 INFO @ Sat, 15 Jan 2022 20:26:25: 2000000 INFO @ Sat, 15 Jan 2022 20:26:27: 9000000 INFO @ Sat, 15 Jan 2022 20:26:31: 3000000 INFO @ Sat, 15 Jan 2022 20:26:32: 10000000 INFO @ Sat, 15 Jan 2022 20:26:37: 4000000 INFO @ Sat, 15 Jan 2022 20:26:38: 11000000 INFO @ Sat, 15 Jan 2022 20:26:42: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:26:42: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:26:42: #1 total tags in treatment: 4388153 INFO @ Sat, 15 Jan 2022 20:26:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:26:42: #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 20:26:42: #1 tags after filtering in treatment: 2179256 INFO @ Sat, 15 Jan 2022 20:26:42: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 20:26:42: #1 finished! INFO @ Sat, 15 Jan 2022 20:26:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:26:42: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:26:42: 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 20:26:42: start model_add_line... INFO @ Sat, 15 Jan 2022 20:26:42: start X-correlation... INFO @ Sat, 15 Jan 2022 20:26:42: end of X-cor INFO @ Sat, 15 Jan 2022 20:26:42: #2 finished! INFO @ Sat, 15 Jan 2022 20:26:42: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Jan 2022 20:26:42: #2 alternative fragment length(s) may be 0,178,182,202,223,574,596 bps INFO @ Sat, 15 Jan 2022 20:26:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.10_model.r INFO @ Sat, 15 Jan 2022 20:26:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:26:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:26:43: 5000000 INFO @ Sat, 15 Jan 2022 20:26:48: 6000000 INFO @ Sat, 15 Jan 2022 20:26:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.10_summits.bed INFO @ Sat, 15 Jan 2022 20:26:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:26:54: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:26:59: 8000000 INFO @ Sat, 15 Jan 2022 20:27:05: 9000000 INFO @ Sat, 15 Jan 2022 20:27:11: 10000000 INFO @ Sat, 15 Jan 2022 20:27:16: 11000000 INFO @ Sat, 15 Jan 2022 20:27:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:27:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:27:21: #1 total tags in treatment: 4388153 INFO @ Sat, 15 Jan 2022 20:27:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:27:21: #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 20:27:21: #1 tags after filtering in treatment: 2179256 INFO @ Sat, 15 Jan 2022 20:27:21: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 20:27:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:27:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:27:21: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:27:21: 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 20:27:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:27:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:27:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:27:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:27:21: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Jan 2022 20:27:21: #2 alternative fragment length(s) may be 0,178,182,202,223,574,596 bps INFO @ Sat, 15 Jan 2022 20:27:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.20_model.r INFO @ Sat, 15 Jan 2022 20:27:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:27:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:27:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:27:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:27:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245432/SRX8245432.20_summits.bed INFO @ Sat, 15 Jan 2022 20:27:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 millis CompletedMACS2peakCalling