Job ID = 10224082 SRX = SRX8952638 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4696835 spots for SRR12458248/SRR12458248.sra Written 4696835 spots for SRR12458248/SRR12458248.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: 00:09:08 4696835 reads; of these: 4696835 (100.00%) were paired; of these: 3551822 (75.62%) aligned concordantly 0 times 894201 (19.04%) aligned concordantly exactly 1 time 250812 (5.34%) aligned concordantly >1 times ---- 3551822 pairs aligned concordantly 0 times; of these: 4421 (0.12%) aligned discordantly 1 time ---- 3547401 pairs aligned 0 times concordantly or discordantly; of these: 7094802 mates make up the pairs; of these: 2867464 (40.42%) aligned 0 times 1330869 (18.76%) aligned exactly 1 time 2896469 (40.83%) aligned >1 times 69.47% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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] 224665 / 1144867 = 0.1962 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 @ Fri, 16 Oct 2020 09:31:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.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 @ Fri, 16 Oct 2020 09:31:56: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:31:56: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:32:01: 1000000 INFO @ Fri, 16 Oct 2020 09:32:05: 2000000 INFO @ Fri, 16 Oct 2020 09:32:09: 3000000 INFO @ Fri, 16 Oct 2020 09:32:12: 4000000 INFO @ Fri, 16 Oct 2020 09:32:16: 5000000 INFO @ Fri, 16 Oct 2020 09:32:20: 6000000 INFO @ Fri, 16 Oct 2020 09:32:21: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:32:21: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:32:21: #1 total tags in treatment: 920360 INFO @ Fri, 16 Oct 2020 09:32:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:32:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:32:21: #1 tags after filtering in treatment: 832068 INFO @ Fri, 16 Oct 2020 09:32:21: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:32:21: #1 finished! INFO @ Fri, 16 Oct 2020 09:32:21: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:32:21: #2 number of paired peaks: 188 WARNING @ Fri, 16 Oct 2020 09:32:21: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Fri, 16 Oct 2020 09:32:21: start model_add_line... INFO @ Fri, 16 Oct 2020 09:32:21: start X-correlation... INFO @ Fri, 16 Oct 2020 09:32:21: end of X-cor INFO @ Fri, 16 Oct 2020 09:32:21: #2 finished! INFO @ Fri, 16 Oct 2020 09:32:21: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Oct 2020 09:32:21: #2 alternative fragment length(s) may be 1,45,98,150,188,202,252,272,323,353,418,440,499,525,570 bps INFO @ Fri, 16 Oct 2020 09:32:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.05_model.r INFO @ Fri, 16 Oct 2020 09:32:21: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:32:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:32:23: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:32:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:32:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:32:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.05_summits.bed INFO @ Fri, 16 Oct 2020 09:32:24: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Fri, 16 Oct 2020 09:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.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 @ Fri, 16 Oct 2020 09:32:26: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:32:26: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:32:30: 1000000 INFO @ Fri, 16 Oct 2020 09:32:34: 2000000 INFO @ Fri, 16 Oct 2020 09:32:38: 3000000 INFO @ Fri, 16 Oct 2020 09:32:41: 4000000 INFO @ Fri, 16 Oct 2020 09:32:45: 5000000 INFO @ Fri, 16 Oct 2020 09:32:49: 6000000 INFO @ Fri, 16 Oct 2020 09:32:49: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:32:49: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:32:49: #1 total tags in treatment: 920360 INFO @ Fri, 16 Oct 2020 09:32:49: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:32:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:32:49: #1 tags after filtering in treatment: 832068 INFO @ Fri, 16 Oct 2020 09:32:49: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:32:49: #1 finished! INFO @ Fri, 16 Oct 2020 09:32:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:32:50: #2 number of paired peaks: 188 WARNING @ Fri, 16 Oct 2020 09:32:50: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Fri, 16 Oct 2020 09:32:50: start model_add_line... INFO @ Fri, 16 Oct 2020 09:32:50: start X-correlation... INFO @ Fri, 16 Oct 2020 09:32:50: end of X-cor INFO @ Fri, 16 Oct 2020 09:32:50: #2 finished! INFO @ Fri, 16 Oct 2020 09:32:50: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Oct 2020 09:32:50: #2 alternative fragment length(s) may be 1,45,98,150,188,202,252,272,323,353,418,440,499,525,570 bps INFO @ Fri, 16 Oct 2020 09:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.10_model.r INFO @ Fri, 16 Oct 2020 09:32:50: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:32:52: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:32:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:32:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:32:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.10_summits.bed INFO @ Fri, 16 Oct 2020 09:32:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Fri, 16 Oct 2020 09:32:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.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 @ Fri, 16 Oct 2020 09:32:56: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:32:56: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:33:01: 1000000 INFO @ Fri, 16 Oct 2020 09:33:06: 2000000 INFO @ Fri, 16 Oct 2020 09:33:11: 3000000 INFO @ Fri, 16 Oct 2020 09:33:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:33:20: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:33:25: 6000000 INFO @ Fri, 16 Oct 2020 09:33:25: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:33:25: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:33:25: #1 total tags in treatment: 920360 INFO @ Fri, 16 Oct 2020 09:33:25: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:33:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:33:25: #1 tags after filtering in treatment: 832068 INFO @ Fri, 16 Oct 2020 09:33:25: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:33:25: #1 finished! INFO @ Fri, 16 Oct 2020 09:33:25: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:33:25: #2 number of paired peaks: 188 WARNING @ Fri, 16 Oct 2020 09:33:25: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Fri, 16 Oct 2020 09:33:25: start model_add_line... INFO @ Fri, 16 Oct 2020 09:33:25: start X-correlation... INFO @ Fri, 16 Oct 2020 09:33:25: end of X-cor INFO @ Fri, 16 Oct 2020 09:33:25: #2 finished! INFO @ Fri, 16 Oct 2020 09:33:25: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Oct 2020 09:33:25: #2 alternative fragment length(s) may be 1,45,98,150,188,202,252,272,323,353,418,440,499,525,570 bps INFO @ Fri, 16 Oct 2020 09:33:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.20_model.r INFO @ Fri, 16 Oct 2020 09:33:25: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:33:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:33:27: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:33:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:33:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:33:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952638/SRX8952638.20_summits.bed INFO @ Fri, 16 Oct 2020 09:33:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (23 records, 4 fields): 1 millis CompletedMACS2peakCalling