Job ID = 14521287 SRX = SRX8952619 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17454208 spots for SRR12458267/SRR12458267.sra Written 17454208 spots for SRR12458267/SRR12458267.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: 00:04:23 17454208 reads; of these: 17454208 (100.00%) were paired; of these: 15265449 (87.46%) aligned concordantly 0 times 1876294 (10.75%) aligned concordantly exactly 1 time 312465 (1.79%) aligned concordantly >1 times ---- 15265449 pairs aligned concordantly 0 times; of these: 513512 (3.36%) aligned discordantly 1 time ---- 14751937 pairs aligned 0 times concordantly or discordantly; of these: 29503874 mates make up the pairs; of these: 27498817 (93.20%) aligned 0 times 1678707 (5.69%) aligned exactly 1 time 326350 (1.11%) aligned >1 times 21.23% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 915394 / 2689554 = 0.3404 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 20:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.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 20:55:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:53: 1000000 INFO @ Sat, 15 Jan 2022 20:55:58: 2000000 INFO @ Sat, 15 Jan 2022 20:56:04: 3000000 INFO @ Sat, 15 Jan 2022 20:56:10: 4000000 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 20:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.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 20:56:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:16: 5000000 INFO @ Sat, 15 Jan 2022 20:56:20: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:56:20: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:56:20: #1 total tags in treatment: 1604181 INFO @ Sat, 15 Jan 2022 20:56:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:56:20: #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 20:56:20: #1 tags after filtering in treatment: 1384694 INFO @ Sat, 15 Jan 2022 20:56:20: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 20:56:20: #1 finished! INFO @ Sat, 15 Jan 2022 20:56:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:56:20: #2 number of paired peaks: 212 WARNING @ Sat, 15 Jan 2022 20:56:20: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 15 Jan 2022 20:56:20: start model_add_line... INFO @ Sat, 15 Jan 2022 20:56:20: start X-correlation... INFO @ Sat, 15 Jan 2022 20:56:20: end of X-cor INFO @ Sat, 15 Jan 2022 20:56:20: #2 finished! INFO @ Sat, 15 Jan 2022 20:56:20: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 20:56:20: #2 alternative fragment length(s) may be 4,242 bps INFO @ Sat, 15 Jan 2022 20:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.05_model.r INFO @ Sat, 15 Jan 2022 20:56:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:56:23: 1000000 INFO @ Sat, 15 Jan 2022 20:56:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.05_summits.bed INFO @ Sat, 15 Jan 2022 20:56:26: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (620 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:56:30: 2000000 INFO @ Sat, 15 Jan 2022 20:56:37: 3000000 INFO @ Sat, 15 Jan 2022 20:56:43: 4000000 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 20:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.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 20:56:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:49: 5000000 INFO @ Sat, 15 Jan 2022 20:56:52: 1000000 INFO @ Sat, 15 Jan 2022 20:56:53: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:56:53: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:56:53: #1 total tags in treatment: 1604181 INFO @ Sat, 15 Jan 2022 20:56:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:56:53: #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 20:56:53: #1 tags after filtering in treatment: 1384694 INFO @ Sat, 15 Jan 2022 20:56:53: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 20:56:53: #1 finished! INFO @ Sat, 15 Jan 2022 20:56:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:56:53: #2 number of paired peaks: 212 WARNING @ Sat, 15 Jan 2022 20:56:53: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 15 Jan 2022 20:56:53: start model_add_line... INFO @ Sat, 15 Jan 2022 20:56:53: start X-correlation... INFO @ Sat, 15 Jan 2022 20:56:53: end of X-cor INFO @ Sat, 15 Jan 2022 20:56:53: #2 finished! INFO @ Sat, 15 Jan 2022 20:56:53: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 20:56:53: #2 alternative fragment length(s) may be 4,242 bps INFO @ Sat, 15 Jan 2022 20:56:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.10_model.r INFO @ Sat, 15 Jan 2022 20:56:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:56:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:56:58: 2000000 INFO @ Sat, 15 Jan 2022 20:56:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:56:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:56:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.10_summits.bed INFO @ Sat, 15 Jan 2022 20:56:59: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:57:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:57:10: 4000000 INFO @ Sat, 15 Jan 2022 20:57:16: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:57:19: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:57:19: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:57:19: #1 total tags in treatment: 1604181 INFO @ Sat, 15 Jan 2022 20:57:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:19: #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 20:57:19: #1 tags after filtering in treatment: 1384694 INFO @ Sat, 15 Jan 2022 20:57:19: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 20:57:19: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:19: #2 number of paired peaks: 212 WARNING @ Sat, 15 Jan 2022 20:57:19: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 15 Jan 2022 20:57:19: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:19: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:19: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:19: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:19: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 20:57:19: #2 alternative fragment length(s) may be 4,242 bps INFO @ Sat, 15 Jan 2022 20:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.20_model.r INFO @ Sat, 15 Jan 2022 20:57:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:57:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952619/SRX8952619.20_summits.bed INFO @ Sat, 15 Jan 2022 20:57:25: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 2 millis CompletedMACS2peakCalling