Job ID = 14520901 SRX = SRX8245437 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12960750 spots for SRR11684648/SRR11684648.sra Written 12960750 spots for SRR11684648/SRR11684648.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: 00:16:27 12960750 reads; of these: 12960750 (100.00%) were paired; of these: 7717241 (59.54%) aligned concordantly 0 times 2881108 (22.23%) aligned concordantly exactly 1 time 2362401 (18.23%) aligned concordantly >1 times ---- 7717241 pairs aligned concordantly 0 times; of these: 148363 (1.92%) aligned discordantly 1 time ---- 7568878 pairs aligned 0 times concordantly or discordantly; of these: 15137756 mates make up the pairs; of these: 10512690 (69.45%) aligned 0 times 2619656 (17.31%) aligned exactly 1 time 2005410 (13.25%) aligned >1 times 59.44% overall alignment rate Time searching: 00:16:27 Overall time: 00:16:27 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] 756999 / 5390660 = 0.1404 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 20:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.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 20:28:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:28:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:28:47: 1000000 INFO @ Sat, 15 Jan 2022 20:28:51: 2000000 INFO @ Sat, 15 Jan 2022 20:28:56: 3000000 INFO @ Sat, 15 Jan 2022 20:29:00: 4000000 INFO @ Sat, 15 Jan 2022 20:29:05: 5000000 INFO @ Sat, 15 Jan 2022 20:29:10: 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 20:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.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 20:29:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:29:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:29:15: 7000000 INFO @ Sat, 15 Jan 2022 20:29:18: 1000000 INFO @ Sat, 15 Jan 2022 20:29:20: 8000000 INFO @ Sat, 15 Jan 2022 20:29:25: 2000000 INFO @ Sat, 15 Jan 2022 20:29:26: 9000000 INFO @ Sat, 15 Jan 2022 20:29:31: 10000000 INFO @ Sat, 15 Jan 2022 20:29:32: 3000000 INFO @ Sat, 15 Jan 2022 20:29:37: 11000000 INFO @ Sat, 15 Jan 2022 20:29:38: 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 20:29:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.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 20:29:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:29:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:29:42: 12000000 INFO @ Sat, 15 Jan 2022 20:29:45: 5000000 INFO @ Sat, 15 Jan 2022 20:29:48: 1000000 INFO @ Sat, 15 Jan 2022 20:29:48: 13000000 INFO @ Sat, 15 Jan 2022 20:29:51: 6000000 INFO @ Sat, 15 Jan 2022 20:29:53: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:29:53: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:29:53: #1 total tags in treatment: 4535994 INFO @ Sat, 15 Jan 2022 20:29:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:29:53: #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 20:29:53: #1 tags after filtering in treatment: 2177427 INFO @ Sat, 15 Jan 2022 20:29:53: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 20:29:53: #1 finished! INFO @ Sat, 15 Jan 2022 20:29:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:29:53: #2 number of paired peaks: 206 WARNING @ Sat, 15 Jan 2022 20:29:53: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Jan 2022 20:29:53: start model_add_line... INFO @ Sat, 15 Jan 2022 20:29:53: start X-correlation... INFO @ Sat, 15 Jan 2022 20:29:53: end of X-cor INFO @ Sat, 15 Jan 2022 20:29:53: #2 finished! INFO @ Sat, 15 Jan 2022 20:29:53: #2 predicted fragment length is 360 bps INFO @ Sat, 15 Jan 2022 20:29:53: #2 alternative fragment length(s) may be 2,327,340,360,388,390 bps INFO @ Sat, 15 Jan 2022 20:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.05_model.r INFO @ Sat, 15 Jan 2022 20:29:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:29:53: 2000000 INFO @ Sat, 15 Jan 2022 20:29:58: 7000000 INFO @ Sat, 15 Jan 2022 20:29:59: 3000000 INFO @ Sat, 15 Jan 2022 20:30:05: 4000000 INFO @ Sat, 15 Jan 2022 20:30:05: 8000000 INFO @ Sat, 15 Jan 2022 20:30:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:30:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:30:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:30:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.05_summits.bed INFO @ Sat, 15 Jan 2022 20:30:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (645 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:30:10: 5000000 INFO @ Sat, 15 Jan 2022 20:30:11: 9000000 INFO @ Sat, 15 Jan 2022 20:30:16: 6000000 INFO @ Sat, 15 Jan 2022 20:30:18: 10000000 INFO @ Sat, 15 Jan 2022 20:30:21: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:30:24: 11000000 INFO @ Sat, 15 Jan 2022 20:30:27: 8000000 INFO @ Sat, 15 Jan 2022 20:30:31: 12000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:30:32: 9000000 INFO @ Sat, 15 Jan 2022 20:30:38: 13000000 INFO @ Sat, 15 Jan 2022 20:30:38: 10000000 INFO @ Sat, 15 Jan 2022 20:30:43: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:30:43: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:30:43: #1 total tags in treatment: 4535994 INFO @ Sat, 15 Jan 2022 20:30:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:30:43: #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 20:30:44: #1 tags after filtering in treatment: 2177427 INFO @ Sat, 15 Jan 2022 20:30:44: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 20:30:44: #1 finished! INFO @ Sat, 15 Jan 2022 20:30:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:30:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:30:44: #2 number of paired peaks: 206 WARNING @ Sat, 15 Jan 2022 20:30:44: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Jan 2022 20:30:44: start model_add_line... INFO @ Sat, 15 Jan 2022 20:30:44: start X-correlation... INFO @ Sat, 15 Jan 2022 20:30:44: end of X-cor INFO @ Sat, 15 Jan 2022 20:30:44: #2 finished! INFO @ Sat, 15 Jan 2022 20:30:44: #2 predicted fragment length is 360 bps INFO @ Sat, 15 Jan 2022 20:30:44: #2 alternative fragment length(s) may be 2,327,340,360,388,390 bps INFO @ Sat, 15 Jan 2022 20:30:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.10_model.r INFO @ Sat, 15 Jan 2022 20:30:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:30:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:30:44: 11000000 INFO @ Sat, 15 Jan 2022 20:30:50: 12000000 INFO @ Sat, 15 Jan 2022 20:30:55: 13000000 INFO @ Sat, 15 Jan 2022 20:30:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.10_summits.bed INFO @ Sat, 15 Jan 2022 20:30:58: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (446 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:31:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:31:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:31:00: #1 total tags in treatment: 4535994 INFO @ Sat, 15 Jan 2022 20:31:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:31:00: #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 20:31:00: #1 tags after filtering in treatment: 2177427 INFO @ Sat, 15 Jan 2022 20:31:00: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 20:31:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:31:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:31:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:31:00: #2 number of paired peaks: 206 WARNING @ Sat, 15 Jan 2022 20:31:00: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Jan 2022 20:31:00: start model_add_line... INFO @ Sat, 15 Jan 2022 20:31:00: start X-correlation... INFO @ Sat, 15 Jan 2022 20:31:00: end of X-cor INFO @ Sat, 15 Jan 2022 20:31:00: #2 finished! INFO @ Sat, 15 Jan 2022 20:31:00: #2 predicted fragment length is 360 bps INFO @ Sat, 15 Jan 2022 20:31:00: #2 alternative fragment length(s) may be 2,327,340,360,388,390 bps INFO @ Sat, 15 Jan 2022 20:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.20_model.r INFO @ Sat, 15 Jan 2022 20:31:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:31:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:31:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245437/SRX8245437.20_summits.bed INFO @ Sat, 15 Jan 2022 20:31:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling