Job ID = 14520897 SRX = SRX8245433 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11701635 spots for SRR11684644/SRR11684644.sra Written 11701635 spots for SRR11684644/SRR11684644.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: 00:20:10 11701635 reads; of these: 11701635 (100.00%) were paired; of these: 5595645 (47.82%) aligned concordantly 0 times 2831220 (24.20%) aligned concordantly exactly 1 time 3274770 (27.99%) aligned concordantly >1 times ---- 5595645 pairs aligned concordantly 0 times; of these: 72070 (1.29%) aligned discordantly 1 time ---- 5523575 pairs aligned 0 times concordantly or discordantly; of these: 11047150 mates make up the pairs; of these: 7321389 (66.27%) aligned 0 times 1788027 (16.19%) aligned exactly 1 time 1937734 (17.54%) aligned >1 times 68.72% overall alignment rate Time searching: 00:20:10 Overall time: 00:20:10 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] 481978 / 6176810 = 0.0780 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 20:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.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 20:31:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:31:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:31:40: 1000000 INFO @ Sat, 15 Jan 2022 20:31:46: 2000000 INFO @ Sat, 15 Jan 2022 20:31:52: 3000000 INFO @ Sat, 15 Jan 2022 20:31:58: 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 20:32:04: 5000000 INFO @ Sat, 15 Jan 2022 20:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.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 20:32:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:32:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:32:10: 1000000 INFO @ Sat, 15 Jan 2022 20:32:11: 6000000 INFO @ Sat, 15 Jan 2022 20:32:16: 2000000 INFO @ Sat, 15 Jan 2022 20:32:17: 7000000 INFO @ Sat, 15 Jan 2022 20:32:22: 3000000 INFO @ Sat, 15 Jan 2022 20:32:24: 8000000 INFO @ Sat, 15 Jan 2022 20:32:27: 4000000 INFO @ Sat, 15 Jan 2022 20:32:31: 9000000 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 20:32:33: 5000000 INFO @ Sat, 15 Jan 2022 20:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.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 20:32:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:32:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:32:38: 10000000 INFO @ Sat, 15 Jan 2022 20:32:39: 6000000 INFO @ Sat, 15 Jan 2022 20:32:40: 1000000 INFO @ Sat, 15 Jan 2022 20:32:45: 11000000 INFO @ Sat, 15 Jan 2022 20:32:45: 7000000 INFO @ Sat, 15 Jan 2022 20:32:46: 2000000 INFO @ Sat, 15 Jan 2022 20:32:51: 8000000 INFO @ Sat, 15 Jan 2022 20:32:52: 12000000 INFO @ Sat, 15 Jan 2022 20:32:52: 3000000 INFO @ Sat, 15 Jan 2022 20:32:57: 9000000 INFO @ Sat, 15 Jan 2022 20:32:58: 4000000 INFO @ Sat, 15 Jan 2022 20:32:58: 13000000 INFO @ Sat, 15 Jan 2022 20:33:03: 10000000 INFO @ Sat, 15 Jan 2022 20:33:03: 5000000 INFO @ Sat, 15 Jan 2022 20:33:05: 14000000 INFO @ Sat, 15 Jan 2022 20:33:09: 6000000 INFO @ Sat, 15 Jan 2022 20:33:10: 11000000 INFO @ Sat, 15 Jan 2022 20:33:12: 15000000 INFO @ Sat, 15 Jan 2022 20:33:13: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:33:13: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:33:13: #1 total tags in treatment: 5625347 INFO @ Sat, 15 Jan 2022 20:33:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:33:13: #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 20:33:13: #1 tags after filtering in treatment: 2379504 INFO @ Sat, 15 Jan 2022 20:33:13: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 15 Jan 2022 20:33:13: #1 finished! INFO @ Sat, 15 Jan 2022 20:33:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:33:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:33:13: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 20:33:13: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 20:33:13: start model_add_line... INFO @ Sat, 15 Jan 2022 20:33:13: start X-correlation... INFO @ Sat, 15 Jan 2022 20:33:13: end of X-cor INFO @ Sat, 15 Jan 2022 20:33:13: #2 finished! INFO @ Sat, 15 Jan 2022 20:33:13: #2 predicted fragment length is 331 bps INFO @ Sat, 15 Jan 2022 20:33:13: #2 alternative fragment length(s) may be 2,331,360 bps INFO @ Sat, 15 Jan 2022 20:33:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.05_model.r INFO @ Sat, 15 Jan 2022 20:33:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:33:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:33:15: 7000000 INFO @ Sat, 15 Jan 2022 20:33:16: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:33:21: 8000000 INFO @ Sat, 15 Jan 2022 20:33:22: 13000000 INFO @ Sat, 15 Jan 2022 20:33:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:33:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:33:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:33:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.05_summits.bed INFO @ Sat, 15 Jan 2022 20:33:26: 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 20:33:27: 9000000 INFO @ Sat, 15 Jan 2022 20:33:28: 14000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:33:33: 10000000 INFO @ Sat, 15 Jan 2022 20:33:34: 15000000 INFO @ Sat, 15 Jan 2022 20:33:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:33:34: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:33:34: #1 total tags in treatment: 5625347 INFO @ Sat, 15 Jan 2022 20:33:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:33:34: #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 20:33:34: #1 tags after filtering in treatment: 2379504 INFO @ Sat, 15 Jan 2022 20:33:34: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 15 Jan 2022 20:33:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:33:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:33:35: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 20:33:35: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 20:33:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:33:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:33:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:33:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:33:35: #2 predicted fragment length is 331 bps INFO @ Sat, 15 Jan 2022 20:33:35: #2 alternative fragment length(s) may be 2,331,360 bps INFO @ Sat, 15 Jan 2022 20:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.10_model.r INFO @ Sat, 15 Jan 2022 20:33:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:33:40: 11000000 INFO @ Sat, 15 Jan 2022 20:33:45: 12000000 INFO @ Sat, 15 Jan 2022 20:33:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.10_summits.bed INFO @ Sat, 15 Jan 2022 20:33:47: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (257 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:33:51: 13000000 INFO @ Sat, 15 Jan 2022 20:33:56: 14000000 INFO @ Sat, 15 Jan 2022 20:34:02: 15000000 INFO @ Sat, 15 Jan 2022 20:34:02: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:34:02: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:34:02: #1 total tags in treatment: 5625347 INFO @ Sat, 15 Jan 2022 20:34:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:34:02: #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 20:34:02: #1 tags after filtering in treatment: 2379504 INFO @ Sat, 15 Jan 2022 20:34:02: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 15 Jan 2022 20:34:02: #1 finished! INFO @ Sat, 15 Jan 2022 20:34:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:34:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:34:02: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 20:34:02: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 20:34:02: start model_add_line... INFO @ Sat, 15 Jan 2022 20:34:02: start X-correlation... INFO @ Sat, 15 Jan 2022 20:34:02: end of X-cor INFO @ Sat, 15 Jan 2022 20:34:02: #2 finished! INFO @ Sat, 15 Jan 2022 20:34:02: #2 predicted fragment length is 331 bps INFO @ Sat, 15 Jan 2022 20:34:02: #2 alternative fragment length(s) may be 2,331,360 bps INFO @ Sat, 15 Jan 2022 20:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.20_model.r INFO @ Sat, 15 Jan 2022 20:34:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:34:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245433/SRX8245433.20_summits.bed INFO @ Sat, 15 Jan 2022 20:34:15: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 1 millis CompletedMACS2peakCalling