Job ID = 14521200 SRX = SRX8245378 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8887029 spots for SRR11684589/SRR11684589.sra Written 8887029 spots for SRR11684589/SRR11684589.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: 00:06:45 8887029 reads; of these: 8887029 (100.00%) were paired; of these: 6317466 (71.09%) aligned concordantly 0 times 1912462 (21.52%) aligned concordantly exactly 1 time 657101 (7.39%) aligned concordantly >1 times ---- 6317466 pairs aligned concordantly 0 times; of these: 81178 (1.28%) aligned discordantly 1 time ---- 6236288 pairs aligned 0 times concordantly or discordantly; of these: 12472576 mates make up the pairs; of these: 7782429 (62.40%) aligned 0 times 3450595 (27.67%) aligned exactly 1 time 1239552 (9.94%) aligned >1 times 56.21% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 196953 / 2650142 = 0.0743 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 20:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.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 20:47:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:47:18: 1000000 INFO @ Sat, 15 Jan 2022 20:47:23: 2000000 INFO @ Sat, 15 Jan 2022 20:47:28: 3000000 INFO @ Sat, 15 Jan 2022 20:47:32: 4000000 INFO @ Sat, 15 Jan 2022 20:47:37: 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 20:47:42: 6000000 INFO @ Sat, 15 Jan 2022 20:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.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 20:47:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:47:47: 7000000 INFO @ Sat, 15 Jan 2022 20:47:49: 1000000 INFO @ Sat, 15 Jan 2022 20:47:53: 8000000 INFO @ Sat, 15 Jan 2022 20:47:55: 2000000 INFO @ Sat, 15 Jan 2022 20:47:58: 9000000 INFO @ Sat, 15 Jan 2022 20:48:00: 3000000 INFO @ Sat, 15 Jan 2022 20:48:02: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:48:02: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:48:02: #1 total tags in treatment: 2376291 INFO @ Sat, 15 Jan 2022 20:48:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:02: #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 20:48:02: #1 tags after filtering in treatment: 1734482 INFO @ Sat, 15 Jan 2022 20:48:02: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:48:02: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:02: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:48:02: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:02: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:02: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:02: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:02: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:02: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Jan 2022 20:48:02: #2 alternative fragment length(s) may be 0,85,144,177,208,241,257,291,356,358 bps INFO @ Sat, 15 Jan 2022 20:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.05_model.r INFO @ Sat, 15 Jan 2022 20:48:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:48:05: 4000000 INFO @ Sat, 15 Jan 2022 20:48:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.05_summits.bed INFO @ Sat, 15 Jan 2022 20:48:09: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:48:10: 5000000 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 20:48:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.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 20:48:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:16: 6000000 INFO @ Sat, 15 Jan 2022 20:48:20: 1000000 INFO @ Sat, 15 Jan 2022 20:48:22: 7000000 INFO @ Sat, 15 Jan 2022 20:48:27: 2000000 INFO @ Sat, 15 Jan 2022 20:48:28: 8000000 INFO @ Sat, 15 Jan 2022 20:48:33: 3000000 INFO @ Sat, 15 Jan 2022 20:48:34: 9000000 INFO @ Sat, 15 Jan 2022 20:48:37: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:48:37: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:48:37: #1 total tags in treatment: 2376291 INFO @ Sat, 15 Jan 2022 20:48:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:37: #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 20:48:37: #1 tags after filtering in treatment: 1734482 INFO @ Sat, 15 Jan 2022 20:48:37: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:48:37: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:38: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:48:38: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:38: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:38: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:38: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:38: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:38: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Jan 2022 20:48:38: #2 alternative fragment length(s) may be 0,85,144,177,208,241,257,291,356,358 bps INFO @ Sat, 15 Jan 2022 20:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.10_model.r INFO @ Sat, 15 Jan 2022 20:48:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:48:39: 4000000 INFO @ Sat, 15 Jan 2022 20:48:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:48:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:48:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:48:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.10_summits.bed INFO @ Sat, 15 Jan 2022 20:48:45: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (106 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:48:45: 5000000 INFO @ Sat, 15 Jan 2022 20:48:51: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:48:57: 7000000 INFO @ Sat, 15 Jan 2022 20:49:03: 8000000 INFO @ Sat, 15 Jan 2022 20:49:09: 9000000 INFO @ Sat, 15 Jan 2022 20:49:12: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:49:12: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:49:12: #1 total tags in treatment: 2376291 INFO @ Sat, 15 Jan 2022 20:49:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:12: #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 20:49:12: #1 tags after filtering in treatment: 1734482 INFO @ Sat, 15 Jan 2022 20:49:12: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:49:12: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:12: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:49:12: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:12: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:12: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:12: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:12: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:12: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Jan 2022 20:49:12: #2 alternative fragment length(s) may be 0,85,144,177,208,241,257,291,356,358 bps INFO @ Sat, 15 Jan 2022 20:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.20_model.r INFO @ Sat, 15 Jan 2022 20:49:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245378/SRX8245378.20_summits.bed INFO @ Sat, 15 Jan 2022 20:49:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling