Job ID = 14520740 SRX = SRX8245502 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12413690 spots for SRR11684713/SRR11684713.sra Written 12413690 spots for SRR11684713/SRR11684713.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: 00:12:37 12413690 reads; of these: 12413690 (100.00%) were paired; of these: 8203552 (66.08%) aligned concordantly 0 times 3456925 (27.85%) aligned concordantly exactly 1 time 753213 (6.07%) aligned concordantly >1 times ---- 8203552 pairs aligned concordantly 0 times; of these: 118650 (1.45%) aligned discordantly 1 time ---- 8084902 pairs aligned 0 times concordantly or discordantly; of these: 16169804 mates make up the pairs; of these: 9770193 (60.42%) aligned 0 times 5186854 (32.08%) aligned exactly 1 time 1212757 (7.50%) aligned >1 times 60.65% overall alignment rate Time searching: 00:12:37 Overall time: 00:12:37 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] 236512 / 4327380 = 0.0547 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 20:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.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 20:04:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:04:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:04:58: 1000000 INFO @ Sat, 15 Jan 2022 20:05:05: 2000000 INFO @ Sat, 15 Jan 2022 20:05:13: 3000000 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 20:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.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 20:05:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:05:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:05:21: 4000000 INFO @ Sat, 15 Jan 2022 20:05:28: 1000000 INFO @ Sat, 15 Jan 2022 20:05:29: 5000000 INFO @ Sat, 15 Jan 2022 20:05:36: 2000000 INFO @ Sat, 15 Jan 2022 20:05:36: 6000000 INFO @ Sat, 15 Jan 2022 20:05:45: 7000000 INFO @ Sat, 15 Jan 2022 20:05:45: 3000000 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 20:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.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 20:05:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:05:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:05:53: 8000000 INFO @ Sat, 15 Jan 2022 20:05:53: 4000000 INFO @ Sat, 15 Jan 2022 20:05:57: 1000000 INFO @ Sat, 15 Jan 2022 20:06:02: 9000000 INFO @ Sat, 15 Jan 2022 20:06:02: 5000000 INFO @ Sat, 15 Jan 2022 20:06:04: 2000000 INFO @ Sat, 15 Jan 2022 20:06:10: 6000000 INFO @ Sat, 15 Jan 2022 20:06:10: 10000000 INFO @ Sat, 15 Jan 2022 20:06:11: 3000000 INFO @ Sat, 15 Jan 2022 20:06:19: 7000000 INFO @ Sat, 15 Jan 2022 20:06:19: 11000000 INFO @ Sat, 15 Jan 2022 20:06:19: 4000000 INFO @ Sat, 15 Jan 2022 20:06:26: 5000000 INFO @ Sat, 15 Jan 2022 20:06:27: 8000000 INFO @ Sat, 15 Jan 2022 20:06:28: 12000000 INFO @ Sat, 15 Jan 2022 20:06:33: 6000000 INFO @ Sat, 15 Jan 2022 20:06:36: 9000000 INFO @ Sat, 15 Jan 2022 20:06:36: 13000000 INFO @ Sat, 15 Jan 2022 20:06:40: 7000000 INFO @ Sat, 15 Jan 2022 20:06:44: 10000000 INFO @ Sat, 15 Jan 2022 20:06:44: 14000000 INFO @ Sat, 15 Jan 2022 20:06:47: 8000000 INFO @ Sat, 15 Jan 2022 20:06:49: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:06:49: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:06:49: #1 total tags in treatment: 3976614 INFO @ Sat, 15 Jan 2022 20:06:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:06:49: #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 20:06:49: #1 tags after filtering in treatment: 2757375 INFO @ Sat, 15 Jan 2022 20:06:49: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 20:06:49: #1 finished! INFO @ Sat, 15 Jan 2022 20:06:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:06:49: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 20:06:49: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 20:06:49: start model_add_line... INFO @ Sat, 15 Jan 2022 20:06:49: start X-correlation... INFO @ Sat, 15 Jan 2022 20:06:49: end of X-cor INFO @ Sat, 15 Jan 2022 20:06:49: #2 finished! INFO @ Sat, 15 Jan 2022 20:06:49: #2 predicted fragment length is 218 bps INFO @ Sat, 15 Jan 2022 20:06:49: #2 alternative fragment length(s) may be 0,47,82,117,155,176,218,237,266,285,315,336,503,563,582 bps INFO @ Sat, 15 Jan 2022 20:06:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.05_model.r INFO @ Sat, 15 Jan 2022 20:06:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:06:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:06:52: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:06:54: 9000000 INFO @ Sat, 15 Jan 2022 20:06:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:07:01: 12000000 INFO @ Sat, 15 Jan 2022 20:07:02: 10000000 INFO @ Sat, 15 Jan 2022 20:07:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.05_summits.bed INFO @ Sat, 15 Jan 2022 20:07:02: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (556 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:07:09: 11000000 INFO @ Sat, 15 Jan 2022 20:07:09: 13000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:07:16: 12000000 INFO @ Sat, 15 Jan 2022 20:07:17: 14000000 INFO @ Sat, 15 Jan 2022 20:07:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:07:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:07:22: #1 total tags in treatment: 3976614 INFO @ Sat, 15 Jan 2022 20:07:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:07:22: #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 20:07:22: #1 tags after filtering in treatment: 2757375 INFO @ Sat, 15 Jan 2022 20:07:22: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 20:07:22: #1 finished! INFO @ Sat, 15 Jan 2022 20:07:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:07:23: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 20:07:23: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 20:07:23: start model_add_line... INFO @ Sat, 15 Jan 2022 20:07:23: start X-correlation... INFO @ Sat, 15 Jan 2022 20:07:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:07:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:07:23: #2 predicted fragment length is 218 bps INFO @ Sat, 15 Jan 2022 20:07:23: #2 alternative fragment length(s) may be 0,47,82,117,155,176,218,237,266,285,315,336,503,563,582 bps INFO @ Sat, 15 Jan 2022 20:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.10_model.r INFO @ Sat, 15 Jan 2022 20:07:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:07:23: 13000000 INFO @ Sat, 15 Jan 2022 20:07:30: 14000000 INFO @ Sat, 15 Jan 2022 20:07:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:07:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:07:34: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:07:34: #1 total tags in treatment: 3976614 INFO @ Sat, 15 Jan 2022 20:07:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:07:34: #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 20:07:34: #1 tags after filtering in treatment: 2757375 INFO @ Sat, 15 Jan 2022 20:07:34: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 20:07:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:07:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:07:35: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 20:07:35: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 20:07:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:07:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:07:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:07:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:07:35: #2 predicted fragment length is 218 bps INFO @ Sat, 15 Jan 2022 20:07:35: #2 alternative fragment length(s) may be 0,47,82,117,155,176,218,237,266,285,315,336,503,563,582 bps INFO @ Sat, 15 Jan 2022 20:07:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.20_model.r INFO @ Sat, 15 Jan 2022 20:07:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:07:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:07:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:07:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.10_summits.bed INFO @ Sat, 15 Jan 2022 20:07:35: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (279 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:07:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245502/SRX8245502.20_summits.bed INFO @ Sat, 15 Jan 2022 20:07:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (83 records, 4 fields): 2 millis CompletedMACS2peakCalling