Job ID = 14520646 SRX = SRX7847363 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34310389 spots for SRR11235545/SRR11235545.sra Written 34310389 spots for SRR11235545/SRR11235545.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: 00:22:10 34310389 reads; of these: 34310389 (100.00%) were paired; of these: 5515525 (16.08%) aligned concordantly 0 times 23359733 (68.08%) aligned concordantly exactly 1 time 5435131 (15.84%) aligned concordantly >1 times ---- 5515525 pairs aligned concordantly 0 times; of these: 66747 (1.21%) aligned discordantly 1 time ---- 5448778 pairs aligned 0 times concordantly or discordantly; of these: 10897556 mates make up the pairs; of these: 9035045 (82.91%) aligned 0 times 1220159 (11.20%) aligned exactly 1 time 642352 (5.89%) aligned >1 times 86.83% overall alignment rate Time searching: 00:22:10 Overall time: 00:22:10 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 16 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] 26809798 / 28840390 = 0.9296 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 20:09:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.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 20:09:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:09:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:09:26: 1000000 INFO @ Sat, 15 Jan 2022 20:09:32: 2000000 INFO @ Sat, 15 Jan 2022 20:09:38: 3000000 INFO @ Sat, 15 Jan 2022 20:09:45: 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 20:09:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.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 20:09:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:09:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:09:51: 5000000 INFO @ Sat, 15 Jan 2022 20:09:57: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:09:57: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:09:57: #1 total tags in treatment: 2037387 INFO @ Sat, 15 Jan 2022 20:09:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:09:57: #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 20:09:57: #1 tags after filtering in treatment: 797533 INFO @ Sat, 15 Jan 2022 20:09:57: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 15 Jan 2022 20:09:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:09:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:09:57: #2 number of paired peaks: 744 WARNING @ Sat, 15 Jan 2022 20:09:57: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Sat, 15 Jan 2022 20:09:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:09:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:09:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:09:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:09:57: #2 predicted fragment length is 142 bps INFO @ Sat, 15 Jan 2022 20:09:57: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 15 Jan 2022 20:09:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.05_model.r INFO @ Sat, 15 Jan 2022 20:09:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:09:58: 1000000 INFO @ Sat, 15 Jan 2022 20:10:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:10:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:10:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:10:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.05_summits.bed INFO @ Sat, 15 Jan 2022 20:10:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1292 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:10:05: 2000000 INFO @ Sat, 15 Jan 2022 20:10:13: 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 20:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.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 20:10:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:10:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:10:20: 4000000 INFO @ Sat, 15 Jan 2022 20:10:27: 1000000 INFO @ Sat, 15 Jan 2022 20:10:27: 5000000 INFO @ Sat, 15 Jan 2022 20:10:34: 2000000 INFO @ Sat, 15 Jan 2022 20:10:35: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:10:35: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:10:35: #1 total tags in treatment: 2037387 INFO @ Sat, 15 Jan 2022 20:10:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:10:35: #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 20:10:35: #1 tags after filtering in treatment: 797533 INFO @ Sat, 15 Jan 2022 20:10:35: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 15 Jan 2022 20:10:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:10:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:10:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:10:35: #2 number of paired peaks: 744 WARNING @ Sat, 15 Jan 2022 20:10:35: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Sat, 15 Jan 2022 20:10:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:10:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:10:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:10:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:10:35: #2 predicted fragment length is 142 bps INFO @ Sat, 15 Jan 2022 20:10:35: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 15 Jan 2022 20:10:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.10_model.r INFO @ Sat, 15 Jan 2022 20:10:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:10:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:10:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:10:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:10:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:10:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.10_summits.bed INFO @ Sat, 15 Jan 2022 20:10:41: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (971 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:10:41: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:10:48: 4000000 INFO @ Sat, 15 Jan 2022 20:10:55: 5000000 INFO @ Sat, 15 Jan 2022 20:11:03: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:11:03: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:11:03: #1 total tags in treatment: 2037387 INFO @ Sat, 15 Jan 2022 20:11:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:11:03: #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 20:11:03: #1 tags after filtering in treatment: 797533 INFO @ Sat, 15 Jan 2022 20:11:03: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 15 Jan 2022 20:11:03: #1 finished! INFO @ Sat, 15 Jan 2022 20:11:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:11:03: #2 number of paired peaks: 744 WARNING @ Sat, 15 Jan 2022 20:11:03: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Sat, 15 Jan 2022 20:11:03: start model_add_line... INFO @ Sat, 15 Jan 2022 20:11:03: start X-correlation... INFO @ Sat, 15 Jan 2022 20:11:03: end of X-cor INFO @ Sat, 15 Jan 2022 20:11:03: #2 finished! INFO @ Sat, 15 Jan 2022 20:11:03: #2 predicted fragment length is 142 bps INFO @ Sat, 15 Jan 2022 20:11:03: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 15 Jan 2022 20:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.20_model.r INFO @ Sat, 15 Jan 2022 20:11:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:11:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:11:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847363/SRX7847363.20_summits.bed INFO @ Sat, 15 Jan 2022 20:11:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (673 records, 4 fields): 8 millis CompletedMACS2peakCalling