Job ID = 14520495 SRX = SRX11781168 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:13:54 prefetch.2.10.7: 1) Downloading 'SRR15481111'... 2022-01-15T10:13:54 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:14:10 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:14:11 prefetch.2.10.7: 'SRR15481111' is valid 2022-01-15T10:14:11 prefetch.2.10.7: 1) 'SRR15481111' was downloaded successfully 2022-01-15T10:14:11 prefetch.2.10.7: 'SRR15481111' has 0 unresolved dependencies Read 8127695 spots for SRR15481111/SRR15481111.sra Written 8127695 spots for SRR15481111/SRR15481111.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: 00:07:29 8127695 reads; of these: 8127695 (100.00%) were paired; of these: 5177374 (63.70%) aligned concordantly 0 times 1729874 (21.28%) aligned concordantly exactly 1 time 1220447 (15.02%) aligned concordantly >1 times ---- 5177374 pairs aligned concordantly 0 times; of these: 33958 (0.66%) aligned discordantly 1 time ---- 5143416 pairs aligned 0 times concordantly or discordantly; of these: 10286832 mates make up the pairs; of these: 5901809 (57.37%) aligned 0 times 2694815 (26.20%) aligned exactly 1 time 1690208 (16.43%) aligned >1 times 63.69% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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_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] 277985 / 2983509 = 0.0932 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 19:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.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 19:25:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:18: 1000000 INFO @ Sat, 15 Jan 2022 19:25:22: 2000000 INFO @ Sat, 15 Jan 2022 19:25:26: 3000000 INFO @ Sat, 15 Jan 2022 19:25:30: 4000000 INFO @ Sat, 15 Jan 2022 19:25:34: 5000000 INFO @ Sat, 15 Jan 2022 19:25:38: 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 19:25:42: 7000000 INFO @ Sat, 15 Jan 2022 19:25:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.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 19:25:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:46: 8000000 INFO @ Sat, 15 Jan 2022 19:25:48: 1000000 INFO @ Sat, 15 Jan 2022 19:25:51: 9000000 INFO @ Sat, 15 Jan 2022 19:25:53: 2000000 INFO @ Sat, 15 Jan 2022 19:25:55: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:25:55: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:25:55: #1 total tags in treatment: 2674389 INFO @ Sat, 15 Jan 2022 19:25:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:25:55: #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 19:25:55: #1 tags after filtering in treatment: 1565905 INFO @ Sat, 15 Jan 2022 19:25:55: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 19:25:55: #1 finished! INFO @ Sat, 15 Jan 2022 19:25:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:25:55: #2 number of paired peaks: 187 WARNING @ Sat, 15 Jan 2022 19:25:55: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 15 Jan 2022 19:25:55: start model_add_line... INFO @ Sat, 15 Jan 2022 19:25:55: start X-correlation... INFO @ Sat, 15 Jan 2022 19:25:55: end of X-cor INFO @ Sat, 15 Jan 2022 19:25:55: #2 finished! INFO @ Sat, 15 Jan 2022 19:25:55: #2 predicted fragment length is 259 bps INFO @ Sat, 15 Jan 2022 19:25:55: #2 alternative fragment length(s) may be 0,259,263,273 bps INFO @ Sat, 15 Jan 2022 19:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.05_model.r INFO @ Sat, 15 Jan 2022 19:25:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:25:58: 3000000 INFO @ Sat, 15 Jan 2022 19:26:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:02: 4000000 INFO @ Sat, 15 Jan 2022 19:26:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.05_summits.bed INFO @ Sat, 15 Jan 2022 19:26:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (305 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:26:07: 5000000 INFO @ Sat, 15 Jan 2022 19:26:11: 6000000 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 19:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.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 19:26:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:26:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:26:16: 7000000 INFO @ Sat, 15 Jan 2022 19:26:18: 1000000 INFO @ Sat, 15 Jan 2022 19:26:20: 8000000 INFO @ Sat, 15 Jan 2022 19:26:23: 2000000 INFO @ Sat, 15 Jan 2022 19:26:25: 9000000 INFO @ Sat, 15 Jan 2022 19:26:28: 3000000 INFO @ Sat, 15 Jan 2022 19:26:29: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:26:29: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:26:29: #1 total tags in treatment: 2674389 INFO @ Sat, 15 Jan 2022 19:26:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:29: #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 19:26:29: #1 tags after filtering in treatment: 1565905 INFO @ Sat, 15 Jan 2022 19:26:29: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 19:26:29: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:29: #2 number of paired peaks: 187 WARNING @ Sat, 15 Jan 2022 19:26:29: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:29: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:29: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:29: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:29: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:29: #2 predicted fragment length is 259 bps INFO @ Sat, 15 Jan 2022 19:26:29: #2 alternative fragment length(s) may be 0,259,263,273 bps INFO @ Sat, 15 Jan 2022 19:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.10_model.r INFO @ Sat, 15 Jan 2022 19:26:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:32: 4000000 INFO @ Sat, 15 Jan 2022 19:26:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.10_summits.bed INFO @ Sat, 15 Jan 2022 19:26:36: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (176 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:26:37: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:26:41: 6000000 INFO @ Sat, 15 Jan 2022 19:26:45: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:26:50: 8000000 INFO @ Sat, 15 Jan 2022 19:26:54: 9000000 INFO @ Sat, 15 Jan 2022 19:26:57: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:26:57: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:26:57: #1 total tags in treatment: 2674389 INFO @ Sat, 15 Jan 2022 19:26:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:57: #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 19:26:57: #1 tags after filtering in treatment: 1565905 INFO @ Sat, 15 Jan 2022 19:26:57: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 19:26:57: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:57: #2 number of paired peaks: 187 WARNING @ Sat, 15 Jan 2022 19:26:57: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:57: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:57: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:58: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:58: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:58: #2 predicted fragment length is 259 bps INFO @ Sat, 15 Jan 2022 19:26:58: #2 alternative fragment length(s) may be 0,259,263,273 bps INFO @ Sat, 15 Jan 2022 19:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.20_model.r INFO @ Sat, 15 Jan 2022 19:26:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:27:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781168/SRX11781168.20_summits.bed INFO @ Sat, 15 Jan 2022 19:27:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 millis CompletedMACS2peakCalling