Job ID = 14520406 SRX = SRX11781132 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:02:36 prefetch.2.10.7: 1) Downloading 'SRR15481075'... 2022-01-15T10:02:36 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:02:57 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:02:58 prefetch.2.10.7: 'SRR15481075' is valid 2022-01-15T10:02:58 prefetch.2.10.7: 1) 'SRR15481075' was downloaded successfully 2022-01-15T10:02:58 prefetch.2.10.7: 'SRR15481075' has 0 unresolved dependencies Read 7503638 spots for SRR15481075/SRR15481075.sra Written 7503638 spots for SRR15481075/SRR15481075.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: 00:04:19 7503638 reads; of these: 7503638 (100.00%) were paired; of these: 4697944 (62.61%) aligned concordantly 0 times 2225579 (29.66%) aligned concordantly exactly 1 time 580115 (7.73%) aligned concordantly >1 times ---- 4697944 pairs aligned concordantly 0 times; of these: 44723 (0.95%) aligned discordantly 1 time ---- 4653221 pairs aligned 0 times concordantly or discordantly; of these: 9306442 mates make up the pairs; of these: 5331813 (57.29%) aligned 0 times 3124321 (33.57%) aligned exactly 1 time 850308 (9.14%) aligned >1 times 64.47% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 152869 / 2849185 = 0.0537 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 19:10:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.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 19:10:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:50: 1000000 INFO @ Sat, 15 Jan 2022 19:10:54: 2000000 INFO @ Sat, 15 Jan 2022 19:10:58: 3000000 INFO @ Sat, 15 Jan 2022 19:11:03: 4000000 INFO @ Sat, 15 Jan 2022 19:11:07: 5000000 INFO @ Sat, 15 Jan 2022 19:11:11: 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 19:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.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 19:11:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:15: 7000000 INFO @ Sat, 15 Jan 2022 19:11:20: 1000000 INFO @ Sat, 15 Jan 2022 19:11:20: 8000000 INFO @ Sat, 15 Jan 2022 19:11:25: 9000000 INFO @ Sat, 15 Jan 2022 19:11:26: 2000000 INFO @ Sat, 15 Jan 2022 19:11:27: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:11:27: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:11:27: #1 total tags in treatment: 2654232 INFO @ Sat, 15 Jan 2022 19:11:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:11:27: #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 19:11:27: #1 tags after filtering in treatment: 2149805 INFO @ Sat, 15 Jan 2022 19:11:27: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:11:27: #1 finished! INFO @ Sat, 15 Jan 2022 19:11:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:11:27: #2 number of paired peaks: 107 WARNING @ Sat, 15 Jan 2022 19:11:27: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 15 Jan 2022 19:11:27: start model_add_line... INFO @ Sat, 15 Jan 2022 19:11:27: start X-correlation... INFO @ Sat, 15 Jan 2022 19:11:27: end of X-cor INFO @ Sat, 15 Jan 2022 19:11:27: #2 finished! INFO @ Sat, 15 Jan 2022 19:11:27: #2 predicted fragment length is 145 bps INFO @ Sat, 15 Jan 2022 19:11:27: #2 alternative fragment length(s) may be 1,50,106,125,130,145,177,204,576 bps INFO @ Sat, 15 Jan 2022 19:11:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.05_model.r INFO @ Sat, 15 Jan 2022 19:11:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:11:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:11:31: 3000000 INFO @ Sat, 15 Jan 2022 19:11:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:11:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:11:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:11:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.05_summits.bed INFO @ Sat, 15 Jan 2022 19:11:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (353 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:11:36: 4000000 INFO @ Sat, 15 Jan 2022 19:11:41: 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 19:11:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.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 19:11:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:46: 6000000 INFO @ Sat, 15 Jan 2022 19:11:50: 1000000 INFO @ Sat, 15 Jan 2022 19:11:52: 7000000 INFO @ Sat, 15 Jan 2022 19:11:56: 2000000 INFO @ Sat, 15 Jan 2022 19:11:58: 8000000 INFO @ Sat, 15 Jan 2022 19:12:00: 3000000 INFO @ Sat, 15 Jan 2022 19:12:03: 9000000 INFO @ Sat, 15 Jan 2022 19:12:05: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:12:05: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:12:05: #1 total tags in treatment: 2654232 INFO @ Sat, 15 Jan 2022 19:12:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:05: #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 19:12:05: #1 tags after filtering in treatment: 2149805 INFO @ Sat, 15 Jan 2022 19:12:05: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:12:05: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:05: 4000000 INFO @ Sat, 15 Jan 2022 19:12:06: #2 number of paired peaks: 107 WARNING @ Sat, 15 Jan 2022 19:12:06: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:06: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:06: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:06: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:06: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:06: #2 predicted fragment length is 145 bps INFO @ Sat, 15 Jan 2022 19:12:06: #2 alternative fragment length(s) may be 1,50,106,125,130,145,177,204,576 bps INFO @ Sat, 15 Jan 2022 19:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.10_model.r INFO @ Sat, 15 Jan 2022 19:12:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:10: 5000000 INFO @ Sat, 15 Jan 2022 19:12:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.10_summits.bed INFO @ Sat, 15 Jan 2022 19:12:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:12:15: 6000000 INFO @ Sat, 15 Jan 2022 19:12:19: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:12:24: 8000000 INFO @ Sat, 15 Jan 2022 19:12:29: 9000000 INFO @ Sat, 15 Jan 2022 19:12:30: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:12:30: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:12:30: #1 total tags in treatment: 2654232 INFO @ Sat, 15 Jan 2022 19:12:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:30: #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 19:12:30: #1 tags after filtering in treatment: 2149805 INFO @ Sat, 15 Jan 2022 19:12:30: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:12:30: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:31: #2 number of paired peaks: 107 WARNING @ Sat, 15 Jan 2022 19:12:31: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:31: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:31: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:31: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:31: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:31: #2 predicted fragment length is 145 bps INFO @ Sat, 15 Jan 2022 19:12:31: #2 alternative fragment length(s) may be 1,50,106,125,130,145,177,204,576 bps INFO @ Sat, 15 Jan 2022 19:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.20_model.r INFO @ Sat, 15 Jan 2022 19:12:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781132/SRX11781132.20_summits.bed INFO @ Sat, 15 Jan 2022 19:12:38: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling