Job ID = 14520492 SRX = SRX11781165 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:13:39 prefetch.2.10.7: 1) Downloading 'SRR15481108'... 2022-01-15T10:13:39 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:13:53 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:13:54 prefetch.2.10.7: 'SRR15481108' is valid 2022-01-15T10:13:54 prefetch.2.10.7: 1) 'SRR15481108' was downloaded successfully 2022-01-15T10:13:54 prefetch.2.10.7: 'SRR15481108' has 0 unresolved dependencies Read 5717063 spots for SRR15481108/SRR15481108.sra Written 5717063 spots for SRR15481108/SRR15481108.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: 00:02:36 5717063 reads; of these: 5717063 (100.00%) were paired; of these: 3524649 (61.65%) aligned concordantly 0 times 1906459 (33.35%) aligned concordantly exactly 1 time 285955 (5.00%) aligned concordantly >1 times ---- 3524649 pairs aligned concordantly 0 times; of these: 34522 (0.98%) aligned discordantly 1 time ---- 3490127 pairs aligned 0 times concordantly or discordantly; of these: 6980254 mates make up the pairs; of these: 3869541 (55.44%) aligned 0 times 2688408 (38.51%) aligned exactly 1 time 422305 (6.05%) aligned >1 times 66.16% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 250994 / 2226273 = 0.1127 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 19:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.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 19:19:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:06: 1000000 INFO @ Sat, 15 Jan 2022 19:19:10: 2000000 INFO @ Sat, 15 Jan 2022 19:19:15: 3000000 INFO @ Sat, 15 Jan 2022 19:19:19: 4000000 INFO @ Sat, 15 Jan 2022 19:19:24: 5000000 INFO @ Sat, 15 Jan 2022 19:19:28: 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 19:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.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 19:19:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:33: 7000000 INFO @ Sat, 15 Jan 2022 19:19:33: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:19:33: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:19:33: #1 total tags in treatment: 1943567 INFO @ Sat, 15 Jan 2022 19:19:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:19:33: #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 19:19:33: #1 tags after filtering in treatment: 1540690 INFO @ Sat, 15 Jan 2022 19:19:33: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:19:33: #1 finished! INFO @ Sat, 15 Jan 2022 19:19:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:19:33: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:19:33: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:19:33: start model_add_line... INFO @ Sat, 15 Jan 2022 19:19:33: start X-correlation... INFO @ Sat, 15 Jan 2022 19:19:33: end of X-cor INFO @ Sat, 15 Jan 2022 19:19:33: #2 finished! INFO @ Sat, 15 Jan 2022 19:19:33: #2 predicted fragment length is 259 bps INFO @ Sat, 15 Jan 2022 19:19:33: #2 alternative fragment length(s) may be 1,230,259 bps INFO @ Sat, 15 Jan 2022 19:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.05_model.r INFO @ Sat, 15 Jan 2022 19:19:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:19:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:19:38: 1000000 INFO @ Sat, 15 Jan 2022 19:19:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:19:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:19:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.05_summits.bed INFO @ Sat, 15 Jan 2022 19:19:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:19:43: 2000000 INFO @ Sat, 15 Jan 2022 19:19:49: 3000000 INFO @ Sat, 15 Jan 2022 19:19:55: 4000000 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 19:20:01: 5000000 INFO @ Sat, 15 Jan 2022 19:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.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 19:20:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:08: 6000000 INFO @ Sat, 15 Jan 2022 19:20:08: 1000000 INFO @ Sat, 15 Jan 2022 19:20:14: 7000000 INFO @ Sat, 15 Jan 2022 19:20:14: 2000000 INFO @ Sat, 15 Jan 2022 19:20:15: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:20:15: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:20:15: #1 total tags in treatment: 1943567 INFO @ Sat, 15 Jan 2022 19:20:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:15: #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 19:20:15: #1 tags after filtering in treatment: 1540690 INFO @ Sat, 15 Jan 2022 19:20:15: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:20:15: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:15: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:20:15: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:20:15: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:15: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:15: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:15: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:15: #2 predicted fragment length is 259 bps INFO @ Sat, 15 Jan 2022 19:20:15: #2 alternative fragment length(s) may be 1,230,259 bps INFO @ Sat, 15 Jan 2022 19:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.10_model.r INFO @ Sat, 15 Jan 2022 19:20:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.10_summits.bed INFO @ Sat, 15 Jan 2022 19:20:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:20:20: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:20:27: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:20:33: 5000000 INFO @ Sat, 15 Jan 2022 19:20:39: 6000000 INFO @ Sat, 15 Jan 2022 19:20:44: 7000000 INFO @ Sat, 15 Jan 2022 19:20:45: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:20:45: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:20:45: #1 total tags in treatment: 1943567 INFO @ Sat, 15 Jan 2022 19:20:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:45: #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 19:20:45: #1 tags after filtering in treatment: 1540690 INFO @ Sat, 15 Jan 2022 19:20:45: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:20:45: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:45: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:20:45: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:20:45: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:45: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:45: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:45: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:45: #2 predicted fragment length is 259 bps INFO @ Sat, 15 Jan 2022 19:20:45: #2 alternative fragment length(s) may be 1,230,259 bps INFO @ Sat, 15 Jan 2022 19:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.20_model.r INFO @ Sat, 15 Jan 2022 19:20:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781165/SRX11781165.20_summits.bed INFO @ Sat, 15 Jan 2022 19:20:50: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 12 millis CompletedMACS2peakCalling