Job ID = 14520373 SRX = SRX11781116 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:01:06 prefetch.2.10.7: 1) Downloading 'SRR15481059'... 2022-01-15T10:01:06 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:02:21 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:02:21 prefetch.2.10.7: 1) 'SRR15481059' was downloaded successfully 2022-01-15T10:02:21 prefetch.2.10.7: 'SRR15481059' has 0 unresolved dependencies Read 10072464 spots for SRR15481059/SRR15481059.sra Written 10072464 spots for SRR15481059/SRR15481059.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: 00:05:17 10072464 reads; of these: 10072464 (100.00%) were paired; of these: 5936874 (58.94%) aligned concordantly 0 times 3543951 (35.18%) aligned concordantly exactly 1 time 591639 (5.87%) aligned concordantly >1 times ---- 5936874 pairs aligned concordantly 0 times; of these: 165392 (2.79%) aligned discordantly 1 time ---- 5771482 pairs aligned 0 times concordantly or discordantly; of these: 11542964 mates make up the pairs; of these: 6971299 (60.39%) aligned 0 times 3821365 (33.11%) aligned exactly 1 time 750300 (6.50%) aligned >1 times 65.39% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 489709 / 4300276 = 0.1139 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 19:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.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 19:12:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:07: 1000000 INFO @ Sat, 15 Jan 2022 19:12:12: 2000000 INFO @ Sat, 15 Jan 2022 19:12:16: 3000000 INFO @ Sat, 15 Jan 2022 19:12:20: 4000000 INFO @ Sat, 15 Jan 2022 19:12:25: 5000000 INFO @ Sat, 15 Jan 2022 19:12:29: 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 19:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.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 19:12:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:34: 7000000 INFO @ Sat, 15 Jan 2022 19:12:38: 1000000 INFO @ Sat, 15 Jan 2022 19:12:39: 8000000 INFO @ Sat, 15 Jan 2022 19:12:43: 2000000 INFO @ Sat, 15 Jan 2022 19:12:44: 9000000 INFO @ Sat, 15 Jan 2022 19:12:48: 3000000 INFO @ Sat, 15 Jan 2022 19:12:48: 10000000 INFO @ Sat, 15 Jan 2022 19:12:52: 4000000 INFO @ Sat, 15 Jan 2022 19:12:53: 11000000 INFO @ Sat, 15 Jan 2022 19:12:57: 5000000 INFO @ Sat, 15 Jan 2022 19:12:58: 12000000 INFO @ Sat, 15 Jan 2022 19:12:59: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:12:59: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:12:59: #1 total tags in treatment: 3658774 INFO @ Sat, 15 Jan 2022 19:12:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:59: #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 19:12:59: #1 tags after filtering in treatment: 2961394 INFO @ Sat, 15 Jan 2022 19:12:59: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:12:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:59: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 19:12:59: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:59: #2 predicted fragment length is 197 bps INFO @ Sat, 15 Jan 2022 19:12:59: #2 alternative fragment length(s) may be 52,86,141,180,182,197,218,221,244,263,287,324,356,388,408,507 bps INFO @ Sat, 15 Jan 2022 19:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.05_model.r INFO @ Sat, 15 Jan 2022 19:12:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:59: #3 Pre-compute pvalue-qvalue table... 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 19:13:02: 6000000 INFO @ Sat, 15 Jan 2022 19:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.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 19:13:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:13:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:13:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:07: 7000000 INFO @ Sat, 15 Jan 2022 19:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.05_summits.bed INFO @ Sat, 15 Jan 2022 19:13:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:13:08: 1000000 INFO @ Sat, 15 Jan 2022 19:13:11: 8000000 INFO @ Sat, 15 Jan 2022 19:13:13: 2000000 INFO @ Sat, 15 Jan 2022 19:13:16: 9000000 INFO @ Sat, 15 Jan 2022 19:13:17: 3000000 INFO @ Sat, 15 Jan 2022 19:13:21: 10000000 INFO @ Sat, 15 Jan 2022 19:13:22: 4000000 INFO @ Sat, 15 Jan 2022 19:13:25: 11000000 INFO @ Sat, 15 Jan 2022 19:13:27: 5000000 INFO @ Sat, 15 Jan 2022 19:13:30: 12000000 INFO @ Sat, 15 Jan 2022 19:13:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:13:31: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:13:31: #1 total tags in treatment: 3658774 INFO @ Sat, 15 Jan 2022 19:13:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:31: #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 19:13:31: #1 tags after filtering in treatment: 2961394 INFO @ Sat, 15 Jan 2022 19:13:31: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:13:31: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:31: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 19:13:31: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:31: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:31: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:31: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:31: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:31: #2 predicted fragment length is 197 bps INFO @ Sat, 15 Jan 2022 19:13:31: #2 alternative fragment length(s) may be 52,86,141,180,182,197,218,221,244,263,287,324,356,388,408,507 bps INFO @ Sat, 15 Jan 2022 19:13:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.10_model.r INFO @ Sat, 15 Jan 2022 19:13:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:31: 6000000 INFO @ Sat, 15 Jan 2022 19:13:36: 7000000 INFO @ Sat, 15 Jan 2022 19:13:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.10_summits.bed INFO @ Sat, 15 Jan 2022 19:13:39: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:13:40: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:13:45: 9000000 INFO @ Sat, 15 Jan 2022 19:13:49: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:13:54: 11000000 INFO @ Sat, 15 Jan 2022 19:13:58: 12000000 INFO @ Sat, 15 Jan 2022 19:13:59: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:13:59: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:13:59: #1 total tags in treatment: 3658774 INFO @ Sat, 15 Jan 2022 19:13:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:59: #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 19:13:59: #1 tags after filtering in treatment: 2961394 INFO @ Sat, 15 Jan 2022 19:13:59: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:13:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:59: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 19:13:59: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:59: #2 predicted fragment length is 197 bps INFO @ Sat, 15 Jan 2022 19:13:59: #2 alternative fragment length(s) may be 52,86,141,180,182,197,218,221,244,263,287,324,356,388,408,507 bps INFO @ Sat, 15 Jan 2022 19:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.20_model.r INFO @ Sat, 15 Jan 2022 19:13:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781116/SRX11781116.20_summits.bed INFO @ Sat, 15 Jan 2022 19:14:07: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 12 millis CompletedMACS2peakCalling