Job ID = 14520644 SRX = SRX7847361 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23489008 spots for SRR11235543/SRR11235543.sra Written 23489008 spots for SRR11235543/SRR11235543.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: 00:09:25 23489008 reads; of these: 23489008 (100.00%) were paired; of these: 4657879 (19.83%) aligned concordantly 0 times 16348273 (69.60%) aligned concordantly exactly 1 time 2482856 (10.57%) aligned concordantly >1 times ---- 4657879 pairs aligned concordantly 0 times; of these: 74817 (1.61%) aligned discordantly 1 time ---- 4583062 pairs aligned 0 times concordantly or discordantly; of these: 9166124 mates make up the pairs; of these: 7737718 (84.42%) aligned 0 times 937252 (10.23%) aligned exactly 1 time 491154 (5.36%) aligned >1 times 83.53% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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 12 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] 17904608 / 18861740 = 0.9493 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 19:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.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 19:47:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:47:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:47:49: 1000000 INFO @ Sat, 15 Jan 2022 19:47:53: 2000000 INFO @ Sat, 15 Jan 2022 19:47:57: 3000000 INFO @ Sat, 15 Jan 2022 19:47:58: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:47:58: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:47:58: #1 total tags in treatment: 989851 INFO @ Sat, 15 Jan 2022 19:47:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:47:58: #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 19:47:58: #1 tags after filtering in treatment: 374651 INFO @ Sat, 15 Jan 2022 19:47:58: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 19:47:58: #1 finished! INFO @ Sat, 15 Jan 2022 19:47:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:47:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:47:59: #2 number of paired peaks: 814 WARNING @ Sat, 15 Jan 2022 19:47:59: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 15 Jan 2022 19:47:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:47:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:47:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:47:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:47:59: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Jan 2022 19:47:59: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Jan 2022 19:47:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.05_model.r INFO @ Sat, 15 Jan 2022 19:47:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:47:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:48:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.05_summits.bed INFO @ Sat, 15 Jan 2022 19:48:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (938 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 19:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.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 19:48:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:48:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:48:19: 1000000 INFO @ Sat, 15 Jan 2022 19:48:23: 2000000 INFO @ Sat, 15 Jan 2022 19:48:27: 3000000 INFO @ Sat, 15 Jan 2022 19:48:28: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:48:28: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:48:28: #1 total tags in treatment: 989851 INFO @ Sat, 15 Jan 2022 19:48:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:48:28: #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 19:48:28: #1 tags after filtering in treatment: 374651 INFO @ Sat, 15 Jan 2022 19:48:28: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 19:48:28: #1 finished! INFO @ Sat, 15 Jan 2022 19:48:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:48:28: #2 number of paired peaks: 814 WARNING @ Sat, 15 Jan 2022 19:48:28: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 15 Jan 2022 19:48:28: start model_add_line... INFO @ Sat, 15 Jan 2022 19:48:28: start X-correlation... INFO @ Sat, 15 Jan 2022 19:48:28: end of X-cor INFO @ Sat, 15 Jan 2022 19:48:28: #2 finished! INFO @ Sat, 15 Jan 2022 19:48:28: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Jan 2022 19:48:28: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Jan 2022 19:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.10_model.r INFO @ Sat, 15 Jan 2022 19:48:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:48:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.10_summits.bed INFO @ Sat, 15 Jan 2022 19:48:30: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 19:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.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 19:48:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:48:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:48:49: 1000000 INFO @ Sat, 15 Jan 2022 19:48:53: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:48:57: 3000000 INFO @ Sat, 15 Jan 2022 19:48:59: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:48:59: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:48:59: #1 total tags in treatment: 989851 INFO @ Sat, 15 Jan 2022 19:48:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:48:59: #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 19:48:59: #1 tags after filtering in treatment: 374651 INFO @ Sat, 15 Jan 2022 19:48:59: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 19:48:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:48:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:48:59: #2 number of paired peaks: 814 WARNING @ Sat, 15 Jan 2022 19:48:59: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 15 Jan 2022 19:48:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:48:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:48:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:48:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:48:59: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Jan 2022 19:48:59: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Jan 2022 19:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.20_model.r INFO @ Sat, 15 Jan 2022 19:48:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:49:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847361/SRX7847361.20_summits.bed INFO @ Sat, 15 Jan 2022 19:49:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 2 millis CompletedMACS2peakCalling