Job ID = 14521309 SRX = SRX8952628 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27209350 spots for SRR12458258/SRR12458258.sra Written 27209350 spots for SRR12458258/SRR12458258.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: 00:08:08 27209350 reads; of these: 27209350 (100.00%) were paired; of these: 25485978 (93.67%) aligned concordantly 0 times 1391241 (5.11%) aligned concordantly exactly 1 time 332131 (1.22%) aligned concordantly >1 times ---- 25485978 pairs aligned concordantly 0 times; of these: 4036201 (15.84%) aligned discordantly 1 time ---- 21449777 pairs aligned 0 times concordantly or discordantly; of these: 42899554 mates make up the pairs; of these: 31516186 (73.47%) aligned 0 times 9871501 (23.01%) aligned exactly 1 time 1511867 (3.52%) aligned >1 times 42.09% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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] 4081491 / 5581757 = 0.7312 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 21:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.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 21:05:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:05:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:05:33: 1000000 INFO @ Sat, 15 Jan 2022 21:05:37: 2000000 INFO @ Sat, 15 Jan 2022 21:05:42: 3000000 INFO @ Sat, 15 Jan 2022 21:05:46: 4000000 INFO @ Sat, 15 Jan 2022 21:05:50: 5000000 INFO @ Sat, 15 Jan 2022 21:05:54: 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 21:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.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 21:05:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:05:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:05:59: 7000000 INFO @ Sat, 15 Jan 2022 21:06:04: 8000000 INFO @ Sat, 15 Jan 2022 21:06:05: 1000000 INFO @ Sat, 15 Jan 2022 21:06:09: 9000000 INFO @ Sat, 15 Jan 2022 21:06:12: 2000000 INFO @ Sat, 15 Jan 2022 21:06:15: 10000000 INFO @ Sat, 15 Jan 2022 21:06:18: 3000000 INFO @ Sat, 15 Jan 2022 21:06:21: 11000000 INFO @ Sat, 15 Jan 2022 21:06:24: 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 21:06:27: 12000000 INFO @ Sat, 15 Jan 2022 21:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.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 21:06:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:06:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:06:30: 5000000 INFO @ Sat, 15 Jan 2022 21:06:33: 13000000 INFO @ Sat, 15 Jan 2022 21:06:35: 1000000 INFO @ Sat, 15 Jan 2022 21:06:36: 6000000 INFO @ Sat, 15 Jan 2022 21:06:38: 14000000 INFO @ Sat, 15 Jan 2022 21:06:41: 2000000 INFO @ Sat, 15 Jan 2022 21:06:43: 7000000 INFO @ Sat, 15 Jan 2022 21:06:43: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 21:06:43: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 21:06:43: #1 total tags in treatment: 1202750 INFO @ Sat, 15 Jan 2022 21:06:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:06:43: #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 21:06:43: #1 tags after filtering in treatment: 915396 INFO @ Sat, 15 Jan 2022 21:06:43: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 21:06:43: #1 finished! INFO @ Sat, 15 Jan 2022 21:06:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:06:43: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 21:06:43: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 15 Jan 2022 21:06:43: start model_add_line... INFO @ Sat, 15 Jan 2022 21:06:43: start X-correlation... INFO @ Sat, 15 Jan 2022 21:06:43: end of X-cor INFO @ Sat, 15 Jan 2022 21:06:43: #2 finished! INFO @ Sat, 15 Jan 2022 21:06:43: #2 predicted fragment length is 304 bps INFO @ Sat, 15 Jan 2022 21:06:43: #2 alternative fragment length(s) may be 3,304 bps INFO @ Sat, 15 Jan 2022 21:06:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.05_model.r INFO @ Sat, 15 Jan 2022 21:06:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:06:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:06:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.05_summits.bed INFO @ Sat, 15 Jan 2022 21:06:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (315 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:06:48: 3000000 INFO @ Sat, 15 Jan 2022 21:06:49: 8000000 INFO @ Sat, 15 Jan 2022 21:06:54: 4000000 INFO @ Sat, 15 Jan 2022 21:06:55: 9000000 INFO @ Sat, 15 Jan 2022 21:07:00: 5000000 INFO @ Sat, 15 Jan 2022 21:07:01: 10000000 INFO @ Sat, 15 Jan 2022 21:07:06: 6000000 INFO @ Sat, 15 Jan 2022 21:07:08: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:07:12: 7000000 INFO @ Sat, 15 Jan 2022 21:07:15: 12000000 INFO @ Sat, 15 Jan 2022 21:07:18: 8000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:07:21: 13000000 INFO @ Sat, 15 Jan 2022 21:07:24: 9000000 INFO @ Sat, 15 Jan 2022 21:07:28: 14000000 INFO @ Sat, 15 Jan 2022 21:07:31: 10000000 INFO @ Sat, 15 Jan 2022 21:07:32: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 21:07:32: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 21:07:32: #1 total tags in treatment: 1202750 INFO @ Sat, 15 Jan 2022 21:07:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:07:32: #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 21:07:32: #1 tags after filtering in treatment: 915396 INFO @ Sat, 15 Jan 2022 21:07:32: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 21:07:32: #1 finished! INFO @ Sat, 15 Jan 2022 21:07:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:07:33: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 21:07:33: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 15 Jan 2022 21:07:33: start model_add_line... INFO @ Sat, 15 Jan 2022 21:07:33: start X-correlation... INFO @ Sat, 15 Jan 2022 21:07:33: end of X-cor INFO @ Sat, 15 Jan 2022 21:07:33: #2 finished! INFO @ Sat, 15 Jan 2022 21:07:33: #2 predicted fragment length is 304 bps INFO @ Sat, 15 Jan 2022 21:07:33: #2 alternative fragment length(s) may be 3,304 bps INFO @ Sat, 15 Jan 2022 21:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.10_model.r INFO @ Sat, 15 Jan 2022 21:07:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:07:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.10_summits.bed INFO @ Sat, 15 Jan 2022 21:07:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:07:37: 11000000 INFO @ Sat, 15 Jan 2022 21:07:43: 12000000 INFO @ Sat, 15 Jan 2022 21:07:49: 13000000 INFO @ Sat, 15 Jan 2022 21:07:55: 14000000 INFO @ Sat, 15 Jan 2022 21:07:59: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 21:07:59: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 21:07:59: #1 total tags in treatment: 1202750 INFO @ Sat, 15 Jan 2022 21:07:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:07:59: #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 21:07:59: #1 tags after filtering in treatment: 915396 INFO @ Sat, 15 Jan 2022 21:07:59: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 21:07:59: #1 finished! INFO @ Sat, 15 Jan 2022 21:07:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:07:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:07:59: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 21:07:59: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 15 Jan 2022 21:07:59: start model_add_line... INFO @ Sat, 15 Jan 2022 21:07:59: start X-correlation... INFO @ Sat, 15 Jan 2022 21:07:59: end of X-cor INFO @ Sat, 15 Jan 2022 21:07:59: #2 finished! INFO @ Sat, 15 Jan 2022 21:07:59: #2 predicted fragment length is 304 bps INFO @ Sat, 15 Jan 2022 21:07:59: #2 alternative fragment length(s) may be 3,304 bps INFO @ Sat, 15 Jan 2022 21:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.20_model.r INFO @ Sat, 15 Jan 2022 21:07:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:08:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952628/SRX8952628.20_summits.bed INFO @ Sat, 15 Jan 2022 21:08:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 millis CompletedMACS2peakCalling