Job ID = 14520378 SRX = SRX11781117 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 'SRR15481060'... 2022-01-15T10:01:06 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:02:04 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:02:04 prefetch.2.10.7: 1) 'SRR15481060' was downloaded successfully 2022-01-15T10:02:04 prefetch.2.10.7: 'SRR15481060' has 0 unresolved dependencies Read 9500099 spots for SRR15481060/SRR15481060.sra Written 9500099 spots for SRR15481060/SRR15481060.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: 00:04:27 9500099 reads; of these: 9500099 (100.00%) were paired; of these: 5251733 (55.28%) aligned concordantly 0 times 3638431 (38.30%) aligned concordantly exactly 1 time 609935 (6.42%) aligned concordantly >1 times ---- 5251733 pairs aligned concordantly 0 times; of these: 132277 (2.52%) aligned discordantly 1 time ---- 5119456 pairs aligned 0 times concordantly or discordantly; of these: 10238912 mates make up the pairs; of these: 6661391 (65.06%) aligned 0 times 2977711 (29.08%) aligned exactly 1 time 599810 (5.86%) aligned >1 times 64.94% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 563585 / 4380011 = 0.1287 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 19:10:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.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 19:10:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:43: 1000000 INFO @ Sat, 15 Jan 2022 19:10:52: 2000000 INFO @ Sat, 15 Jan 2022 19:10:59: 3000000 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 19:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.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 19:11:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:05: 4000000 INFO @ Sat, 15 Jan 2022 19:11:12: 1000000 INFO @ Sat, 15 Jan 2022 19:11:12: 5000000 INFO @ Sat, 15 Jan 2022 19:11:19: 2000000 INFO @ Sat, 15 Jan 2022 19:11:20: 6000000 INFO @ Sat, 15 Jan 2022 19:11:26: 3000000 INFO @ Sat, 15 Jan 2022 19:11:27: 7000000 INFO @ Sat, 15 Jan 2022 19:11:33: 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 19:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.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 19:11:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:35: 8000000 INFO @ Sat, 15 Jan 2022 19:11:40: 5000000 INFO @ Sat, 15 Jan 2022 19:11:42: 1000000 INFO @ Sat, 15 Jan 2022 19:11:43: 9000000 INFO @ Sat, 15 Jan 2022 19:11:47: 6000000 INFO @ Sat, 15 Jan 2022 19:11:49: 2000000 INFO @ Sat, 15 Jan 2022 19:11:50: 10000000 INFO @ Sat, 15 Jan 2022 19:11:54: 7000000 INFO @ Sat, 15 Jan 2022 19:11:56: 3000000 INFO @ Sat, 15 Jan 2022 19:11:58: 11000000 INFO @ Sat, 15 Jan 2022 19:11:59: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:11:59: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:11:59: #1 total tags in treatment: 3696193 INFO @ Sat, 15 Jan 2022 19:11:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:11:59: #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 19:11:59: #1 tags after filtering in treatment: 2854190 INFO @ Sat, 15 Jan 2022 19:11:59: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 19:11:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:11:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:00: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 19:12:00: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:00: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:00: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:00: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:00: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:00: #2 predicted fragment length is 234 bps INFO @ Sat, 15 Jan 2022 19:12:00: #2 alternative fragment length(s) may be 0,52,92,124,155,204,234,273,302,304,323,344,382,518 bps INFO @ Sat, 15 Jan 2022 19:12:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.05_model.r INFO @ Sat, 15 Jan 2022 19:12:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:02: 8000000 INFO @ Sat, 15 Jan 2022 19:12:03: 4000000 INFO @ Sat, 15 Jan 2022 19:12:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.05_summits.bed INFO @ Sat, 15 Jan 2022 19:12:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:12:09: 9000000 INFO @ Sat, 15 Jan 2022 19:12:10: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:12:16: 10000000 INFO @ Sat, 15 Jan 2022 19:12:17: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:12:23: 11000000 INFO @ Sat, 15 Jan 2022 19:12:24: 7000000 INFO @ Sat, 15 Jan 2022 19:12:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:12:24: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:12:24: #1 total tags in treatment: 3696193 INFO @ Sat, 15 Jan 2022 19:12:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:24: #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 19:12:24: #1 tags after filtering in treatment: 2854190 INFO @ Sat, 15 Jan 2022 19:12:24: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 19:12:24: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:24: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 19:12:24: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:24: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:24: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:24: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:24: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:24: #2 predicted fragment length is 234 bps INFO @ Sat, 15 Jan 2022 19:12:24: #2 alternative fragment length(s) may be 0,52,92,124,155,204,234,273,302,304,323,344,382,518 bps INFO @ Sat, 15 Jan 2022 19:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.10_model.r INFO @ Sat, 15 Jan 2022 19:12:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:31: 8000000 INFO @ Sat, 15 Jan 2022 19:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.10_summits.bed INFO @ Sat, 15 Jan 2022 19:12:32: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (19 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:12:37: 9000000 INFO @ Sat, 15 Jan 2022 19:12:44: 10000000 INFO @ Sat, 15 Jan 2022 19:12:50: 11000000 INFO @ Sat, 15 Jan 2022 19:12:51: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:12:51: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:12:51: #1 total tags in treatment: 3696193 INFO @ Sat, 15 Jan 2022 19:12:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:51: #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 19:12:51: #1 tags after filtering in treatment: 2854190 INFO @ Sat, 15 Jan 2022 19:12:51: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 19:12:51: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:51: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 19:12:51: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:51: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:51: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:52: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:52: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:52: #2 predicted fragment length is 234 bps INFO @ Sat, 15 Jan 2022 19:12:52: #2 alternative fragment length(s) may be 0,52,92,124,155,204,234,273,302,304,323,344,382,518 bps INFO @ Sat, 15 Jan 2022 19:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.20_model.r INFO @ Sat, 15 Jan 2022 19:12:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781117/SRX11781117.20_summits.bed INFO @ Sat, 15 Jan 2022 19:12:59: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling