Job ID = 14520367 SRX = SRX11781112 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:00:36 prefetch.2.10.7: 1) Downloading 'SRR15481055'... 2022-01-15T10:00:36 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:13 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:13 prefetch.2.10.7: 1) 'SRR15481055' was downloaded successfully 2022-01-15T10:01:13 prefetch.2.10.7: 'SRR15481055' has 0 unresolved dependencies Read 8911858 spots for SRR15481055/SRR15481055.sra Written 8911858 spots for SRR15481055/SRR15481055.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: 00:00:01 Multiseed full-index search: 00:06:25 8911858 reads; of these: 8911858 (100.00%) were paired; of these: 4852771 (54.45%) aligned concordantly 0 times 3081425 (34.58%) aligned concordantly exactly 1 time 977662 (10.97%) aligned concordantly >1 times ---- 4852771 pairs aligned concordantly 0 times; of these: 204110 (4.21%) aligned discordantly 1 time ---- 4648661 pairs aligned 0 times concordantly or discordantly; of these: 9297322 mates make up the pairs; of these: 5635426 (60.61%) aligned 0 times 2647958 (28.48%) aligned exactly 1 time 1013938 (10.91%) aligned >1 times 68.38% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 442450 / 4262288 = 0.1038 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 19:11:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.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 19:11:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:47: 1000000 INFO @ Sat, 15 Jan 2022 19:11:52: 2000000 INFO @ Sat, 15 Jan 2022 19:11:57: 3000000 INFO @ Sat, 15 Jan 2022 19:12:02: 4000000 INFO @ Sat, 15 Jan 2022 19:12:07: 5000000 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 19:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.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 19:12:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:13: 6000000 INFO @ Sat, 15 Jan 2022 19:12:17: 1000000 INFO @ Sat, 15 Jan 2022 19:12:19: 7000000 INFO @ Sat, 15 Jan 2022 19:12:23: 2000000 INFO @ Sat, 15 Jan 2022 19:12:24: 8000000 INFO @ Sat, 15 Jan 2022 19:12:29: 3000000 INFO @ Sat, 15 Jan 2022 19:12:30: 9000000 INFO @ Sat, 15 Jan 2022 19:12:34: 4000000 INFO @ Sat, 15 Jan 2022 19:12:36: 10000000 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 19:12:40: 5000000 INFO @ Sat, 15 Jan 2022 19:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.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 19:12:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:42: 11000000 INFO @ Sat, 15 Jan 2022 19:12:43: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:12:43: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:12:43: #1 total tags in treatment: 3630734 INFO @ Sat, 15 Jan 2022 19:12:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:43: #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 19:12:43: #1 tags after filtering in treatment: 2673523 INFO @ Sat, 15 Jan 2022 19:12:43: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:12:43: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:44: #2 number of paired peaks: 128 WARNING @ Sat, 15 Jan 2022 19:12:44: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:44: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:44: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:44: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:44: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:44: #2 predicted fragment length is 255 bps INFO @ Sat, 15 Jan 2022 19:12:44: #2 alternative fragment length(s) may be 1,189,222,255 bps INFO @ Sat, 15 Jan 2022 19:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.05_model.r INFO @ Sat, 15 Jan 2022 19:12:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:46: 6000000 INFO @ Sat, 15 Jan 2022 19:12:47: 1000000 INFO @ Sat, 15 Jan 2022 19:12:51: 7000000 INFO @ Sat, 15 Jan 2022 19:12:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:53: 2000000 INFO @ Sat, 15 Jan 2022 19:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.05_summits.bed INFO @ Sat, 15 Jan 2022 19:12:56: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (254 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:12:57: 8000000 INFO @ Sat, 15 Jan 2022 19:12:59: 3000000 INFO @ Sat, 15 Jan 2022 19:13:03: 9000000 INFO @ Sat, 15 Jan 2022 19:13:04: 4000000 INFO @ Sat, 15 Jan 2022 19:13:08: 10000000 INFO @ Sat, 15 Jan 2022 19:13:10: 5000000 INFO @ Sat, 15 Jan 2022 19:13:14: 11000000 INFO @ Sat, 15 Jan 2022 19:13:15: 6000000 INFO @ Sat, 15 Jan 2022 19:13:16: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:13:16: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:13:16: #1 total tags in treatment: 3630734 INFO @ Sat, 15 Jan 2022 19:13:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:16: #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 19:13:16: #1 tags after filtering in treatment: 2673523 INFO @ Sat, 15 Jan 2022 19:13:16: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:13:16: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:16: #2 number of paired peaks: 128 WARNING @ Sat, 15 Jan 2022 19:13:16: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:16: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:16: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:16: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:16: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:16: #2 predicted fragment length is 255 bps INFO @ Sat, 15 Jan 2022 19:13:16: #2 alternative fragment length(s) may be 1,189,222,255 bps INFO @ Sat, 15 Jan 2022 19:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.10_model.r INFO @ Sat, 15 Jan 2022 19:13:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:13:21: 7000000 INFO @ Sat, 15 Jan 2022 19:13:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.10_summits.bed INFO @ Sat, 15 Jan 2022 19:13:26: Done! INFO @ Sat, 15 Jan 2022 19:13:26: 8000000 pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:13:31: 9000000 INFO @ Sat, 15 Jan 2022 19:13:36: 10000000 INFO @ Sat, 15 Jan 2022 19:13:41: 11000000 INFO @ Sat, 15 Jan 2022 19:13:43: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:13:43: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:13:43: #1 total tags in treatment: 3630734 INFO @ Sat, 15 Jan 2022 19:13:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:43: #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 19:13:43: #1 tags after filtering in treatment: 2673523 INFO @ Sat, 15 Jan 2022 19:13:43: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:13:43: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:43: #2 number of paired peaks: 128 WARNING @ Sat, 15 Jan 2022 19:13:43: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:43: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:43: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:43: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:43: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:43: #2 predicted fragment length is 255 bps INFO @ Sat, 15 Jan 2022 19:13:43: #2 alternative fragment length(s) may be 1,189,222,255 bps INFO @ Sat, 15 Jan 2022 19:13:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.20_model.r INFO @ Sat, 15 Jan 2022 19:13:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781112/SRX11781112.20_summits.bed INFO @ Sat, 15 Jan 2022 19:13:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (70 records, 4 fields): 20 millis CompletedMACS2peakCalling