Job ID = 10224054 SRX = SRX8952611 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14138512 spots for SRR12458275/SRR12458275.sra Written 14138512 spots for SRR12458275/SRR12458275.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: 00:47:01 14138512 reads; of these: 14138512 (100.00%) were paired; of these: 9926674 (70.21%) aligned concordantly 0 times 1636759 (11.58%) aligned concordantly exactly 1 time 2575079 (18.21%) aligned concordantly >1 times ---- 9926674 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 9926674 pairs aligned 0 times concordantly or discordantly; of these: 19853348 mates make up the pairs; of these: 4344452 (21.88%) aligned 0 times 7205555 (36.29%) aligned exactly 1 time 8303341 (41.82%) aligned >1 times 84.64% overall alignment rate Time searching: 00:47:01 Overall time: 00:47:01 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] 3325774 / 4208285 = 0.7903 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:07:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.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 @ Fri, 16 Oct 2020 10:07:48: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:07:48: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:07:52: 1000000 INFO @ Fri, 16 Oct 2020 10:07:55: 2000000 INFO @ Fri, 16 Oct 2020 10:07:59: 3000000 INFO @ Fri, 16 Oct 2020 10:08:02: 4000000 INFO @ Fri, 16 Oct 2020 10:08:06: 5000000 INFO @ Fri, 16 Oct 2020 10:08:10: 6000000 INFO @ Fri, 16 Oct 2020 10:08:13: 7000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:08:17: 8000000 INFO @ Fri, 16 Oct 2020 10:08:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.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 @ Fri, 16 Oct 2020 10:08:18: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:08:18: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:08:20: 9000000 INFO @ Fri, 16 Oct 2020 10:08:22: 1000000 INFO @ Fri, 16 Oct 2020 10:08:24: 10000000 INFO @ Fri, 16 Oct 2020 10:08:25: 2000000 INFO @ Fri, 16 Oct 2020 10:08:27: 11000000 INFO @ Fri, 16 Oct 2020 10:08:29: 3000000 INFO @ Fri, 16 Oct 2020 10:08:31: 12000000 INFO @ Fri, 16 Oct 2020 10:08:32: 4000000 INFO @ Fri, 16 Oct 2020 10:08:34: 13000000 INFO @ Fri, 16 Oct 2020 10:08:36: 5000000 INFO @ Fri, 16 Oct 2020 10:08:38: 14000000 INFO @ Fri, 16 Oct 2020 10:08:40: 6000000 INFO @ Fri, 16 Oct 2020 10:08:41: 15000000 INFO @ Fri, 16 Oct 2020 10:08:44: 7000000 INFO @ Fri, 16 Oct 2020 10:08:45: 16000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:08:47: 8000000 INFO @ Fri, 16 Oct 2020 10:08:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.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 @ Fri, 16 Oct 2020 10:08:48: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:08:48: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:08:48: 17000000 INFO @ Fri, 16 Oct 2020 10:08:49: #1 tag size is determined as 20 bps INFO @ Fri, 16 Oct 2020 10:08:49: #1 tag size = 20 INFO @ Fri, 16 Oct 2020 10:08:49: #1 total tags in treatment: 886064 INFO @ Fri, 16 Oct 2020 10:08:49: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:08:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:08:49: #1 tags after filtering in treatment: 684709 INFO @ Fri, 16 Oct 2020 10:08:49: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 16 Oct 2020 10:08:49: #1 finished! INFO @ Fri, 16 Oct 2020 10:08:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:08:49: #2 number of paired peaks: 228 WARNING @ Fri, 16 Oct 2020 10:08:49: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Fri, 16 Oct 2020 10:08:49: start model_add_line... INFO @ Fri, 16 Oct 2020 10:08:49: start X-correlation... INFO @ Fri, 16 Oct 2020 10:08:49: end of X-cor INFO @ Fri, 16 Oct 2020 10:08:49: #2 finished! INFO @ Fri, 16 Oct 2020 10:08:49: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 10:08:49: #2 alternative fragment length(s) may be 2,179,217,236,260 bps INFO @ Fri, 16 Oct 2020 10:08:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.05_model.r INFO @ Fri, 16 Oct 2020 10:08:49: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:08:51: 9000000 INFO @ Fri, 16 Oct 2020 10:08:52: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:08:52: 1000000 INFO @ Fri, 16 Oct 2020 10:08:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.05_peaks.xls INFO @ Fri, 16 Oct 2020 10:08:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:08:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.05_summits.bed INFO @ Fri, 16 Oct 2020 10:08:52: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:08:55: 10000000 INFO @ Fri, 16 Oct 2020 10:08:56: 2000000 INFO @ Fri, 16 Oct 2020 10:08:58: 11000000 INFO @ Fri, 16 Oct 2020 10:09:00: 3000000 INFO @ Fri, 16 Oct 2020 10:09:02: 12000000 INFO @ Fri, 16 Oct 2020 10:09:05: 4000000 INFO @ Fri, 16 Oct 2020 10:09:05: 13000000 INFO @ Fri, 16 Oct 2020 10:09:09: 14000000 INFO @ Fri, 16 Oct 2020 10:09:09: 5000000 INFO @ Fri, 16 Oct 2020 10:09:13: 15000000 INFO @ Fri, 16 Oct 2020 10:09:14: 6000000 INFO @ Fri, 16 Oct 2020 10:09:16: 16000000 INFO @ Fri, 16 Oct 2020 10:09:18: 7000000 INFO @ Fri, 16 Oct 2020 10:09:20: 17000000 INFO @ Fri, 16 Oct 2020 10:09:21: #1 tag size is determined as 20 bps INFO @ Fri, 16 Oct 2020 10:09:21: #1 tag size = 20 INFO @ Fri, 16 Oct 2020 10:09:21: #1 total tags in treatment: 886064 INFO @ Fri, 16 Oct 2020 10:09:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:09:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:09:21: #1 tags after filtering in treatment: 684709 INFO @ Fri, 16 Oct 2020 10:09:21: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 16 Oct 2020 10:09:21: #1 finished! INFO @ Fri, 16 Oct 2020 10:09:21: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:09:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:09:21: #2 number of paired peaks: 228 WARNING @ Fri, 16 Oct 2020 10:09:21: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Fri, 16 Oct 2020 10:09:21: start model_add_line... INFO @ Fri, 16 Oct 2020 10:09:21: start X-correlation... INFO @ Fri, 16 Oct 2020 10:09:21: end of X-cor INFO @ Fri, 16 Oct 2020 10:09:21: #2 finished! INFO @ Fri, 16 Oct 2020 10:09:21: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 10:09:21: #2 alternative fragment length(s) may be 2,179,217,236,260 bps INFO @ Fri, 16 Oct 2020 10:09:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.10_model.r INFO @ Fri, 16 Oct 2020 10:09:21: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:09:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:09:22: 8000000 INFO @ Fri, 16 Oct 2020 10:09:23: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.10_peaks.xls INFO @ Fri, 16 Oct 2020 10:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.10_summits.bed INFO @ Fri, 16 Oct 2020 10:09:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (172 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:09:26: 9000000 INFO @ Fri, 16 Oct 2020 10:09:30: 10000000 INFO @ Fri, 16 Oct 2020 10:09:34: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 10:09:38: 12000000 INFO @ Fri, 16 Oct 2020 10:09:42: 13000000 INFO @ Fri, 16 Oct 2020 10:09:46: 14000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 10:09:50: 15000000 INFO @ Fri, 16 Oct 2020 10:09:54: 16000000 INFO @ Fri, 16 Oct 2020 10:09:58: 17000000 INFO @ Fri, 16 Oct 2020 10:09:59: #1 tag size is determined as 20 bps INFO @ Fri, 16 Oct 2020 10:09:59: #1 tag size = 20 INFO @ Fri, 16 Oct 2020 10:09:59: #1 total tags in treatment: 886064 INFO @ Fri, 16 Oct 2020 10:09:59: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:09:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:09:59: #1 tags after filtering in treatment: 684709 INFO @ Fri, 16 Oct 2020 10:09:59: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 16 Oct 2020 10:09:59: #1 finished! INFO @ Fri, 16 Oct 2020 10:09:59: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:09:59: #2 number of paired peaks: 228 WARNING @ Fri, 16 Oct 2020 10:09:59: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Fri, 16 Oct 2020 10:09:59: start model_add_line... INFO @ Fri, 16 Oct 2020 10:09:59: start X-correlation... INFO @ Fri, 16 Oct 2020 10:09:59: end of X-cor INFO @ Fri, 16 Oct 2020 10:09:59: #2 finished! INFO @ Fri, 16 Oct 2020 10:09:59: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 10:09:59: #2 alternative fragment length(s) may be 2,179,217,236,260 bps INFO @ Fri, 16 Oct 2020 10:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.20_model.r INFO @ Fri, 16 Oct 2020 10:09:59: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:10:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:10:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.20_peaks.xls INFO @ Fri, 16 Oct 2020 10:10:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:10:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952611/SRX8952611.20_summits.bed INFO @ Fri, 16 Oct 2020 10:10:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (80 records, 4 fields): 2 millis CompletedMACS2peakCalling