Job ID = 10224098 SRX = SRX8952653 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7934305 spots for SRR12458233/SRR12458233.sra Written 7934305 spots for SRR12458233/SRR12458233.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: 00:02:22 7934305 reads; of these: 7934305 (100.00%) were paired; of these: 5562884 (70.11%) aligned concordantly 0 times 2024916 (25.52%) aligned concordantly exactly 1 time 346505 (4.37%) aligned concordantly >1 times ---- 5562884 pairs aligned concordantly 0 times; of these: 351559 (6.32%) aligned discordantly 1 time ---- 5211325 pairs aligned 0 times concordantly or discordantly; of these: 10422650 mates make up the pairs; of these: 8674794 (83.23%) aligned 0 times 1498676 (14.38%) aligned exactly 1 time 249180 (2.39%) aligned >1 times 45.33% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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_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] 474914 / 2709395 = 0.1753 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 09:30:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.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 09:30:12: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:30:12: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:30:18: 1000000 INFO @ Fri, 16 Oct 2020 09:30:23: 2000000 INFO @ Fri, 16 Oct 2020 09:30:28: 3000000 INFO @ Fri, 16 Oct 2020 09:30:34: 4000000 INFO @ Fri, 16 Oct 2020 09:30:39: 5000000 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 09:30:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.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 09:30:42: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:30:42: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:30:45: 6000000 INFO @ Fri, 16 Oct 2020 09:30:46: #1 tag size is determined as 43 bps INFO @ Fri, 16 Oct 2020 09:30:46: #1 tag size = 43 INFO @ Fri, 16 Oct 2020 09:30:46: #1 total tags in treatment: 2088419 INFO @ Fri, 16 Oct 2020 09:30:46: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:30:46: #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 09:30:46: #1 tags after filtering in treatment: 1815462 INFO @ Fri, 16 Oct 2020 09:30:46: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 09:30:46: #1 finished! INFO @ Fri, 16 Oct 2020 09:30:46: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:30:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:30:46: #2 number of paired peaks: 167 WARNING @ Fri, 16 Oct 2020 09:30:46: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 16 Oct 2020 09:30:46: start model_add_line... INFO @ Fri, 16 Oct 2020 09:30:46: start X-correlation... INFO @ Fri, 16 Oct 2020 09:30:46: end of X-cor INFO @ Fri, 16 Oct 2020 09:30:46: #2 finished! INFO @ Fri, 16 Oct 2020 09:30:46: #2 predicted fragment length is 183 bps INFO @ Fri, 16 Oct 2020 09:30:46: #2 alternative fragment length(s) may be 0,123,144,166,183,208,227,440,592 bps INFO @ Fri, 16 Oct 2020 09:30:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05_model.r INFO @ Fri, 16 Oct 2020 09:30:46: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:30:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:30:49: 1000000 INFO @ Fri, 16 Oct 2020 09:30:50: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:30:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:30:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:30:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05_summits.bed INFO @ Fri, 16 Oct 2020 09:30:52: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:30:55: 2000000 INFO @ Fri, 16 Oct 2020 09:31:01: 3000000 INFO @ Fri, 16 Oct 2020 09:31:08: 4000000 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 09:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.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 09:31:12: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:31:12: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:31:15: 5000000 INFO @ Fri, 16 Oct 2020 09:31:19: 1000000 INFO @ Fri, 16 Oct 2020 09:31:22: 6000000 INFO @ Fri, 16 Oct 2020 09:31:23: #1 tag size is determined as 43 bps INFO @ Fri, 16 Oct 2020 09:31:23: #1 tag size = 43 INFO @ Fri, 16 Oct 2020 09:31:23: #1 total tags in treatment: 2088419 INFO @ Fri, 16 Oct 2020 09:31:23: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:31:23: #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 09:31:23: #1 tags after filtering in treatment: 1815462 INFO @ Fri, 16 Oct 2020 09:31:23: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 09:31:23: #1 finished! INFO @ Fri, 16 Oct 2020 09:31:23: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:31:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:31:24: #2 number of paired peaks: 167 WARNING @ Fri, 16 Oct 2020 09:31:24: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 16 Oct 2020 09:31:24: start model_add_line... INFO @ Fri, 16 Oct 2020 09:31:24: start X-correlation... INFO @ Fri, 16 Oct 2020 09:31:24: end of X-cor INFO @ Fri, 16 Oct 2020 09:31:24: #2 finished! INFO @ Fri, 16 Oct 2020 09:31:24: #2 predicted fragment length is 183 bps INFO @ Fri, 16 Oct 2020 09:31:24: #2 alternative fragment length(s) may be 0,123,144,166,183,208,227,440,592 bps INFO @ Fri, 16 Oct 2020 09:31:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10_model.r INFO @ Fri, 16 Oct 2020 09:31:24: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:31:26: 2000000 INFO @ Fri, 16 Oct 2020 09:31:28: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10_summits.bed INFO @ Fri, 16 Oct 2020 09:31:29: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:31:32: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:31:38: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:31:44: 5000000 INFO @ Fri, 16 Oct 2020 09:31:51: 6000000 INFO @ Fri, 16 Oct 2020 09:31:52: #1 tag size is determined as 43 bps INFO @ Fri, 16 Oct 2020 09:31:52: #1 tag size = 43 INFO @ Fri, 16 Oct 2020 09:31:52: #1 total tags in treatment: 2088419 INFO @ Fri, 16 Oct 2020 09:31:52: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:31:52: #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 09:31:53: #1 tags after filtering in treatment: 1815462 INFO @ Fri, 16 Oct 2020 09:31:53: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 09:31:53: #1 finished! INFO @ Fri, 16 Oct 2020 09:31:53: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:31:53: #2 number of paired peaks: 167 WARNING @ Fri, 16 Oct 2020 09:31:53: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 16 Oct 2020 09:31:53: start model_add_line... INFO @ Fri, 16 Oct 2020 09:31:53: start X-correlation... INFO @ Fri, 16 Oct 2020 09:31:53: end of X-cor INFO @ Fri, 16 Oct 2020 09:31:53: #2 finished! INFO @ Fri, 16 Oct 2020 09:31:53: #2 predicted fragment length is 183 bps INFO @ Fri, 16 Oct 2020 09:31:53: #2 alternative fragment length(s) may be 0,123,144,166,183,208,227,440,592 bps INFO @ Fri, 16 Oct 2020 09:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20_model.r INFO @ Fri, 16 Oct 2020 09:31:53: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:31:57: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20_summits.bed INFO @ Fri, 16 Oct 2020 09:31:58: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (40 records, 4 fields): 1 millis CompletedMACS2peakCalling