Job ID = 14521391 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: 00:02:20 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: 00:02:20 Overall time: 00:02:20 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:00:48: # 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 @ Sat, 15 Jan 2022 21:00:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:00:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:00:54: 1000000 INFO @ Sat, 15 Jan 2022 21:01:00: 2000000 INFO @ Sat, 15 Jan 2022 21:01:06: 3000000 INFO @ Sat, 15 Jan 2022 21:01:12: 4000000 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 21:01:18: 5000000 INFO @ Sat, 15 Jan 2022 21:01:18: # 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 @ Sat, 15 Jan 2022 21:01:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:24: 6000000 INFO @ Sat, 15 Jan 2022 21:01:24: 1000000 INFO @ Sat, 15 Jan 2022 21:01:25: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 21:01:25: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 21:01:25: #1 total tags in treatment: 2088419 INFO @ Sat, 15 Jan 2022 21:01:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:25: #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 21:01:25: #1 tags after filtering in treatment: 1815462 INFO @ Sat, 15 Jan 2022 21:01:25: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:01:25: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:26: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 21:01:26: 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 @ Sat, 15 Jan 2022 21:01:26: start model_add_line... INFO @ Sat, 15 Jan 2022 21:01:26: start X-correlation... INFO @ Sat, 15 Jan 2022 21:01:26: end of X-cor INFO @ Sat, 15 Jan 2022 21:01:26: #2 finished! INFO @ Sat, 15 Jan 2022 21:01:26: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 21:01:26: #2 alternative fragment length(s) may be 0,123,144,166,183,208,227,440,592 bps INFO @ Sat, 15 Jan 2022 21:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05_model.r INFO @ Sat, 15 Jan 2022 21:01:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:01:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:01:30: 2000000 INFO @ Sat, 15 Jan 2022 21:01:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:01:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:01:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.05_summits.bed INFO @ Sat, 15 Jan 2022 21:01:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:01:35: 3000000 INFO @ Sat, 15 Jan 2022 21:01:40: 4000000 INFO @ Sat, 15 Jan 2022 21:01:45: 5000000 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 21:01:48: # 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 @ Sat, 15 Jan 2022 21:01:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:51: 6000000 INFO @ Sat, 15 Jan 2022 21:01:53: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 21:01:53: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 21:01:53: #1 total tags in treatment: 2088419 INFO @ Sat, 15 Jan 2022 21:01:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:53: #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 21:01:53: #1 tags after filtering in treatment: 1815462 INFO @ Sat, 15 Jan 2022 21:01:53: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:01:53: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:53: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 21:01:53: 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 @ Sat, 15 Jan 2022 21:01:53: start model_add_line... INFO @ Sat, 15 Jan 2022 21:01:53: start X-correlation... INFO @ Sat, 15 Jan 2022 21:01:53: end of X-cor INFO @ Sat, 15 Jan 2022 21:01:53: #2 finished! INFO @ Sat, 15 Jan 2022 21:01:53: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 21:01:53: #2 alternative fragment length(s) may be 0,123,144,166,183,208,227,440,592 bps INFO @ Sat, 15 Jan 2022 21:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10_model.r INFO @ Sat, 15 Jan 2022 21:01:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:01:55: 1000000 INFO @ Sat, 15 Jan 2022 21:01:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:01:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:01:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:01:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.10_summits.bed INFO @ Sat, 15 Jan 2022 21:01:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:02:00: 2000000 INFO @ Sat, 15 Jan 2022 21:02:05: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:02:10: 4000000 INFO @ Sat, 15 Jan 2022 21:02:16: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:02:21: 6000000 INFO @ Sat, 15 Jan 2022 21:02:22: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 21:02:22: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 21:02:22: #1 total tags in treatment: 2088419 INFO @ Sat, 15 Jan 2022 21:02:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:02:22: #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 21:02:22: #1 tags after filtering in treatment: 1815462 INFO @ Sat, 15 Jan 2022 21:02:22: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:02:22: #1 finished! INFO @ Sat, 15 Jan 2022 21:02:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:02:22: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 21:02:22: 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 @ Sat, 15 Jan 2022 21:02:22: start model_add_line... INFO @ Sat, 15 Jan 2022 21:02:22: start X-correlation... INFO @ Sat, 15 Jan 2022 21:02:22: end of X-cor INFO @ Sat, 15 Jan 2022 21:02:22: #2 finished! INFO @ Sat, 15 Jan 2022 21:02:22: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 21:02:22: #2 alternative fragment length(s) may be 0,123,144,166,183,208,227,440,592 bps INFO @ Sat, 15 Jan 2022 21:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20_model.r INFO @ Sat, 15 Jan 2022 21:02:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:02:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952653/SRX8952653.20_summits.bed INFO @ Sat, 15 Jan 2022 21:02:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 1 millis CompletedMACS2peakCalling