Job ID = 14520631 SRX = SRX7847358 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18531280 spots for SRR11235540/SRR11235540.sra Written 18531280 spots for SRR11235540/SRR11235540.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: 00:10:27 18531280 reads; of these: 18531280 (100.00%) were paired; of these: 2986572 (16.12%) aligned concordantly 0 times 13507428 (72.89%) aligned concordantly exactly 1 time 2037280 (10.99%) aligned concordantly >1 times ---- 2986572 pairs aligned concordantly 0 times; of these: 108696 (3.64%) aligned discordantly 1 time ---- 2877876 pairs aligned 0 times concordantly or discordantly; of these: 5755752 mates make up the pairs; of these: 4344576 (75.48%) aligned 0 times 945801 (16.43%) aligned exactly 1 time 465375 (8.09%) aligned >1 times 88.28% overall alignment rate Time searching: 00:10:27 Overall time: 00:10:27 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 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] 14712708 / 15610459 = 0.9425 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 19:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.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 19:46:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:46:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:46:14: 1000000 INFO @ Sat, 15 Jan 2022 19:46:19: 2000000 INFO @ Sat, 15 Jan 2022 19:46:23: 3000000 INFO @ Sat, 15 Jan 2022 19:46:24: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:46:24: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:46:24: #1 total tags in treatment: 926972 INFO @ Sat, 15 Jan 2022 19:46:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:46:24: #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 19:46:24: #1 tags after filtering in treatment: 324492 INFO @ Sat, 15 Jan 2022 19:46:24: #1 Redundant rate of treatment: 0.65 INFO @ Sat, 15 Jan 2022 19:46:24: #1 finished! INFO @ Sat, 15 Jan 2022 19:46:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:46:25: #2 number of paired peaks: 732 WARNING @ Sat, 15 Jan 2022 19:46:25: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 15 Jan 2022 19:46:25: start model_add_line... INFO @ Sat, 15 Jan 2022 19:46:25: start X-correlation... INFO @ Sat, 15 Jan 2022 19:46:25: end of X-cor INFO @ Sat, 15 Jan 2022 19:46:25: #2 finished! INFO @ Sat, 15 Jan 2022 19:46:25: #2 predicted fragment length is 137 bps INFO @ Sat, 15 Jan 2022 19:46:25: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 15 Jan 2022 19:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.05_model.r INFO @ Sat, 15 Jan 2022 19:46:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:46:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:46:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:46:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:46:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.05_summits.bed INFO @ Sat, 15 Jan 2022 19:46:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (802 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 19:46:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.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 19:46:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:46:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:46:44: 1000000 INFO @ Sat, 15 Jan 2022 19:46:48: 2000000 INFO @ Sat, 15 Jan 2022 19:46:53: 3000000 INFO @ Sat, 15 Jan 2022 19:46:54: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:46:54: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:46:54: #1 total tags in treatment: 926972 INFO @ Sat, 15 Jan 2022 19:46:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:46:54: #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 19:46:54: #1 tags after filtering in treatment: 324492 INFO @ Sat, 15 Jan 2022 19:46:54: #1 Redundant rate of treatment: 0.65 INFO @ Sat, 15 Jan 2022 19:46:54: #1 finished! INFO @ Sat, 15 Jan 2022 19:46:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:46:54: #2 number of paired peaks: 732 WARNING @ Sat, 15 Jan 2022 19:46:54: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 15 Jan 2022 19:46:54: start model_add_line... INFO @ Sat, 15 Jan 2022 19:46:54: start X-correlation... INFO @ Sat, 15 Jan 2022 19:46:54: end of X-cor INFO @ Sat, 15 Jan 2022 19:46:54: #2 finished! INFO @ Sat, 15 Jan 2022 19:46:54: #2 predicted fragment length is 137 bps INFO @ Sat, 15 Jan 2022 19:46:54: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 15 Jan 2022 19:46:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.10_model.r INFO @ Sat, 15 Jan 2022 19:46:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:46:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.10_summits.bed INFO @ Sat, 15 Jan 2022 19:46:56: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (601 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 19:47:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.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 19:47:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:47:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:47:14: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:47:18: 2000000 INFO @ Sat, 15 Jan 2022 19:47:23: 3000000 INFO @ Sat, 15 Jan 2022 19:47:24: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:47:24: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:47:24: #1 total tags in treatment: 926972 INFO @ Sat, 15 Jan 2022 19:47:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:47:24: #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 19:47:24: #1 tags after filtering in treatment: 324492 INFO @ Sat, 15 Jan 2022 19:47:24: #1 Redundant rate of treatment: 0.65 INFO @ Sat, 15 Jan 2022 19:47:24: #1 finished! INFO @ Sat, 15 Jan 2022 19:47:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:47:24: #2 number of paired peaks: 732 WARNING @ Sat, 15 Jan 2022 19:47:24: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 15 Jan 2022 19:47:24: start model_add_line... INFO @ Sat, 15 Jan 2022 19:47:24: start X-correlation... INFO @ Sat, 15 Jan 2022 19:47:24: end of X-cor INFO @ Sat, 15 Jan 2022 19:47:24: #2 finished! INFO @ Sat, 15 Jan 2022 19:47:24: #2 predicted fragment length is 137 bps INFO @ Sat, 15 Jan 2022 19:47:24: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 15 Jan 2022 19:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.20_model.r INFO @ Sat, 15 Jan 2022 19:47:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:47:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847358/SRX7847358.20_summits.bed INFO @ Sat, 15 Jan 2022 19:47:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 2 millis CompletedMACS2peakCalling