Job ID = 14519783 SRX = SRX9390803 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1080151 spots for SRR12926698/SRR12926698.sra Written 1080151 spots for SRR12926698/SRR12926698.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: 00:00:49 1080151 reads; of these: 1080151 (100.00%) were paired; of these: 625992 (57.95%) aligned concordantly 0 times 311972 (28.88%) aligned concordantly exactly 1 time 142187 (13.16%) aligned concordantly >1 times ---- 625992 pairs aligned concordantly 0 times; of these: 83496 (13.34%) aligned discordantly 1 time ---- 542496 pairs aligned 0 times concordantly or discordantly; of these: 1084992 mates make up the pairs; of these: 481136 (44.34%) aligned 0 times 165675 (15.27%) aligned exactly 1 time 438181 (40.39%) aligned >1 times 77.73% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 116497 / 534137 = 0.2181 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 17:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.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 17:46:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:46:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:46:16: 1000000 INFO @ Sat, 15 Jan 2022 17:46:18: #1 tag size is determined as 58 bps INFO @ Sat, 15 Jan 2022 17:46:18: #1 tag size = 58 INFO @ Sat, 15 Jan 2022 17:46:18: #1 total tags in treatment: 352095 INFO @ Sat, 15 Jan 2022 17:46:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:46:18: #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 17:46:18: #1 tags after filtering in treatment: 283815 INFO @ Sat, 15 Jan 2022 17:46:18: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 17:46:18: #1 finished! INFO @ Sat, 15 Jan 2022 17:46:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:46:18: #2 number of paired peaks: 122 WARNING @ Sat, 15 Jan 2022 17:46:18: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 15 Jan 2022 17:46:18: start model_add_line... INFO @ Sat, 15 Jan 2022 17:46:18: start X-correlation... INFO @ Sat, 15 Jan 2022 17:46:18: end of X-cor INFO @ Sat, 15 Jan 2022 17:46:18: #2 finished! INFO @ Sat, 15 Jan 2022 17:46:18: #2 predicted fragment length is 140 bps INFO @ Sat, 15 Jan 2022 17:46:18: #2 alternative fragment length(s) may be 10,63,103,140,189,584 bps INFO @ Sat, 15 Jan 2022 17:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.05_model.r INFO @ Sat, 15 Jan 2022 17:46:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:46:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:46:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.05_summits.bed INFO @ Sat, 15 Jan 2022 17:46:19: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (312 records, 4 fields): 2 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 17:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.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 17:46:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:46:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:46:47: 1000000 INFO @ Sat, 15 Jan 2022 17:46:50: #1 tag size is determined as 58 bps INFO @ Sat, 15 Jan 2022 17:46:50: #1 tag size = 58 INFO @ Sat, 15 Jan 2022 17:46:50: #1 total tags in treatment: 352095 INFO @ Sat, 15 Jan 2022 17:46:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:46:50: #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 17:46:50: #1 tags after filtering in treatment: 283815 INFO @ Sat, 15 Jan 2022 17:46:50: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 17:46:50: #1 finished! INFO @ Sat, 15 Jan 2022 17:46:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:46:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:46:50: #2 number of paired peaks: 122 WARNING @ Sat, 15 Jan 2022 17:46:50: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 15 Jan 2022 17:46:50: start model_add_line... INFO @ Sat, 15 Jan 2022 17:46:50: start X-correlation... INFO @ Sat, 15 Jan 2022 17:46:50: end of X-cor INFO @ Sat, 15 Jan 2022 17:46:50: #2 finished! INFO @ Sat, 15 Jan 2022 17:46:50: #2 predicted fragment length is 140 bps INFO @ Sat, 15 Jan 2022 17:46:50: #2 alternative fragment length(s) may be 10,63,103,140,189,584 bps INFO @ Sat, 15 Jan 2022 17:46:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.10_model.r INFO @ Sat, 15 Jan 2022 17:46:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:46:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:46:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:46:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:46:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.10_summits.bed INFO @ Sat, 15 Jan 2022 17:46:51: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (53 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 17:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.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 17:47:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:47:11: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:47:16: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:47:19: #1 tag size is determined as 58 bps INFO @ Sat, 15 Jan 2022 17:47:19: #1 tag size = 58 INFO @ Sat, 15 Jan 2022 17:47:19: #1 total tags in treatment: 352095 INFO @ Sat, 15 Jan 2022 17:47:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:47:19: #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 17:47:19: #1 tags after filtering in treatment: 283815 INFO @ Sat, 15 Jan 2022 17:47:19: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 17:47:19: #1 finished! INFO @ Sat, 15 Jan 2022 17:47:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:47:19: #2 number of paired peaks: 122 WARNING @ Sat, 15 Jan 2022 17:47:19: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 15 Jan 2022 17:47:19: start model_add_line... INFO @ Sat, 15 Jan 2022 17:47:19: start X-correlation... INFO @ Sat, 15 Jan 2022 17:47:19: end of X-cor INFO @ Sat, 15 Jan 2022 17:47:19: #2 finished! INFO @ Sat, 15 Jan 2022 17:47:19: #2 predicted fragment length is 140 bps INFO @ Sat, 15 Jan 2022 17:47:19: #2 alternative fragment length(s) may be 10,63,103,140,189,584 bps INFO @ Sat, 15 Jan 2022 17:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.20_model.r INFO @ Sat, 15 Jan 2022 17:47:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:47:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390803/SRX9390803.20_summits.bed INFO @ Sat, 15 Jan 2022 17:47:20: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 21 millis CompletedMACS2peakCalling