Job ID = 14521518 SRX = SRX10468495 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2766555 spots for SRR14094806/SRR14094806.sra Written 2766555 spots for SRR14094806/SRR14094806.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: 00:00:39 2766555 reads; of these: 2766555 (100.00%) were paired; of these: 2069625 (74.81%) aligned concordantly 0 times 446184 (16.13%) aligned concordantly exactly 1 time 250746 (9.06%) aligned concordantly >1 times ---- 2069625 pairs aligned concordantly 0 times; of these: 9394 (0.45%) aligned discordantly 1 time ---- 2060231 pairs aligned 0 times concordantly or discordantly; of these: 4120462 mates make up the pairs; of these: 4071786 (98.82%) aligned 0 times 21570 (0.52%) aligned exactly 1 time 27106 (0.66%) aligned >1 times 26.41% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 23300 / 704926 = 0.0331 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 21:07:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.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 21:07:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:07:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:07:22: 1000000 INFO @ Sat, 15 Jan 2022 21:07:24: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:07:24: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:07:24: #1 total tags in treatment: 673766 INFO @ Sat, 15 Jan 2022 21:07:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:07:24: #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 21:07:24: #1 tags after filtering in treatment: 496809 INFO @ Sat, 15 Jan 2022 21:07:24: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:07:24: #1 finished! INFO @ Sat, 15 Jan 2022 21:07:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:07:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:07:24: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 21:07:24: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 21:07:24: start model_add_line... INFO @ Sat, 15 Jan 2022 21:07:24: start X-correlation... INFO @ Sat, 15 Jan 2022 21:07:24: end of X-cor INFO @ Sat, 15 Jan 2022 21:07:24: #2 finished! INFO @ Sat, 15 Jan 2022 21:07:24: #2 predicted fragment length is 127 bps INFO @ Sat, 15 Jan 2022 21:07:24: #2 alternative fragment length(s) may be 4,97,127 bps INFO @ Sat, 15 Jan 2022 21:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.05_model.r INFO @ Sat, 15 Jan 2022 21:07:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:07:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:07:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.05_summits.bed INFO @ Sat, 15 Jan 2022 21:07:27: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (319 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 21:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.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 21:07:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:07:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:07:54: 1000000 INFO @ Sat, 15 Jan 2022 21:07:57: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:07:57: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:07:57: #1 total tags in treatment: 673766 INFO @ Sat, 15 Jan 2022 21:07:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:07:57: #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 21:07:57: #1 tags after filtering in treatment: 496809 INFO @ Sat, 15 Jan 2022 21:07:57: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:07:57: #1 finished! INFO @ Sat, 15 Jan 2022 21:07:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:07:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:07:57: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 21:07:57: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 21:07:57: start model_add_line... INFO @ Sat, 15 Jan 2022 21:07:57: start X-correlation... INFO @ Sat, 15 Jan 2022 21:07:57: end of X-cor INFO @ Sat, 15 Jan 2022 21:07:57: #2 finished! INFO @ Sat, 15 Jan 2022 21:07:57: #2 predicted fragment length is 127 bps INFO @ Sat, 15 Jan 2022 21:07:57: #2 alternative fragment length(s) may be 4,97,127 bps INFO @ Sat, 15 Jan 2022 21:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.10_model.r INFO @ Sat, 15 Jan 2022 21:07:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:07:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:07:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.10_summits.bed INFO @ Sat, 15 Jan 2022 21:08:00: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 2 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 21:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.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 21:08:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:08:15: #1 read treatment tags... 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 21:08:23: 1000000 INFO @ Sat, 15 Jan 2022 21:08:26: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:08:26: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:08:26: #1 total tags in treatment: 673766 INFO @ Sat, 15 Jan 2022 21:08:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:08:26: #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 21:08:26: #1 tags after filtering in treatment: 496809 INFO @ Sat, 15 Jan 2022 21:08:26: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:08:26: #1 finished! INFO @ Sat, 15 Jan 2022 21:08:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:08:26: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 21:08:26: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 21:08:26: start model_add_line... INFO @ Sat, 15 Jan 2022 21:08:26: start X-correlation... INFO @ Sat, 15 Jan 2022 21:08:26: end of X-cor INFO @ Sat, 15 Jan 2022 21:08:26: #2 finished! INFO @ Sat, 15 Jan 2022 21:08:26: #2 predicted fragment length is 127 bps INFO @ Sat, 15 Jan 2022 21:08:26: #2 alternative fragment length(s) may be 4,97,127 bps INFO @ Sat, 15 Jan 2022 21:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.20_model.r INFO @ Sat, 15 Jan 2022 21:08:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:08:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:08:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468495/SRX10468495.20_summits.bed INFO @ Sat, 15 Jan 2022 21:08:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 3 millis CompletedMACS2peakCalling