Job ID = 14521303 SRX = SRX8952622 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4524103 spots for SRR12458264/SRR12458264.sra Written 4524103 spots for SRR12458264/SRR12458264.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: 00:01:27 4524103 reads; of these: 4524103 (100.00%) were paired; of these: 3560861 (78.71%) aligned concordantly 0 times 840259 (18.57%) aligned concordantly exactly 1 time 122983 (2.72%) aligned concordantly >1 times ---- 3560861 pairs aligned concordantly 0 times; of these: 76122 (2.14%) aligned discordantly 1 time ---- 3484739 pairs aligned 0 times concordantly or discordantly; of these: 6969478 mates make up the pairs; of these: 6561082 (94.14%) aligned 0 times 322570 (4.63%) aligned exactly 1 time 85826 (1.23%) aligned >1 times 27.49% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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_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] 236114 / 1028324 = 0.2296 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 20:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.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 20:51:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:51:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:51:26: 1000000 INFO @ Sat, 15 Jan 2022 20:51:33: 2000000 INFO @ Sat, 15 Jan 2022 20:51:33: #1 tag size is determined as 44 bps INFO @ Sat, 15 Jan 2022 20:51:33: #1 tag size = 44 INFO @ Sat, 15 Jan 2022 20:51:33: #1 total tags in treatment: 744461 INFO @ Sat, 15 Jan 2022 20:51:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:33: #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 20:51:33: #1 tags after filtering in treatment: 667369 INFO @ Sat, 15 Jan 2022 20:51:33: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 20:51:33: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:33: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 20:51:33: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:33: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:33: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:33: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:33: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:33: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Jan 2022 20:51:33: #2 alternative fragment length(s) may be 2,60,213,247,588 bps INFO @ Sat, 15 Jan 2022 20:51:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.05_model.r INFO @ Sat, 15 Jan 2022 20:51:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:51:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.05_summits.bed INFO @ Sat, 15 Jan 2022 20:51:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (208 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 20:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.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 20:51:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:51:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:51:56: 1000000 INFO @ Sat, 15 Jan 2022 20:52:04: 2000000 INFO @ Sat, 15 Jan 2022 20:52:04: #1 tag size is determined as 44 bps INFO @ Sat, 15 Jan 2022 20:52:04: #1 tag size = 44 INFO @ Sat, 15 Jan 2022 20:52:04: #1 total tags in treatment: 744461 INFO @ Sat, 15 Jan 2022 20:52:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:04: #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 20:52:04: #1 tags after filtering in treatment: 667369 INFO @ Sat, 15 Jan 2022 20:52:04: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 20:52:04: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:04: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 20:52:04: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:04: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:04: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:04: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:04: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:04: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Jan 2022 20:52:04: #2 alternative fragment length(s) may be 2,60,213,247,588 bps INFO @ Sat, 15 Jan 2022 20:52:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.10_model.r INFO @ Sat, 15 Jan 2022 20:52:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.10_summits.bed INFO @ Sat, 15 Jan 2022 20:52:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (103 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 20:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.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 20:52:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:52:19: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:52:27: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:52:35: 2000000 INFO @ Sat, 15 Jan 2022 20:52:35: #1 tag size is determined as 44 bps INFO @ Sat, 15 Jan 2022 20:52:35: #1 tag size = 44 INFO @ Sat, 15 Jan 2022 20:52:35: #1 total tags in treatment: 744461 INFO @ Sat, 15 Jan 2022 20:52:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:52:35: #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 20:52:36: #1 tags after filtering in treatment: 667369 INFO @ Sat, 15 Jan 2022 20:52:36: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 20:52:36: #1 finished! INFO @ Sat, 15 Jan 2022 20:52:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:52:36: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 20:52:36: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 15 Jan 2022 20:52:36: start model_add_line... INFO @ Sat, 15 Jan 2022 20:52:36: start X-correlation... INFO @ Sat, 15 Jan 2022 20:52:36: end of X-cor INFO @ Sat, 15 Jan 2022 20:52:36: #2 finished! INFO @ Sat, 15 Jan 2022 20:52:36: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Jan 2022 20:52:36: #2 alternative fragment length(s) may be 2,60,213,247,588 bps INFO @ Sat, 15 Jan 2022 20:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.20_model.r INFO @ Sat, 15 Jan 2022 20:52:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:52:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:52:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:52:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:52:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952622/SRX8952622.20_summits.bed INFO @ Sat, 15 Jan 2022 20:52:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 72 millis CompletedMACS2peakCalling