Job ID = 14520675 SRX = SRX7847374 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6031670 spots for SRR11235556/SRR11235556.sra Written 6031670 spots for SRR11235556/SRR11235556.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: 00:03:29 6031670 reads; of these: 6031670 (100.00%) were paired; of these: 1364998 (22.63%) aligned concordantly 0 times 3416841 (56.65%) aligned concordantly exactly 1 time 1249831 (20.72%) aligned concordantly >1 times ---- 1364998 pairs aligned concordantly 0 times; of these: 5054 (0.37%) aligned discordantly 1 time ---- 1359944 pairs aligned 0 times concordantly or discordantly; of these: 2719888 mates make up the pairs; of these: 2440920 (89.74%) aligned 0 times 146758 (5.40%) aligned exactly 1 time 132210 (4.86%) aligned >1 times 79.77% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 4543384 / 4655535 = 0.9759 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 19:41:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.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 19:41:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:41:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:41:09: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 19:41:09: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 19:41:09: #1 total tags in treatment: 127046 INFO @ Sat, 15 Jan 2022 19:41:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:41:09: #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 19:41:09: #1 tags after filtering in treatment: 64973 INFO @ Sat, 15 Jan 2022 19:41:09: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 15 Jan 2022 19:41:09: #1 finished! INFO @ Sat, 15 Jan 2022 19:41:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:41:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:41:09: #2 number of paired peaks: 558 WARNING @ Sat, 15 Jan 2022 19:41:09: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sat, 15 Jan 2022 19:41:09: start model_add_line... INFO @ Sat, 15 Jan 2022 19:41:09: start X-correlation... INFO @ Sat, 15 Jan 2022 19:41:09: end of X-cor INFO @ Sat, 15 Jan 2022 19:41:09: #2 finished! INFO @ Sat, 15 Jan 2022 19:41:09: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 19:41:09: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 15 Jan 2022 19:41:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.05_model.r INFO @ Sat, 15 Jan 2022 19:41:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:41:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:41:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:41:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:41:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:41:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.05_summits.bed INFO @ Sat, 15 Jan 2022 19:41:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (465 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 19:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.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 19:41:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:41:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:41:39: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 19:41:39: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 19:41:39: #1 total tags in treatment: 127046 INFO @ Sat, 15 Jan 2022 19:41:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:41:39: #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 19:41:39: #1 tags after filtering in treatment: 64973 INFO @ Sat, 15 Jan 2022 19:41:39: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 15 Jan 2022 19:41:39: #1 finished! INFO @ Sat, 15 Jan 2022 19:41:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:41:39: #2 number of paired peaks: 558 WARNING @ Sat, 15 Jan 2022 19:41:39: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sat, 15 Jan 2022 19:41:39: start model_add_line... INFO @ Sat, 15 Jan 2022 19:41:39: start X-correlation... INFO @ Sat, 15 Jan 2022 19:41:39: end of X-cor INFO @ Sat, 15 Jan 2022 19:41:39: #2 finished! INFO @ Sat, 15 Jan 2022 19:41:39: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 19:41:39: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 15 Jan 2022 19:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.10_model.r INFO @ Sat, 15 Jan 2022 19:41:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:41:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:41:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:41:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:41:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.10_summits.bed INFO @ Sat, 15 Jan 2022 19:41:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (297 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 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 19:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.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 19:42:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:42:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:42:10: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 19:42:10: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 19:42:10: #1 total tags in treatment: 127046 INFO @ Sat, 15 Jan 2022 19:42:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:42:10: #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 19:42:10: #1 tags after filtering in treatment: 64973 INFO @ Sat, 15 Jan 2022 19:42:10: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 15 Jan 2022 19:42:10: #1 finished! INFO @ Sat, 15 Jan 2022 19:42:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:42:10: #2 number of paired peaks: 558 WARNING @ Sat, 15 Jan 2022 19:42:10: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sat, 15 Jan 2022 19:42:10: start model_add_line... INFO @ Sat, 15 Jan 2022 19:42:10: start X-correlation... INFO @ Sat, 15 Jan 2022 19:42:10: end of X-cor INFO @ Sat, 15 Jan 2022 19:42:10: #2 finished! INFO @ Sat, 15 Jan 2022 19:42:10: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 19:42:10: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 15 Jan 2022 19:42:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.20_model.r INFO @ Sat, 15 Jan 2022 19:42:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:42:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:42:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:42:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:42:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:42:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847374/SRX7847374.20_summits.bed INFO @ Sat, 15 Jan 2022 19:42:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 2 millis CompletedMACS2peakCalling