Job ID = 12531680 SRX = SRX4555051 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10720288 spots for SRR7696750/SRR7696750.sra Written 10720288 spots for SRR7696750/SRR7696750.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: 00:15:25 10720288 reads; of these: 10720288 (100.00%) were paired; of these: 639044 (5.96%) aligned concordantly 0 times 4007695 (37.38%) aligned concordantly exactly 1 time 6073549 (56.65%) aligned concordantly >1 times ---- 639044 pairs aligned concordantly 0 times; of these: 40270 (6.30%) aligned discordantly 1 time ---- 598774 pairs aligned 0 times concordantly or discordantly; of these: 1197548 mates make up the pairs; of these: 833233 (69.58%) aligned 0 times 181099 (15.12%) aligned exactly 1 time 183216 (15.30%) aligned >1 times 96.11% overall alignment rate Time searching: 00:15:25 Overall time: 00:15:25 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 16 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] 2675041 / 4835413 = 0.5532 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.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, 17 Apr 2021 09:29:01: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:29:01: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:08: 1000000 INFO @ Sat, 17 Apr 2021 09:29:16: 2000000 INFO @ Sat, 17 Apr 2021 09:29:23: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.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, 17 Apr 2021 09:29:30: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:29:30: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:31: 4000000 INFO @ Sat, 17 Apr 2021 09:29:39: 5000000 INFO @ Sat, 17 Apr 2021 09:29:39: 1000000 INFO @ Sat, 17 Apr 2021 09:29:47: 6000000 INFO @ Sat, 17 Apr 2021 09:29:48: 2000000 INFO @ Sat, 17 Apr 2021 09:29:55: 7000000 INFO @ Sat, 17 Apr 2021 09:29:56: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.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, 17 Apr 2021 09:30:01: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:30:01: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:30:02: 8000000 INFO @ Sat, 17 Apr 2021 09:30:05: 4000000 INFO @ Sat, 17 Apr 2021 09:30:10: 1000000 INFO @ Sat, 17 Apr 2021 09:30:10: 9000000 INFO @ Sat, 17 Apr 2021 09:30:14: 5000000 INFO @ Sat, 17 Apr 2021 09:30:19: 2000000 INFO @ Sat, 17 Apr 2021 09:30:19: 10000000 INFO @ Sat, 17 Apr 2021 09:30:21: 6000000 INFO @ Sat, 17 Apr 2021 09:30:27: 11000000 INFO @ Sat, 17 Apr 2021 09:30:28: 3000000 INFO @ Sat, 17 Apr 2021 09:30:30: 7000000 INFO @ Sat, 17 Apr 2021 09:30:35: 12000000 INFO @ Sat, 17 Apr 2021 09:30:37: 4000000 INFO @ Sat, 17 Apr 2021 09:30:38: 8000000 INFO @ Sat, 17 Apr 2021 09:30:43: 13000000 INFO @ Sat, 17 Apr 2021 09:30:46: 9000000 INFO @ Sat, 17 Apr 2021 09:30:46: 5000000 INFO @ Sat, 17 Apr 2021 09:30:52: 14000000 INFO @ Sat, 17 Apr 2021 09:30:54: 6000000 INFO @ Sat, 17 Apr 2021 09:30:54: 10000000 INFO @ Sat, 17 Apr 2021 09:31:01: 15000000 INFO @ Sat, 17 Apr 2021 09:31:02: 11000000 INFO @ Sat, 17 Apr 2021 09:31:03: 7000000 INFO @ Sat, 17 Apr 2021 09:31:03: #1 tag size is determined as 144 bps INFO @ Sat, 17 Apr 2021 09:31:03: #1 tag size = 144 INFO @ Sat, 17 Apr 2021 09:31:03: #1 total tags in treatment: 7411823 INFO @ Sat, 17 Apr 2021 09:31:03: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:31:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:31:04: #1 tags after filtering in treatment: 1719400 INFO @ Sat, 17 Apr 2021 09:31:04: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 17 Apr 2021 09:31:04: #1 finished! INFO @ Sat, 17 Apr 2021 09:31:04: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:31:04: #2 number of paired peaks: 161 WARNING @ Sat, 17 Apr 2021 09:31:04: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 17 Apr 2021 09:31:04: start model_add_line... INFO @ Sat, 17 Apr 2021 09:31:04: start X-correlation... INFO @ Sat, 17 Apr 2021 09:31:04: end of X-cor INFO @ Sat, 17 Apr 2021 09:31:04: #2 finished! INFO @ Sat, 17 Apr 2021 09:31:04: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:31:04: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sat, 17 Apr 2021 09:31:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.05_model.r WARNING @ Sat, 17 Apr 2021 09:31:04: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:31:04: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sat, 17 Apr 2021 09:31:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:31:04: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:31:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:31:07: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.05_summits.bed INFO @ Sat, 17 Apr 2021 09:31:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1710 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:31:10: 12000000 INFO @ Sat, 17 Apr 2021 09:31:10: 8000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:31:17: 13000000 INFO @ Sat, 17 Apr 2021 09:31:18: 9000000 INFO @ Sat, 17 Apr 2021 09:31:25: 14000000 INFO @ Sat, 17 Apr 2021 09:31:26: 10000000 INFO @ Sat, 17 Apr 2021 09:31:34: 11000000 INFO @ Sat, 17 Apr 2021 09:31:34: 15000000 INFO @ Sat, 17 Apr 2021 09:31:37: #1 tag size is determined as 144 bps INFO @ Sat, 17 Apr 2021 09:31:37: #1 tag size = 144 INFO @ Sat, 17 Apr 2021 09:31:37: #1 total tags in treatment: 7411823 INFO @ Sat, 17 Apr 2021 09:31:37: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:31:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:31:37: #1 tags after filtering in treatment: 1719400 INFO @ Sat, 17 Apr 2021 09:31:37: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 17 Apr 2021 09:31:37: #1 finished! INFO @ Sat, 17 Apr 2021 09:31:37: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:31:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:31:37: #2 number of paired peaks: 161 WARNING @ Sat, 17 Apr 2021 09:31:37: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 17 Apr 2021 09:31:37: start model_add_line... INFO @ Sat, 17 Apr 2021 09:31:37: start X-correlation... INFO @ Sat, 17 Apr 2021 09:31:37: end of X-cor INFO @ Sat, 17 Apr 2021 09:31:37: #2 finished! INFO @ Sat, 17 Apr 2021 09:31:37: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:31:37: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sat, 17 Apr 2021 09:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.10_model.r WARNING @ Sat, 17 Apr 2021 09:31:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:31:37: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sat, 17 Apr 2021 09:31:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:31:37: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:31:41: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:31:42: 12000000 INFO @ Sat, 17 Apr 2021 09:31:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:31:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:31:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.10_summits.bed INFO @ Sat, 17 Apr 2021 09:31:42: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (819 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:31:50: 13000000 INFO @ Sat, 17 Apr 2021 09:31:57: 14000000 INFO @ Sat, 17 Apr 2021 09:32:05: 15000000 INFO @ Sat, 17 Apr 2021 09:32:07: #1 tag size is determined as 144 bps INFO @ Sat, 17 Apr 2021 09:32:07: #1 tag size = 144 INFO @ Sat, 17 Apr 2021 09:32:07: #1 total tags in treatment: 7411823 INFO @ Sat, 17 Apr 2021 09:32:07: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:32:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:32:07: #1 tags after filtering in treatment: 1719400 INFO @ Sat, 17 Apr 2021 09:32:07: #1 Redundant rate of treatment: 0.77 INFO @ Sat, 17 Apr 2021 09:32:07: #1 finished! INFO @ Sat, 17 Apr 2021 09:32:07: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:32:07: #2 number of paired peaks: 161 WARNING @ Sat, 17 Apr 2021 09:32:07: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 17 Apr 2021 09:32:07: start model_add_line... INFO @ Sat, 17 Apr 2021 09:32:07: start X-correlation... INFO @ Sat, 17 Apr 2021 09:32:07: end of X-cor INFO @ Sat, 17 Apr 2021 09:32:07: #2 finished! INFO @ Sat, 17 Apr 2021 09:32:07: #2 predicted fragment length is 46 bps INFO @ Sat, 17 Apr 2021 09:32:07: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sat, 17 Apr 2021 09:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.20_model.r WARNING @ Sat, 17 Apr 2021 09:32:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:32:07: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sat, 17 Apr 2021 09:32:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:32:07: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:32:10: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:32:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:32:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555051/SRX4555051.20_summits.bed INFO @ Sat, 17 Apr 2021 09:32:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling