Job ID = 14520770 SRX = SRX9038694 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 41868114 spots for SRR12549475/SRR12549475.sra Written 41868114 spots for SRR12549475/SRR12549475.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: 00:43:10 41868114 reads; of these: 41868114 (100.00%) were paired; of these: 28998770 (69.26%) aligned concordantly 0 times 3010163 (7.19%) aligned concordantly exactly 1 time 9859181 (23.55%) aligned concordantly >1 times ---- 28998770 pairs aligned concordantly 0 times; of these: 205040 (0.71%) aligned discordantly 1 time ---- 28793730 pairs aligned 0 times concordantly or discordantly; of these: 57587460 mates make up the pairs; of these: 55459514 (96.30%) aligned 0 times 241961 (0.42%) aligned exactly 1 time 1885985 (3.27%) aligned >1 times 33.77% overall alignment rate Time searching: 00:43:10 Overall time: 00:43:10 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 24 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] 7107083 / 13044111 = 0.5448 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 21:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.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 21:41:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:27: 1000000 INFO @ Sat, 15 Jan 2022 21:41:36: 2000000 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 21:41:45: 3000000 INFO @ Sat, 15 Jan 2022 21:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.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 21:41:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:55: 4000000 INFO @ Sat, 15 Jan 2022 21:42:00: 1000000 INFO @ Sat, 15 Jan 2022 21:42:04: 5000000 INFO @ Sat, 15 Jan 2022 21:42:12: 2000000 INFO @ Sat, 15 Jan 2022 21:42:13: 6000000 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 21:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.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 21:42:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:42:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:42:24: 7000000 INFO @ Sat, 15 Jan 2022 21:42:25: 3000000 INFO @ Sat, 15 Jan 2022 21:42:28: 1000000 INFO @ Sat, 15 Jan 2022 21:42:37: 4000000 INFO @ Sat, 15 Jan 2022 21:42:37: 2000000 INFO @ Sat, 15 Jan 2022 21:42:38: 8000000 INFO @ Sat, 15 Jan 2022 21:42:47: 3000000 INFO @ Sat, 15 Jan 2022 21:42:49: 5000000 INFO @ Sat, 15 Jan 2022 21:42:52: 9000000 INFO @ Sat, 15 Jan 2022 21:42:57: 4000000 INFO @ Sat, 15 Jan 2022 21:43:02: 6000000 INFO @ Sat, 15 Jan 2022 21:43:03: 10000000 INFO @ Sat, 15 Jan 2022 21:43:07: 5000000 INFO @ Sat, 15 Jan 2022 21:43:14: 7000000 INFO @ Sat, 15 Jan 2022 21:43:15: 11000000 INFO @ Sat, 15 Jan 2022 21:43:17: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:43:26: 12000000 INFO @ Sat, 15 Jan 2022 21:43:26: 8000000 INFO @ Sat, 15 Jan 2022 21:43:28: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:43:37: 13000000 INFO @ Sat, 15 Jan 2022 21:43:38: 9000000 INFO @ Sat, 15 Jan 2022 21:43:39: 8000000 INFO @ Sat, 15 Jan 2022 21:43:48: 14000000 INFO @ Sat, 15 Jan 2022 21:43:49: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 21:43:49: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 21:43:49: #1 total tags in treatment: 5790051 INFO @ Sat, 15 Jan 2022 21:43:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:43:49: #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 21:43:49: #1 tags after filtering in treatment: 1875203 INFO @ Sat, 15 Jan 2022 21:43:49: #1 Redundant rate of treatment: 0.68 INFO @ Sat, 15 Jan 2022 21:43:49: #1 finished! INFO @ Sat, 15 Jan 2022 21:43:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:43:49: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 21:43:49: 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 21:43:49: start model_add_line... INFO @ Sat, 15 Jan 2022 21:43:49: start X-correlation... INFO @ Sat, 15 Jan 2022 21:43:49: end of X-cor INFO @ Sat, 15 Jan 2022 21:43:49: #2 finished! INFO @ Sat, 15 Jan 2022 21:43:49: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 21:43:49: #2 alternative fragment length(s) may be 254 bps INFO @ Sat, 15 Jan 2022 21:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05_model.r WARNING @ Sat, 15 Jan 2022 21:43:49: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:43:49: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Sat, 15 Jan 2022 21:43:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:43:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:43:49: 9000000 INFO @ Sat, 15 Jan 2022 21:43:52: 10000000 INFO @ Sat, 15 Jan 2022 21:43:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:43:59: 10000000 INFO @ Sat, 15 Jan 2022 21:43:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:43:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:43:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05_summits.bed INFO @ Sat, 15 Jan 2022 21:43:59: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1236 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:44:05: 11000000 INFO @ Sat, 15 Jan 2022 21:44:08: 11000000 INFO @ Sat, 15 Jan 2022 21:44:18: 12000000 INFO @ Sat, 15 Jan 2022 21:44:18: 12000000 INFO @ Sat, 15 Jan 2022 21:44:29: 13000000 INFO @ Sat, 15 Jan 2022 21:44:30: 13000000 INFO @ Sat, 15 Jan 2022 21:44:39: 14000000 INFO @ Sat, 15 Jan 2022 21:44:39: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 21:44:39: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 21:44:39: #1 total tags in treatment: 5790051 INFO @ Sat, 15 Jan 2022 21:44:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:44:39: #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 21:44:40: #1 tags after filtering in treatment: 1875203 INFO @ Sat, 15 Jan 2022 21:44:40: #1 Redundant rate of treatment: 0.68 INFO @ Sat, 15 Jan 2022 21:44:40: #1 finished! INFO @ Sat, 15 Jan 2022 21:44:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:44:40: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 21:44:40: 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 21:44:40: start model_add_line... INFO @ Sat, 15 Jan 2022 21:44:40: start X-correlation... INFO @ Sat, 15 Jan 2022 21:44:40: end of X-cor INFO @ Sat, 15 Jan 2022 21:44:40: #2 finished! INFO @ Sat, 15 Jan 2022 21:44:40: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 21:44:40: #2 alternative fragment length(s) may be 254 bps INFO @ Sat, 15 Jan 2022 21:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20_model.r WARNING @ Sat, 15 Jan 2022 21:44:40: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:44:40: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Sat, 15 Jan 2022 21:44:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:44:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:44:41: 14000000 INFO @ Sat, 15 Jan 2022 21:44:41: #1 tag size is determined as 151 bps INFO @ Sat, 15 Jan 2022 21:44:41: #1 tag size = 151 INFO @ Sat, 15 Jan 2022 21:44:41: #1 total tags in treatment: 5790051 INFO @ Sat, 15 Jan 2022 21:44:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:44:41: #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 21:44:41: #1 tags after filtering in treatment: 1875203 INFO @ Sat, 15 Jan 2022 21:44:41: #1 Redundant rate of treatment: 0.68 INFO @ Sat, 15 Jan 2022 21:44:41: #1 finished! INFO @ Sat, 15 Jan 2022 21:44:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:44:42: #2 number of paired peaks: 194 WARNING @ Sat, 15 Jan 2022 21:44:42: 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 21:44:42: start model_add_line... INFO @ Sat, 15 Jan 2022 21:44:42: start X-correlation... INFO @ Sat, 15 Jan 2022 21:44:42: end of X-cor INFO @ Sat, 15 Jan 2022 21:44:42: #2 finished! INFO @ Sat, 15 Jan 2022 21:44:42: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 21:44:42: #2 alternative fragment length(s) may be 254 bps INFO @ Sat, 15 Jan 2022 21:44:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10_model.r WARNING @ Sat, 15 Jan 2022 21:44:42: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:44:42: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Sat, 15 Jan 2022 21:44:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:44:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:44:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:44:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20_summits.bed INFO @ Sat, 15 Jan 2022 21:44:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (512 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:44:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:44:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:44:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10_summits.bed INFO @ Sat, 15 Jan 2022 21:44:51: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (861 records, 4 fields): 4 millis CompletedMACS2peakCalling