Job ID = 10224113 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: 00:26:56 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: 00:26:56 Overall time: 00:26:56 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:08:09: # 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 @ Fri, 16 Oct 2020 10:08:09: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:08:09: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:08:17: 1000000 INFO @ Fri, 16 Oct 2020 10:08:24: 2000000 INFO @ Fri, 16 Oct 2020 10:08:31: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:08:38: 4000000 INFO @ Fri, 16 Oct 2020 10:08:39: # 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 @ Fri, 16 Oct 2020 10:08:39: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:08:39: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:08:46: 5000000 INFO @ Fri, 16 Oct 2020 10:08:48: 1000000 INFO @ Fri, 16 Oct 2020 10:08:55: 6000000 INFO @ Fri, 16 Oct 2020 10:08:57: 2000000 INFO @ Fri, 16 Oct 2020 10:09:03: 7000000 INFO @ Fri, 16 Oct 2020 10:09:05: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:09:09: # 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 @ Fri, 16 Oct 2020 10:09:09: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:09:09: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:09:12: 8000000 INFO @ Fri, 16 Oct 2020 10:09:14: 4000000 INFO @ Fri, 16 Oct 2020 10:09:18: 1000000 INFO @ Fri, 16 Oct 2020 10:09:21: 9000000 INFO @ Fri, 16 Oct 2020 10:09:22: 5000000 INFO @ Fri, 16 Oct 2020 10:09:27: 2000000 INFO @ Fri, 16 Oct 2020 10:09:29: 10000000 INFO @ Fri, 16 Oct 2020 10:09:31: 6000000 INFO @ Fri, 16 Oct 2020 10:09:36: 3000000 INFO @ Fri, 16 Oct 2020 10:09:38: 11000000 INFO @ Fri, 16 Oct 2020 10:09:40: 7000000 INFO @ Fri, 16 Oct 2020 10:09:44: 4000000 INFO @ Fri, 16 Oct 2020 10:09:46: 12000000 INFO @ Fri, 16 Oct 2020 10:09:48: 8000000 INFO @ Fri, 16 Oct 2020 10:09:53: 5000000 INFO @ Fri, 16 Oct 2020 10:09:55: 13000000 INFO @ Fri, 16 Oct 2020 10:09:57: 9000000 INFO @ Fri, 16 Oct 2020 10:10:01: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 10:10:04: 14000000 INFO @ Fri, 16 Oct 2020 10:10:05: #1 tag size is determined as 151 bps INFO @ Fri, 16 Oct 2020 10:10:05: #1 tag size = 151 INFO @ Fri, 16 Oct 2020 10:10:05: #1 total tags in treatment: 5790051 INFO @ Fri, 16 Oct 2020 10:10:05: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:10:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:10:05: #1 tags after filtering in treatment: 1875203 INFO @ Fri, 16 Oct 2020 10:10:05: #1 Redundant rate of treatment: 0.68 INFO @ Fri, 16 Oct 2020 10:10:05: #1 finished! INFO @ Fri, 16 Oct 2020 10:10:05: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:10:05: #2 number of paired peaks: 194 WARNING @ Fri, 16 Oct 2020 10:10:05: 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 @ Fri, 16 Oct 2020 10:10:05: start model_add_line... INFO @ Fri, 16 Oct 2020 10:10:05: start X-correlation... INFO @ Fri, 16 Oct 2020 10:10:05: end of X-cor INFO @ Fri, 16 Oct 2020 10:10:05: #2 finished! INFO @ Fri, 16 Oct 2020 10:10:05: #2 predicted fragment length is 254 bps INFO @ Fri, 16 Oct 2020 10:10:05: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 16 Oct 2020 10:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05_model.r WARNING @ Fri, 16 Oct 2020 10:10:05: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 10:10:05: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Fri, 16 Oct 2020 10:10:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 10:10:05: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:10:05: 10000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 10:10:10: 7000000 INFO @ Fri, 16 Oct 2020 10:10:11: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:10:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05_peaks.xls INFO @ Fri, 16 Oct 2020 10:10:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:10:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.05_summits.bed INFO @ Fri, 16 Oct 2020 10:10:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1236 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:10:14: 11000000 INFO @ Fri, 16 Oct 2020 10:10:19: 8000000 INFO @ Fri, 16 Oct 2020 10:10:22: 12000000 INFO @ Fri, 16 Oct 2020 10:10:27: 9000000 INFO @ Fri, 16 Oct 2020 10:10:31: 13000000 INFO @ Fri, 16 Oct 2020 10:10:36: 10000000 INFO @ Fri, 16 Oct 2020 10:10:40: 14000000 INFO @ Fri, 16 Oct 2020 10:10:40: #1 tag size is determined as 151 bps INFO @ Fri, 16 Oct 2020 10:10:40: #1 tag size = 151 INFO @ Fri, 16 Oct 2020 10:10:40: #1 total tags in treatment: 5790051 INFO @ Fri, 16 Oct 2020 10:10:40: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:10:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:10:40: #1 tags after filtering in treatment: 1875203 INFO @ Fri, 16 Oct 2020 10:10:40: #1 Redundant rate of treatment: 0.68 INFO @ Fri, 16 Oct 2020 10:10:40: #1 finished! INFO @ Fri, 16 Oct 2020 10:10:40: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:10:40: #2 number of paired peaks: 194 WARNING @ Fri, 16 Oct 2020 10:10:40: 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 @ Fri, 16 Oct 2020 10:10:40: start model_add_line... INFO @ Fri, 16 Oct 2020 10:10:40: start X-correlation... INFO @ Fri, 16 Oct 2020 10:10:40: end of X-cor INFO @ Fri, 16 Oct 2020 10:10:40: #2 finished! INFO @ Fri, 16 Oct 2020 10:10:40: #2 predicted fragment length is 254 bps INFO @ Fri, 16 Oct 2020 10:10:40: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 16 Oct 2020 10:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10_model.r WARNING @ Fri, 16 Oct 2020 10:10:40: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 10:10:40: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Fri, 16 Oct 2020 10:10:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 10:10:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:10:44: 11000000 INFO @ Fri, 16 Oct 2020 10:10:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:10:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10_peaks.xls INFO @ Fri, 16 Oct 2020 10:10:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:10:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.10_summits.bed INFO @ Fri, 16 Oct 2020 10:10:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (861 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:10:52: 12000000 INFO @ Fri, 16 Oct 2020 10:11:00: 13000000 INFO @ Fri, 16 Oct 2020 10:11:07: 14000000 INFO @ Fri, 16 Oct 2020 10:11:08: #1 tag size is determined as 151 bps INFO @ Fri, 16 Oct 2020 10:11:08: #1 tag size = 151 INFO @ Fri, 16 Oct 2020 10:11:08: #1 total tags in treatment: 5790051 INFO @ Fri, 16 Oct 2020 10:11:08: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:11:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:11:08: #1 tags after filtering in treatment: 1875203 INFO @ Fri, 16 Oct 2020 10:11:08: #1 Redundant rate of treatment: 0.68 INFO @ Fri, 16 Oct 2020 10:11:08: #1 finished! INFO @ Fri, 16 Oct 2020 10:11:08: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:11:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:11:08: #2 number of paired peaks: 194 WARNING @ Fri, 16 Oct 2020 10:11:08: 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 @ Fri, 16 Oct 2020 10:11:08: start model_add_line... INFO @ Fri, 16 Oct 2020 10:11:08: start X-correlation... INFO @ Fri, 16 Oct 2020 10:11:08: end of X-cor INFO @ Fri, 16 Oct 2020 10:11:08: #2 finished! INFO @ Fri, 16 Oct 2020 10:11:08: #2 predicted fragment length is 254 bps INFO @ Fri, 16 Oct 2020 10:11:08: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 16 Oct 2020 10:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20_model.r WARNING @ Fri, 16 Oct 2020 10:11:08: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 10:11:08: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Fri, 16 Oct 2020 10:11:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 10:11:08: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:11:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:11:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20_peaks.xls INFO @ Fri, 16 Oct 2020 10:11:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:11:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9038694/SRX9038694.20_summits.bed INFO @ Fri, 16 Oct 2020 10:11:16: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (512 records, 4 fields): 2 millis CompletedMACS2peakCalling