Job ID = 14520421 SRX = SRX11781020 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:03:21 prefetch.2.10.7: 1) Downloading 'SRR15480963'... 2022-01-15T10:03:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:03:55 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:03:57 prefetch.2.10.7: 'SRR15480963' is valid 2022-01-15T10:03:57 prefetch.2.10.7: 1) 'SRR15480963' was downloaded successfully 2022-01-15T10:03:57 prefetch.2.10.7: 'SRR15480963' has 0 unresolved dependencies Read 8963197 spots for SRR15480963/SRR15480963.sra Written 8963197 spots for SRR15480963/SRR15480963.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: 00:09:29 8963197 reads; of these: 8963197 (100.00%) were paired; of these: 1738202 (19.39%) aligned concordantly 0 times 6042251 (67.41%) aligned concordantly exactly 1 time 1182744 (13.20%) aligned concordantly >1 times ---- 1738202 pairs aligned concordantly 0 times; of these: 94569 (5.44%) aligned discordantly 1 time ---- 1643633 pairs aligned 0 times concordantly or discordantly; of these: 3287266 mates make up the pairs; of these: 2783162 (84.66%) aligned 0 times 454104 (13.81%) aligned exactly 1 time 50000 (1.52%) aligned >1 times 84.47% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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_sort_core] merging from 8 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] 2398477 / 7306745 = 0.3283 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 19:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.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 19:19:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:11: 1000000 INFO @ Sat, 15 Jan 2022 19:19:17: 2000000 INFO @ Sat, 15 Jan 2022 19:19:23: 3000000 INFO @ Sat, 15 Jan 2022 19:19:29: 4000000 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 19:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.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 19:19:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:35: 5000000 INFO @ Sat, 15 Jan 2022 19:19:42: 6000000 INFO @ Sat, 15 Jan 2022 19:19:43: 1000000 INFO @ Sat, 15 Jan 2022 19:19:49: 2000000 INFO @ Sat, 15 Jan 2022 19:19:50: 7000000 INFO @ Sat, 15 Jan 2022 19:19:55: 3000000 INFO @ Sat, 15 Jan 2022 19:19:56: 8000000 INFO @ Sat, 15 Jan 2022 19:20:02: 4000000 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 19:20:03: 9000000 INFO @ Sat, 15 Jan 2022 19:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.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 19:20:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:08: 5000000 INFO @ Sat, 15 Jan 2022 19:20:11: 10000000 INFO @ Sat, 15 Jan 2022 19:20:12: 1000000 INFO @ Sat, 15 Jan 2022 19:20:13: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:20:13: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:20:13: #1 total tags in treatment: 4854733 INFO @ Sat, 15 Jan 2022 19:20:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:13: #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 19:20:13: #1 tags after filtering in treatment: 2726606 INFO @ Sat, 15 Jan 2022 19:20:13: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 19:20:13: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:13: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:20:13: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:20:13: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:13: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:14: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:14: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:14: #2 predicted fragment length is 137 bps INFO @ Sat, 15 Jan 2022 19:20:14: #2 alternative fragment length(s) may be 83,119,137,221,236,261,263,298,329,350,379,430,503,530,567,583 bps INFO @ Sat, 15 Jan 2022 19:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.05_model.r WARNING @ Sat, 15 Jan 2022 19:20:14: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:20:14: #2 You may need to consider one of the other alternative d(s): 83,119,137,221,236,261,263,298,329,350,379,430,503,530,567,583 WARNING @ Sat, 15 Jan 2022 19:20:14: #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 19:20:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:15: 6000000 INFO @ Sat, 15 Jan 2022 19:20:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:20:20: 2000000 INFO @ Sat, 15 Jan 2022 19:20:21: 7000000 INFO @ Sat, 15 Jan 2022 19:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.05_summits.bed INFO @ Sat, 15 Jan 2022 19:20:22: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:20:26: 8000000 INFO @ Sat, 15 Jan 2022 19:20:28: 3000000 INFO @ Sat, 15 Jan 2022 19:20:32: 9000000 INFO @ Sat, 15 Jan 2022 19:20:36: 4000000 INFO @ Sat, 15 Jan 2022 19:20:39: 10000000 INFO @ Sat, 15 Jan 2022 19:20:41: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:20:41: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:20:41: #1 total tags in treatment: 4854733 INFO @ Sat, 15 Jan 2022 19:20:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:41: #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 19:20:41: #1 tags after filtering in treatment: 2726606 INFO @ Sat, 15 Jan 2022 19:20:41: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 19:20:41: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:42: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:20:42: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:20:42: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:42: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:42: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:42: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:42: #2 predicted fragment length is 137 bps INFO @ Sat, 15 Jan 2022 19:20:42: #2 alternative fragment length(s) may be 83,119,137,221,236,261,263,298,329,350,379,430,503,530,567,583 bps INFO @ Sat, 15 Jan 2022 19:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.10_model.r WARNING @ Sat, 15 Jan 2022 19:20:42: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:20:42: #2 You may need to consider one of the other alternative d(s): 83,119,137,221,236,261,263,298,329,350,379,430,503,530,567,583 WARNING @ Sat, 15 Jan 2022 19:20:42: #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 19:20:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:43: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:20:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:20:50: 6000000 INFO @ Sat, 15 Jan 2022 19:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.10_summits.bed INFO @ Sat, 15 Jan 2022 19:20:50: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:20:57: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:21:03: 8000000 INFO @ Sat, 15 Jan 2022 19:21:10: 9000000 INFO @ Sat, 15 Jan 2022 19:21:17: 10000000 INFO @ Sat, 15 Jan 2022 19:21:19: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:21:19: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:21:19: #1 total tags in treatment: 4854733 INFO @ Sat, 15 Jan 2022 19:21:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:21:19: #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 19:21:20: #1 tags after filtering in treatment: 2726606 INFO @ Sat, 15 Jan 2022 19:21:20: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 19:21:20: #1 finished! INFO @ Sat, 15 Jan 2022 19:21:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:21:20: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:21:20: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:21:20: start model_add_line... INFO @ Sat, 15 Jan 2022 19:21:20: start X-correlation... INFO @ Sat, 15 Jan 2022 19:21:20: end of X-cor INFO @ Sat, 15 Jan 2022 19:21:20: #2 finished! INFO @ Sat, 15 Jan 2022 19:21:20: #2 predicted fragment length is 137 bps INFO @ Sat, 15 Jan 2022 19:21:20: #2 alternative fragment length(s) may be 83,119,137,221,236,261,263,298,329,350,379,430,503,530,567,583 bps INFO @ Sat, 15 Jan 2022 19:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.20_model.r WARNING @ Sat, 15 Jan 2022 19:21:20: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:21:20: #2 You may need to consider one of the other alternative d(s): 83,119,137,221,236,261,263,298,329,350,379,430,503,530,567,583 WARNING @ Sat, 15 Jan 2022 19:21:20: #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 19:21:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781020/SRX11781020.20_summits.bed INFO @ Sat, 15 Jan 2022 19:21:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (41 records, 4 fields): 16 millis CompletedMACS2peakCalling