Job ID = 14520569 SRX = SRX11781064 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:22:31 prefetch.2.10.7: 1) Downloading 'SRR15481007'... 2022-01-15T10:22:32 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:23:24 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:23:24 prefetch.2.10.7: 1) 'SRR15481007' was downloaded successfully 2022-01-15T10:23:24 prefetch.2.10.7: 'SRR15481007' has 0 unresolved dependencies Read 11615248 spots for SRR15481007/SRR15481007.sra Written 11615248 spots for SRR15481007/SRR15481007.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: 00:33:47 11615248 reads; of these: 11615248 (100.00%) were paired; of these: 1877982 (16.17%) aligned concordantly 0 times 3685707 (31.73%) aligned concordantly exactly 1 time 6051559 (52.10%) aligned concordantly >1 times ---- 1877982 pairs aligned concordantly 0 times; of these: 28398 (1.51%) aligned discordantly 1 time ---- 1849584 pairs aligned 0 times concordantly or discordantly; of these: 3699168 mates make up the pairs; of these: 2827128 (76.43%) aligned 0 times 325610 (8.80%) aligned exactly 1 time 546430 (14.77%) aligned >1 times 87.83% overall alignment rate Time searching: 00:33:47 Overall time: 00:33:47 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 12 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] 1152399 / 9764850 = 0.1180 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 20:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.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 20:07:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:07:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:01: 1000000 INFO @ Sat, 15 Jan 2022 20:08:08: 2000000 INFO @ Sat, 15 Jan 2022 20:08:14: 3000000 INFO @ Sat, 15 Jan 2022 20:08:20: 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 20:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.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 20:08:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:08:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:26: 5000000 INFO @ Sat, 15 Jan 2022 20:08:34: 1000000 INFO @ Sat, 15 Jan 2022 20:08:34: 6000000 INFO @ Sat, 15 Jan 2022 20:08:42: 7000000 INFO @ Sat, 15 Jan 2022 20:08:43: 2000000 INFO @ Sat, 15 Jan 2022 20:08:51: 8000000 INFO @ Sat, 15 Jan 2022 20:08:52: 3000000 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 20:08:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.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 20:08:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:08:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:59: 9000000 INFO @ Sat, 15 Jan 2022 20:09:01: 4000000 INFO @ Sat, 15 Jan 2022 20:09:04: 1000000 INFO @ Sat, 15 Jan 2022 20:09:07: 10000000 INFO @ Sat, 15 Jan 2022 20:09:10: 5000000 INFO @ Sat, 15 Jan 2022 20:09:14: 2000000 INFO @ Sat, 15 Jan 2022 20:09:16: 11000000 INFO @ Sat, 15 Jan 2022 20:09:19: 6000000 INFO @ Sat, 15 Jan 2022 20:09:23: 3000000 INFO @ Sat, 15 Jan 2022 20:09:24: 12000000 INFO @ Sat, 15 Jan 2022 20:09:28: 7000000 INFO @ Sat, 15 Jan 2022 20:09:32: 4000000 INFO @ Sat, 15 Jan 2022 20:09:32: 13000000 INFO @ Sat, 15 Jan 2022 20:09:38: 8000000 INFO @ Sat, 15 Jan 2022 20:09:40: 14000000 INFO @ Sat, 15 Jan 2022 20:09:41: 5000000 INFO @ Sat, 15 Jan 2022 20:09:47: 9000000 INFO @ Sat, 15 Jan 2022 20:09:49: 15000000 INFO @ Sat, 15 Jan 2022 20:09:50: 6000000 INFO @ Sat, 15 Jan 2022 20:09:56: 10000000 INFO @ Sat, 15 Jan 2022 20:09:57: 16000000 INFO @ Sat, 15 Jan 2022 20:09:59: 7000000 INFO @ Sat, 15 Jan 2022 20:10:05: 11000000 INFO @ Sat, 15 Jan 2022 20:10:05: 17000000 INFO @ Sat, 15 Jan 2022 20:10:08: 8000000 INFO @ Sat, 15 Jan 2022 20:10:13: 18000000 INFO @ Sat, 15 Jan 2022 20:10:14: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:10:14: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:10:14: #1 total tags in treatment: 8586004 INFO @ Sat, 15 Jan 2022 20:10:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:10:14: #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 20:10:14: #1 tags after filtering in treatment: 3175093 INFO @ Sat, 15 Jan 2022 20:10:14: #1 Redundant rate of treatment: 0.63 INFO @ Sat, 15 Jan 2022 20:10:14: #1 finished! INFO @ Sat, 15 Jan 2022 20:10:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:10:14: 12000000 INFO @ Sat, 15 Jan 2022 20:10:14: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 20:10:14: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 20:10:14: start model_add_line... INFO @ Sat, 15 Jan 2022 20:10:14: start X-correlation... INFO @ Sat, 15 Jan 2022 20:10:14: end of X-cor INFO @ Sat, 15 Jan 2022 20:10:14: #2 finished! INFO @ Sat, 15 Jan 2022 20:10:14: #2 predicted fragment length is 114 bps INFO @ Sat, 15 Jan 2022 20:10:14: #2 alternative fragment length(s) may be 36,43,49,79,99,114,161,181,196,232,234,277,328 bps INFO @ Sat, 15 Jan 2022 20:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.05_model.r WARNING @ Sat, 15 Jan 2022 20:10:14: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:10:14: #2 You may need to consider one of the other alternative d(s): 36,43,49,79,99,114,161,181,196,232,234,277,328 WARNING @ Sat, 15 Jan 2022 20:10:14: #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 20:10:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:10:17: 9000000 INFO @ Sat, 15 Jan 2022 20:10:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:10:23: 13000000 INFO @ Sat, 15 Jan 2022 20:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.05_summits.bed INFO @ Sat, 15 Jan 2022 20:10:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (629 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:10:26: 10000000 INFO @ Sat, 15 Jan 2022 20:10:32: 14000000 INFO @ Sat, 15 Jan 2022 20:10:35: 11000000 INFO @ Sat, 15 Jan 2022 20:10:41: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:10:44: 12000000 INFO @ Sat, 15 Jan 2022 20:10:50: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:10:53: 13000000 INFO @ Sat, 15 Jan 2022 20:10:59: 17000000 INFO @ Sat, 15 Jan 2022 20:11:02: 14000000 INFO @ Sat, 15 Jan 2022 20:11:08: 18000000 INFO @ Sat, 15 Jan 2022 20:11:08: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:11:08: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:11:08: #1 total tags in treatment: 8586004 INFO @ Sat, 15 Jan 2022 20:11:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:11:08: #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 20:11:09: #1 tags after filtering in treatment: 3175093 INFO @ Sat, 15 Jan 2022 20:11:09: #1 Redundant rate of treatment: 0.63 INFO @ Sat, 15 Jan 2022 20:11:09: #1 finished! INFO @ Sat, 15 Jan 2022 20:11:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:11:09: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 20:11:09: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 20:11:09: start model_add_line... INFO @ Sat, 15 Jan 2022 20:11:09: start X-correlation... INFO @ Sat, 15 Jan 2022 20:11:09: end of X-cor INFO @ Sat, 15 Jan 2022 20:11:09: #2 finished! INFO @ Sat, 15 Jan 2022 20:11:09: #2 predicted fragment length is 114 bps INFO @ Sat, 15 Jan 2022 20:11:09: #2 alternative fragment length(s) may be 36,43,49,79,99,114,161,181,196,232,234,277,328 bps INFO @ Sat, 15 Jan 2022 20:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.10_model.r WARNING @ Sat, 15 Jan 2022 20:11:09: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:11:09: #2 You may need to consider one of the other alternative d(s): 36,43,49,79,99,114,161,181,196,232,234,277,328 WARNING @ Sat, 15 Jan 2022 20:11:09: #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 20:11:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:11:10: 15000000 INFO @ Sat, 15 Jan 2022 20:11:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:11:18: 16000000 INFO @ Sat, 15 Jan 2022 20:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.10_summits.bed INFO @ Sat, 15 Jan 2022 20:11:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (247 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:11:26: 17000000 INFO @ Sat, 15 Jan 2022 20:11:34: 18000000 INFO @ Sat, 15 Jan 2022 20:11:34: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:11:34: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:11:34: #1 total tags in treatment: 8586004 INFO @ Sat, 15 Jan 2022 20:11:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:11:34: #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 20:11:35: #1 tags after filtering in treatment: 3175093 INFO @ Sat, 15 Jan 2022 20:11:35: #1 Redundant rate of treatment: 0.63 INFO @ Sat, 15 Jan 2022 20:11:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:11:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:11:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:11:35: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 20:11:35: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 20:11:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:11:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:11:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:11:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:11:35: #2 predicted fragment length is 114 bps INFO @ Sat, 15 Jan 2022 20:11:35: #2 alternative fragment length(s) may be 36,43,49,79,99,114,161,181,196,232,234,277,328 bps INFO @ Sat, 15 Jan 2022 20:11:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.20_model.r WARNING @ Sat, 15 Jan 2022 20:11:35: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:11:35: #2 You may need to consider one of the other alternative d(s): 36,43,49,79,99,114,161,181,196,232,234,277,328 WARNING @ Sat, 15 Jan 2022 20:11:35: #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 20:11:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:11:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:11:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:11:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:11:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:11:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781064/SRX11781064.20_summits.bed INFO @ Sat, 15 Jan 2022 20:11:45: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (47 records, 4 fields): 2 millis CompletedMACS2peakCalling