Job ID = 14520598 SRX = SRX11781076 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:25:20 prefetch.2.10.7: 1) Downloading 'SRR15481019'... 2022-01-15T10:25:20 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:26:14 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:26:14 prefetch.2.10.7: 1) 'SRR15481019' was downloaded successfully 2022-01-15T10:26:14 prefetch.2.10.7: 'SRR15481019' has 0 unresolved dependencies Read 13236934 spots for SRR15481019/SRR15481019.sra Written 13236934 spots for SRR15481019/SRR15481019.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: 00:25:27 13236934 reads; of these: 13236934 (100.00%) were paired; of these: 4205174 (31.77%) aligned concordantly 0 times 4312585 (32.58%) aligned concordantly exactly 1 time 4719175 (35.65%) aligned concordantly >1 times ---- 4205174 pairs aligned concordantly 0 times; of these: 44082 (1.05%) aligned discordantly 1 time ---- 4161092 pairs aligned 0 times concordantly or discordantly; of these: 8322184 mates make up the pairs; of these: 7294918 (87.66%) aligned 0 times 502467 (6.04%) aligned exactly 1 time 524799 (6.31%) aligned >1 times 72.44% overall alignment rate Time searching: 00:25:27 Overall time: 00:25:27 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] 1191691 / 9075032 = 0.1313 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 19:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.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 19:59:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:19: 1000000 INFO @ Sat, 15 Jan 2022 19:59:24: 2000000 INFO @ Sat, 15 Jan 2022 19:59:29: 3000000 INFO @ Sat, 15 Jan 2022 19:59:35: 4000000 INFO @ Sat, 15 Jan 2022 19:59:40: 5000000 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 19:59:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.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 19:59:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:45: 6000000 INFO @ Sat, 15 Jan 2022 19:59:49: 1000000 INFO @ Sat, 15 Jan 2022 19:59:51: 7000000 INFO @ Sat, 15 Jan 2022 19:59:55: 2000000 INFO @ Sat, 15 Jan 2022 19:59:57: 8000000 INFO @ Sat, 15 Jan 2022 20:00:01: 3000000 INFO @ Sat, 15 Jan 2022 20:00:03: 9000000 INFO @ Sat, 15 Jan 2022 20:00:07: 4000000 INFO @ Sat, 15 Jan 2022 20:00:08: 10000000 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 20:00:12: 5000000 INFO @ Sat, 15 Jan 2022 20:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.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 20:00:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:00:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:00:14: 11000000 INFO @ Sat, 15 Jan 2022 20:00:18: 6000000 INFO @ Sat, 15 Jan 2022 20:00:20: 12000000 INFO @ Sat, 15 Jan 2022 20:00:21: 1000000 INFO @ Sat, 15 Jan 2022 20:00:24: 7000000 INFO @ Sat, 15 Jan 2022 20:00:27: 13000000 INFO @ Sat, 15 Jan 2022 20:00:28: 2000000 INFO @ Sat, 15 Jan 2022 20:00:30: 8000000 INFO @ Sat, 15 Jan 2022 20:00:33: 14000000 INFO @ Sat, 15 Jan 2022 20:00:35: 3000000 INFO @ Sat, 15 Jan 2022 20:00:37: 9000000 INFO @ Sat, 15 Jan 2022 20:00:39: 15000000 INFO @ Sat, 15 Jan 2022 20:00:42: 4000000 INFO @ Sat, 15 Jan 2022 20:00:43: 10000000 INFO @ Sat, 15 Jan 2022 20:00:45: 16000000 INFO @ Sat, 15 Jan 2022 20:00:49: 5000000 INFO @ Sat, 15 Jan 2022 20:00:49: 11000000 INFO @ Sat, 15 Jan 2022 20:00:50: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:00:50: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:00:50: #1 total tags in treatment: 7842776 INFO @ Sat, 15 Jan 2022 20:00:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:00:50: #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 20:00:50: #1 tags after filtering in treatment: 3316469 INFO @ Sat, 15 Jan 2022 20:00:50: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 15 Jan 2022 20:00:50: #1 finished! INFO @ Sat, 15 Jan 2022 20:00:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:00:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:00:50: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:00:50: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:00:50: start model_add_line... INFO @ Sat, 15 Jan 2022 20:00:50: start X-correlation... INFO @ Sat, 15 Jan 2022 20:00:50: end of X-cor INFO @ Sat, 15 Jan 2022 20:00:50: #2 finished! INFO @ Sat, 15 Jan 2022 20:00:50: #2 predicted fragment length is 62 bps INFO @ Sat, 15 Jan 2022 20:00:50: #2 alternative fragment length(s) may be 62,103,125,149,174,213,242,245,268,304,310,337,376,468,481,530,580 bps INFO @ Sat, 15 Jan 2022 20:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.05_model.r WARNING @ Sat, 15 Jan 2022 20:00:50: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:00:50: #2 You may need to consider one of the other alternative d(s): 62,103,125,149,174,213,242,245,268,304,310,337,376,468,481,530,580 WARNING @ Sat, 15 Jan 2022 20:00:50: #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 20:00:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:00:55: 12000000 INFO @ Sat, 15 Jan 2022 20:00:56: 6000000 INFO @ Sat, 15 Jan 2022 20:00:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:00:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:00:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:00:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.05_summits.bed INFO @ Sat, 15 Jan 2022 20:00:58: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (473 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:01:01: 13000000 INFO @ Sat, 15 Jan 2022 20:01:03: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:01:07: 14000000 INFO @ Sat, 15 Jan 2022 20:01:09: 8000000 INFO @ Sat, 15 Jan 2022 20:01:14: 15000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:01:16: 9000000 INFO @ Sat, 15 Jan 2022 20:01:20: 16000000 INFO @ Sat, 15 Jan 2022 20:01:23: 10000000 INFO @ Sat, 15 Jan 2022 20:01:24: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:01:24: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:01:24: #1 total tags in treatment: 7842776 INFO @ Sat, 15 Jan 2022 20:01:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:01:24: #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 20:01:24: #1 tags after filtering in treatment: 3316469 INFO @ Sat, 15 Jan 2022 20:01:24: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 15 Jan 2022 20:01:24: #1 finished! INFO @ Sat, 15 Jan 2022 20:01:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:01:25: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:01:25: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:01:25: start model_add_line... INFO @ Sat, 15 Jan 2022 20:01:25: start X-correlation... INFO @ Sat, 15 Jan 2022 20:01:25: end of X-cor INFO @ Sat, 15 Jan 2022 20:01:25: #2 finished! INFO @ Sat, 15 Jan 2022 20:01:25: #2 predicted fragment length is 62 bps INFO @ Sat, 15 Jan 2022 20:01:25: #2 alternative fragment length(s) may be 62,103,125,149,174,213,242,245,268,304,310,337,376,468,481,530,580 bps INFO @ Sat, 15 Jan 2022 20:01:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.10_model.r WARNING @ Sat, 15 Jan 2022 20:01:25: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:01:25: #2 You may need to consider one of the other alternative d(s): 62,103,125,149,174,213,242,245,268,304,310,337,376,468,481,530,580 WARNING @ Sat, 15 Jan 2022 20:01:25: #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 20:01:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:01:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:01:30: 11000000 INFO @ Sat, 15 Jan 2022 20:01:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.10_summits.bed INFO @ Sat, 15 Jan 2022 20:01:33: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:01:36: 12000000 INFO @ Sat, 15 Jan 2022 20:01:43: 13000000 INFO @ Sat, 15 Jan 2022 20:01:49: 14000000 INFO @ Sat, 15 Jan 2022 20:01:56: 15000000 INFO @ Sat, 15 Jan 2022 20:02:02: 16000000 INFO @ Sat, 15 Jan 2022 20:02:07: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:02:07: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:02:07: #1 total tags in treatment: 7842776 INFO @ Sat, 15 Jan 2022 20:02:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:02:07: #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 20:02:07: #1 tags after filtering in treatment: 3316469 INFO @ Sat, 15 Jan 2022 20:02:07: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 15 Jan 2022 20:02:07: #1 finished! INFO @ Sat, 15 Jan 2022 20:02:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:02:08: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:02:08: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:02:08: start model_add_line... INFO @ Sat, 15 Jan 2022 20:02:08: start X-correlation... INFO @ Sat, 15 Jan 2022 20:02:08: end of X-cor INFO @ Sat, 15 Jan 2022 20:02:08: #2 finished! INFO @ Sat, 15 Jan 2022 20:02:08: #2 predicted fragment length is 62 bps INFO @ Sat, 15 Jan 2022 20:02:08: #2 alternative fragment length(s) may be 62,103,125,149,174,213,242,245,268,304,310,337,376,468,481,530,580 bps INFO @ Sat, 15 Jan 2022 20:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.20_model.r WARNING @ Sat, 15 Jan 2022 20:02:08: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:02:08: #2 You may need to consider one of the other alternative d(s): 62,103,125,149,174,213,242,245,268,304,310,337,376,468,481,530,580 WARNING @ Sat, 15 Jan 2022 20:02:08: #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 20:02:08: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:02:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:02:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781076/SRX11781076.20_summits.bed INFO @ Sat, 15 Jan 2022 20:02:17: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling