Job ID = 14520595 SRX = SRX11781073 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:25:19 prefetch.2.10.7: 1) Downloading 'SRR15481016'... 2022-01-15T10:25:19 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:26:16 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:26:16 prefetch.2.10.7: 1) 'SRR15481016' was downloaded successfully 2022-01-15T10:26:16 prefetch.2.10.7: 'SRR15481016' has 0 unresolved dependencies Read 11842475 spots for SRR15481016/SRR15481016.sra Written 11842475 spots for SRR15481016/SRR15481016.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: 00:21:38 11842475 reads; of these: 11842475 (100.00%) were paired; of these: 1775022 (14.99%) aligned concordantly 0 times 9122365 (77.03%) aligned concordantly exactly 1 time 945088 (7.98%) aligned concordantly >1 times ---- 1775022 pairs aligned concordantly 0 times; of these: 158292 (8.92%) aligned discordantly 1 time ---- 1616730 pairs aligned 0 times concordantly or discordantly; of these: 3233460 mates make up the pairs; of these: 2236546 (69.17%) aligned 0 times 861140 (26.63%) aligned exactly 1 time 135774 (4.20%) aligned >1 times 90.56% overall alignment rate Time searching: 00:21:38 Overall time: 00:21:38 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] 2044003 / 10224853 = 0.1999 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 20:02:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.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 20:02:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:02:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:02:21: 1000000 INFO @ Sat, 15 Jan 2022 20:02:28: 2000000 INFO @ Sat, 15 Jan 2022 20:02:34: 3000000 INFO @ Sat, 15 Jan 2022 20:02:41: 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 20:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.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 20:02:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:02:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:02:48: 5000000 INFO @ Sat, 15 Jan 2022 20:02:52: 1000000 INFO @ Sat, 15 Jan 2022 20:02:55: 6000000 INFO @ Sat, 15 Jan 2022 20:02:59: 2000000 INFO @ Sat, 15 Jan 2022 20:03:02: 7000000 INFO @ Sat, 15 Jan 2022 20:03:07: 3000000 INFO @ Sat, 15 Jan 2022 20:03:09: 8000000 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 20:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.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 20:03:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:03:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:03:14: 4000000 INFO @ Sat, 15 Jan 2022 20:03:16: 9000000 INFO @ Sat, 15 Jan 2022 20:03:22: 1000000 INFO @ Sat, 15 Jan 2022 20:03:22: 5000000 INFO @ Sat, 15 Jan 2022 20:03:23: 10000000 INFO @ Sat, 15 Jan 2022 20:03:30: 6000000 INFO @ Sat, 15 Jan 2022 20:03:30: 2000000 INFO @ Sat, 15 Jan 2022 20:03:31: 11000000 INFO @ Sat, 15 Jan 2022 20:03:37: 7000000 INFO @ Sat, 15 Jan 2022 20:03:38: 3000000 INFO @ Sat, 15 Jan 2022 20:03:38: 12000000 INFO @ Sat, 15 Jan 2022 20:03:45: 8000000 INFO @ Sat, 15 Jan 2022 20:03:45: 13000000 INFO @ Sat, 15 Jan 2022 20:03:46: 4000000 INFO @ Sat, 15 Jan 2022 20:03:53: 9000000 INFO @ Sat, 15 Jan 2022 20:03:53: 14000000 INFO @ Sat, 15 Jan 2022 20:03:54: 5000000 INFO @ Sat, 15 Jan 2022 20:04:00: 15000000 INFO @ Sat, 15 Jan 2022 20:04:00: 10000000 INFO @ Sat, 15 Jan 2022 20:04:01: 6000000 INFO @ Sat, 15 Jan 2022 20:04:08: 16000000 INFO @ Sat, 15 Jan 2022 20:04:08: 11000000 INFO @ Sat, 15 Jan 2022 20:04:09: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:04:15: 17000000 INFO @ Sat, 15 Jan 2022 20:04:16: 12000000 INFO @ Sat, 15 Jan 2022 20:04:17: 8000000 INFO @ Sat, 15 Jan 2022 20:04:18: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:04:18: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:04:18: #1 total tags in treatment: 8038245 INFO @ Sat, 15 Jan 2022 20:04:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:04:18: #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 20:04:18: #1 tags after filtering in treatment: 4728732 INFO @ Sat, 15 Jan 2022 20:04:18: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 20:04:18: #1 finished! INFO @ Sat, 15 Jan 2022 20:04:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:04:18: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 20:04:18: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 20:04:18: start model_add_line... INFO @ Sat, 15 Jan 2022 20:04:18: start X-correlation... INFO @ Sat, 15 Jan 2022 20:04:18: end of X-cor INFO @ Sat, 15 Jan 2022 20:04:18: #2 finished! INFO @ Sat, 15 Jan 2022 20:04:18: #2 predicted fragment length is 65 bps INFO @ Sat, 15 Jan 2022 20:04:18: #2 alternative fragment length(s) may be 65,127,149,177,215,234,250,271,288,331,360,377,408,425,438,462,484,508,544,547,573,578 bps INFO @ Sat, 15 Jan 2022 20:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.05_model.r WARNING @ Sat, 15 Jan 2022 20:04:18: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:04:18: #2 You may need to consider one of the other alternative d(s): 65,127,149,177,215,234,250,271,288,331,360,377,408,425,438,462,484,508,544,547,573,578 WARNING @ Sat, 15 Jan 2022 20:04:18: #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 20:04:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:04:23: 13000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:04:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:04:25: 9000000 INFO @ Sat, 15 Jan 2022 20:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.05_summits.bed INFO @ Sat, 15 Jan 2022 20:04:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:04:31: 14000000 INFO @ Sat, 15 Jan 2022 20:04:32: 10000000 INFO @ Sat, 15 Jan 2022 20:04:39: 15000000 INFO @ Sat, 15 Jan 2022 20:04:40: 11000000 INFO @ Sat, 15 Jan 2022 20:04:46: 16000000 INFO @ Sat, 15 Jan 2022 20:04:48: 12000000 INFO @ Sat, 15 Jan 2022 20:04:54: 17000000 INFO @ Sat, 15 Jan 2022 20:04:55: 13000000 INFO @ Sat, 15 Jan 2022 20:04:57: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:04:57: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:04:57: #1 total tags in treatment: 8038245 INFO @ Sat, 15 Jan 2022 20:04:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:04:57: #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 20:04:57: #1 tags after filtering in treatment: 4728732 INFO @ Sat, 15 Jan 2022 20:04:57: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 20:04:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:04:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:04:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:04:57: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 20:04:57: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 20:04:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:04:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:04:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:04:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:04:57: #2 predicted fragment length is 65 bps INFO @ Sat, 15 Jan 2022 20:04:57: #2 alternative fragment length(s) may be 65,127,149,177,215,234,250,271,288,331,360,377,408,425,438,462,484,508,544,547,573,578 bps INFO @ Sat, 15 Jan 2022 20:04:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.10_model.r WARNING @ Sat, 15 Jan 2022 20:04:57: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:04:57: #2 You may need to consider one of the other alternative d(s): 65,127,149,177,215,234,250,271,288,331,360,377,408,425,438,462,484,508,544,547,573,578 WARNING @ Sat, 15 Jan 2022 20:04:57: #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 20:04:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:04:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:05:02: 14000000 INFO @ Sat, 15 Jan 2022 20:05:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:05:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:05:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.10_summits.bed INFO @ Sat, 15 Jan 2022 20:05:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:05:09: 15000000 INFO @ Sat, 15 Jan 2022 20:05:16: 16000000 INFO @ Sat, 15 Jan 2022 20:05:23: 17000000 INFO @ Sat, 15 Jan 2022 20:05:26: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:05:26: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:05:26: #1 total tags in treatment: 8038245 INFO @ Sat, 15 Jan 2022 20:05:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:05:26: #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 20:05:26: #1 tags after filtering in treatment: 4728732 INFO @ Sat, 15 Jan 2022 20:05:26: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 20:05:26: #1 finished! INFO @ Sat, 15 Jan 2022 20:05:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:05:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:05:26: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 20:05:26: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 20:05:26: start model_add_line... INFO @ Sat, 15 Jan 2022 20:05:26: start X-correlation... INFO @ Sat, 15 Jan 2022 20:05:26: end of X-cor INFO @ Sat, 15 Jan 2022 20:05:26: #2 finished! INFO @ Sat, 15 Jan 2022 20:05:26: #2 predicted fragment length is 65 bps INFO @ Sat, 15 Jan 2022 20:05:26: #2 alternative fragment length(s) may be 65,127,149,177,215,234,250,271,288,331,360,377,408,425,438,462,484,508,544,547,573,578 bps INFO @ Sat, 15 Jan 2022 20:05:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.20_model.r WARNING @ Sat, 15 Jan 2022 20:05:26: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:05:26: #2 You may need to consider one of the other alternative d(s): 65,127,149,177,215,234,250,271,288,331,360,377,408,425,438,462,484,508,544,547,573,578 WARNING @ Sat, 15 Jan 2022 20:05:26: #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 20:05:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:05:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:05:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781073/SRX11781073.20_summits.bed INFO @ Sat, 15 Jan 2022 20:05:35: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling