Job ID = 14520450 SRX = SRX11781030 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:07:21 prefetch.2.10.7: 1) Downloading 'SRR15480973'... 2022-01-15T10:07:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:07:53 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:07:54 prefetch.2.10.7: 'SRR15480973' is valid 2022-01-15T10:07:54 prefetch.2.10.7: 1) 'SRR15480973' was downloaded successfully 2022-01-15T10:07:54 prefetch.2.10.7: 'SRR15480973' has 0 unresolved dependencies Read 8168266 spots for SRR15480973/SRR15480973.sra Written 8168266 spots for SRR15480973/SRR15480973.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: 00:08:54 8168266 reads; of these: 8168266 (100.00%) were paired; of these: 1832367 (22.43%) aligned concordantly 0 times 5792585 (70.92%) aligned concordantly exactly 1 time 543314 (6.65%) aligned concordantly >1 times ---- 1832367 pairs aligned concordantly 0 times; of these: 138563 (7.56%) aligned discordantly 1 time ---- 1693804 pairs aligned 0 times concordantly or discordantly; of these: 3387608 mates make up the pairs; of these: 2791641 (82.41%) aligned 0 times 558384 (16.48%) aligned exactly 1 time 37583 (1.11%) aligned >1 times 82.91% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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] 2668286 / 6455816 = 0.4133 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 19:21:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.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 19:21:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:21:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:22:03: 1000000 INFO @ Sat, 15 Jan 2022 19:22:09: 2000000 INFO @ Sat, 15 Jan 2022 19:22:15: 3000000 INFO @ Sat, 15 Jan 2022 19:22:22: 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 19:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.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 19:22:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:22:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:22:28: 5000000 INFO @ Sat, 15 Jan 2022 19:22:34: 1000000 INFO @ Sat, 15 Jan 2022 19:22:34: 6000000 INFO @ Sat, 15 Jan 2022 19:22:40: 2000000 INFO @ Sat, 15 Jan 2022 19:22:41: 7000000 INFO @ Sat, 15 Jan 2022 19:22:46: 3000000 INFO @ Sat, 15 Jan 2022 19:22:48: 8000000 INFO @ Sat, 15 Jan 2022 19:22:49: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:22:49: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:22:49: #1 total tags in treatment: 3724195 INFO @ Sat, 15 Jan 2022 19:22:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:22:49: #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 19:22:49: #1 tags after filtering in treatment: 1857112 INFO @ Sat, 15 Jan 2022 19:22:49: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 19:22:49: #1 finished! INFO @ Sat, 15 Jan 2022 19:22:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:22:49: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 19:22:49: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 19:22:49: start model_add_line... INFO @ Sat, 15 Jan 2022 19:22:49: start X-correlation... INFO @ Sat, 15 Jan 2022 19:22:49: end of X-cor INFO @ Sat, 15 Jan 2022 19:22:49: #2 finished! INFO @ Sat, 15 Jan 2022 19:22:49: #2 predicted fragment length is 73 bps INFO @ Sat, 15 Jan 2022 19:22:49: #2 alternative fragment length(s) may be 73,95,124,158,238,293,327,349,380,442,537,574 bps INFO @ Sat, 15 Jan 2022 19:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.05_model.r WARNING @ Sat, 15 Jan 2022 19:22:50: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:22:50: #2 You may need to consider one of the other alternative d(s): 73,95,124,158,238,293,327,349,380,442,537,574 WARNING @ Sat, 15 Jan 2022 19:22:50: #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 19:22:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:22:53: 4000000 INFO @ Sat, 15 Jan 2022 19:22:53: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Sat, 15 Jan 2022 19:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.05_peaks.narrowPeak 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 19:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.05_summits.bed INFO @ Sat, 15 Jan 2022 19:22:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:22:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.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 19:22:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:22:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:22:58: 5000000 INFO @ Sat, 15 Jan 2022 19:23:04: 1000000 INFO @ Sat, 15 Jan 2022 19:23:04: 6000000 INFO @ Sat, 15 Jan 2022 19:23:10: 7000000 INFO @ Sat, 15 Jan 2022 19:23:10: 2000000 INFO @ Sat, 15 Jan 2022 19:23:15: 8000000 INFO @ Sat, 15 Jan 2022 19:23:16: 3000000 INFO @ Sat, 15 Jan 2022 19:23:17: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:23:17: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:23:17: #1 total tags in treatment: 3724195 INFO @ Sat, 15 Jan 2022 19:23:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:23:17: #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 19:23:17: #1 tags after filtering in treatment: 1857112 INFO @ Sat, 15 Jan 2022 19:23:17: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 19:23:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:23:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:23:17: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 19:23:17: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 19:23:17: start model_add_line... INFO @ Sat, 15 Jan 2022 19:23:17: start X-correlation... INFO @ Sat, 15 Jan 2022 19:23:17: end of X-cor INFO @ Sat, 15 Jan 2022 19:23:17: #2 finished! INFO @ Sat, 15 Jan 2022 19:23:17: #2 predicted fragment length is 73 bps INFO @ Sat, 15 Jan 2022 19:23:17: #2 alternative fragment length(s) may be 73,95,124,158,238,293,327,349,380,442,537,574 bps INFO @ Sat, 15 Jan 2022 19:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.10_model.r WARNING @ Sat, 15 Jan 2022 19:23:17: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:23:17: #2 You may need to consider one of the other alternative d(s): 73,95,124,158,238,293,327,349,380,442,537,574 WARNING @ Sat, 15 Jan 2022 19:23:17: #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 19:23:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:23:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:23:21: 4000000 INFO @ Sat, 15 Jan 2022 19:23:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:23:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:23:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.10_summits.bed INFO @ Sat, 15 Jan 2022 19:23:22: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:23:27: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:23:32: 6000000 INFO @ Sat, 15 Jan 2022 19:23:38: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:23:43: 8000000 INFO @ Sat, 15 Jan 2022 19:23:45: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:23:45: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:23:45: #1 total tags in treatment: 3724195 INFO @ Sat, 15 Jan 2022 19:23:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:23:45: #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 19:23:45: #1 tags after filtering in treatment: 1857112 INFO @ Sat, 15 Jan 2022 19:23:45: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 19:23:45: #1 finished! INFO @ Sat, 15 Jan 2022 19:23:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:23:45: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 19:23:45: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 19:23:45: start model_add_line... INFO @ Sat, 15 Jan 2022 19:23:45: start X-correlation... INFO @ Sat, 15 Jan 2022 19:23:45: end of X-cor INFO @ Sat, 15 Jan 2022 19:23:45: #2 finished! INFO @ Sat, 15 Jan 2022 19:23:45: #2 predicted fragment length is 73 bps INFO @ Sat, 15 Jan 2022 19:23:45: #2 alternative fragment length(s) may be 73,95,124,158,238,293,327,349,380,442,537,574 bps INFO @ Sat, 15 Jan 2022 19:23:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.20_model.r WARNING @ Sat, 15 Jan 2022 19:23:45: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:23:45: #2 You may need to consider one of the other alternative d(s): 73,95,124,158,238,293,327,349,380,442,537,574 WARNING @ Sat, 15 Jan 2022 19:23:45: #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 19:23:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:23:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:23:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781030/SRX11781030.20_summits.bed INFO @ Sat, 15 Jan 2022 19:23:50: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (20 records, 4 fields): 15 millis CompletedMACS2peakCalling