Job ID = 14520455 SRX = SRX11781035 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:08:22 prefetch.2.10.7: 1) Downloading 'SRR15480978'... 2022-01-15T10:08:22 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:08:52 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:08:53 prefetch.2.10.7: 'SRR15480978' is valid 2022-01-15T10:08:53 prefetch.2.10.7: 1) 'SRR15480978' was downloaded successfully 2022-01-15T10:08:53 prefetch.2.10.7: 'SRR15480978' has 0 unresolved dependencies Read 7368899 spots for SRR15480978/SRR15480978.sra Written 7368899 spots for SRR15480978/SRR15480978.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: 00:05:41 7368899 reads; of these: 7368899 (100.00%) were paired; of these: 1358465 (18.44%) aligned concordantly 0 times 4429327 (60.11%) aligned concordantly exactly 1 time 1581107 (21.46%) aligned concordantly >1 times ---- 1358465 pairs aligned concordantly 0 times; of these: 185087 (13.62%) aligned discordantly 1 time ---- 1173378 pairs aligned 0 times concordantly or discordantly; of these: 2346756 mates make up the pairs; of these: 1671307 (71.22%) aligned 0 times 477000 (20.33%) aligned exactly 1 time 198449 (8.46%) aligned >1 times 88.66% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 507073 / 6165830 = 0.0822 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 19:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.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 19:19:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:39: 1000000 INFO @ Sat, 15 Jan 2022 19:19:45: 2000000 INFO @ Sat, 15 Jan 2022 19:19:51: 3000000 INFO @ Sat, 15 Jan 2022 19:19:57: 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 19:20:03: 5000000 INFO @ Sat, 15 Jan 2022 19:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.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 19:20:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:08: 1000000 INFO @ Sat, 15 Jan 2022 19:20:09: 6000000 INFO @ Sat, 15 Jan 2022 19:20:13: 2000000 INFO @ Sat, 15 Jan 2022 19:20:15: 7000000 INFO @ Sat, 15 Jan 2022 19:20:18: 3000000 INFO @ Sat, 15 Jan 2022 19:20:21: 8000000 INFO @ Sat, 15 Jan 2022 19:20:23: 4000000 INFO @ Sat, 15 Jan 2022 19:20:28: 9000000 INFO @ Sat, 15 Jan 2022 19:20:28: 5000000 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 19:20:33: 6000000 INFO @ Sat, 15 Jan 2022 19:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.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 19:20:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:34: 10000000 INFO @ Sat, 15 Jan 2022 19:20:38: 7000000 INFO @ Sat, 15 Jan 2022 19:20:40: 1000000 INFO @ Sat, 15 Jan 2022 19:20:40: 11000000 INFO @ Sat, 15 Jan 2022 19:20:43: 8000000 INFO @ Sat, 15 Jan 2022 19:20:46: 12000000 INFO @ Sat, 15 Jan 2022 19:20:46: 2000000 INFO @ Sat, 15 Jan 2022 19:20:46: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:20:46: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:20:46: #1 total tags in treatment: 5512280 INFO @ Sat, 15 Jan 2022 19:20:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:46: #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 19:20:46: #1 tags after filtering in treatment: 3835086 INFO @ Sat, 15 Jan 2022 19:20:46: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 19:20:46: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:46: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 19:20:47: 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 19:20:47: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:47: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:47: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:47: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:47: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:20:47: #2 alternative fragment length(s) may be 0,18,63,86,128,197,235,263,288,351,421,487,524,558 bps INFO @ Sat, 15 Jan 2022 19:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.05_model.r WARNING @ Sat, 15 Jan 2022 19:20:47: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:20:47: #2 You may need to consider one of the other alternative d(s): 0,18,63,86,128,197,235,263,288,351,421,487,524,558 WARNING @ Sat, 15 Jan 2022 19:20:47: #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 19:20:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:48: 9000000 INFO @ Sat, 15 Jan 2022 19:20:52: 3000000 INFO @ Sat, 15 Jan 2022 19:20:53: 10000000 INFO @ Sat, 15 Jan 2022 19:20:58: 11000000 INFO @ Sat, 15 Jan 2022 19:20:58: 4000000 INFO @ Sat, 15 Jan 2022 19:21:03: 12000000 INFO @ Sat, 15 Jan 2022 19:21:03: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:21:03: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:21:03: #1 total tags in treatment: 5512280 INFO @ Sat, 15 Jan 2022 19:21:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:21:03: #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 19:21:03: #1 tags after filtering in treatment: 3835086 INFO @ Sat, 15 Jan 2022 19:21:03: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 19:21:03: #1 finished! INFO @ Sat, 15 Jan 2022 19:21:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:21:03: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 19:21:03: 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 19:21:03: start model_add_line... INFO @ Sat, 15 Jan 2022 19:21:03: start X-correlation... INFO @ Sat, 15 Jan 2022 19:21:03: end of X-cor INFO @ Sat, 15 Jan 2022 19:21:03: #2 finished! INFO @ Sat, 15 Jan 2022 19:21:03: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:21:03: #2 alternative fragment length(s) may be 0,18,63,86,128,197,235,263,288,351,421,487,524,558 bps INFO @ Sat, 15 Jan 2022 19:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781035/SRX11781035.10_model.r WARNING @ Sat, 15 Jan 2022 19:21:03: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:21:03: #2 You may need to consider one of the other alternative d(s): 0,18,63,86,128,197,235,263,288,351,421,487,524,558 WARNING @ Sat, 15 Jan 2022 19:21:03: #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 19:21:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:04: 5000000 INFO @ Sat, 15 Jan 2022 19:21:10: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:21:16: 7000000 INFO @ Sat, 15 Jan 2022 19:21:22: 8000000 BigWig に変換しました。 /var/spool/uge/at155/job_scripts/14520455: line 297: 124536 Terminated MACS $i /var/spool/uge/at155/job_scripts/14520455: line 297: 13684 Terminated MACS $i /var/spool/uge/at155/job_scripts/14520455: line 297: 26627 Terminated MACS $i ls: cannot access SRX11781035.05.bed: No such file or directory mv: cannot stat ‘SRX11781035.05.bed’: No such file or directory mv: cannot stat ‘SRX11781035.05.bb’: No such file or directory ls: cannot access SRX11781035.10.bed: No such file or directory mv: cannot stat ‘SRX11781035.10.bed’: No such file or directory mv: cannot stat ‘SRX11781035.10.bb’: No such file or directory ls: cannot access SRX11781035.20.bed: No such file or directory mv: cannot stat ‘SRX11781035.20.bed’: No such file or directory mv: cannot stat ‘SRX11781035.20.bb’: No such file or directory