Job ID = 14520482 SRX = SRX11781046 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:12:38 prefetch.2.10.7: 1) Downloading 'SRR15480989'... 2022-01-15T10:12:38 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:13:09 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:13:10 prefetch.2.10.7: 'SRR15480989' is valid 2022-01-15T10:13:10 prefetch.2.10.7: 1) 'SRR15480989' was downloaded successfully 2022-01-15T10:13:10 prefetch.2.10.7: 'SRR15480989' has 0 unresolved dependencies Read 7139865 spots for SRR15480989/SRR15480989.sra Written 7139865 spots for SRR15480989/SRR15480989.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: 00:06:32 7139865 reads; of these: 7139865 (100.00%) were paired; of these: 2043164 (28.62%) aligned concordantly 0 times 3073437 (43.05%) aligned concordantly exactly 1 time 2023264 (28.34%) aligned concordantly >1 times ---- 2043164 pairs aligned concordantly 0 times; of these: 338241 (16.55%) aligned discordantly 1 time ---- 1704923 pairs aligned 0 times concordantly or discordantly; of these: 3409846 mates make up the pairs; of these: 2057090 (60.33%) aligned 0 times 686080 (20.12%) aligned exactly 1 time 666676 (19.55%) aligned >1 times 85.59% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 1127203 / 5346643 = 0.2108 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 19:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.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 19:24:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:24:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:24:36: 1000000 INFO @ Sat, 15 Jan 2022 19:24:43: 2000000 INFO @ Sat, 15 Jan 2022 19:24:49: 3000000 INFO @ Sat, 15 Jan 2022 19:24:56: 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 19:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.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 19:25:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:03: 5000000 INFO @ Sat, 15 Jan 2022 19:25:07: 1000000 INFO @ Sat, 15 Jan 2022 19:25:10: 6000000 INFO @ Sat, 15 Jan 2022 19:25:13: 2000000 INFO @ Sat, 15 Jan 2022 19:25:17: 7000000 INFO @ Sat, 15 Jan 2022 19:25:20: 3000000 INFO @ Sat, 15 Jan 2022 19:25:24: 8000000 INFO @ Sat, 15 Jan 2022 19:25:27: 4000000 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 19:25:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.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 19:25:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:31: 9000000 INFO @ Sat, 15 Jan 2022 19:25:34: 5000000 INFO @ Sat, 15 Jan 2022 19:25:36: 1000000 INFO @ Sat, 15 Jan 2022 19:25:38: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:25:38: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:25:38: #1 total tags in treatment: 4017541 INFO @ Sat, 15 Jan 2022 19:25:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:25:38: #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 19:25:38: #1 tags after filtering in treatment: 1990176 INFO @ Sat, 15 Jan 2022 19:25:38: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 19:25:38: #1 finished! INFO @ Sat, 15 Jan 2022 19:25:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:25:38: #2 number of paired peaks: 200 WARNING @ Sat, 15 Jan 2022 19:25:38: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 15 Jan 2022 19:25:38: start model_add_line... INFO @ Sat, 15 Jan 2022 19:25:38: start X-correlation... INFO @ Sat, 15 Jan 2022 19:25:38: end of X-cor INFO @ Sat, 15 Jan 2022 19:25:38: #2 finished! INFO @ Sat, 15 Jan 2022 19:25:38: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:25:38: #2 alternative fragment length(s) may be 0,16,33,57,79,88,116,141,143,153,188,252,289,362,563,571,577 bps INFO @ Sat, 15 Jan 2022 19:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.05_model.r WARNING @ Sat, 15 Jan 2022 19:25:38: #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 19:25:38: #2 You may need to consider one of the other alternative d(s): 0,16,33,57,79,88,116,141,143,153,188,252,289,362,563,571,577 WARNING @ Sat, 15 Jan 2022 19:25:38: #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 19:25:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:25:41: 6000000 INFO @ Sat, 15 Jan 2022 19:25:42: 2000000 INFO @ Sat, 15 Jan 2022 19:25:48: 7000000 INFO @ Sat, 15 Jan 2022 19:25:48: 3000000 INFO @ Sat, 15 Jan 2022 19:25:54: 4000000 INFO @ Sat, 15 Jan 2022 19:25:54: 8000000 INFO @ Sat, 15 Jan 2022 19:26:01: 5000000 INFO @ Sat, 15 Jan 2022 19:26:01: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:26:07: 6000000 INFO @ Sat, 15 Jan 2022 19:26:08: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:26:08: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:26:08: #1 total tags in treatment: 4017541 INFO @ Sat, 15 Jan 2022 19:26:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:08: #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 19:26:08: #1 tags after filtering in treatment: 1990176 INFO @ Sat, 15 Jan 2022 19:26:08: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 19:26:08: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:08: #2 number of paired peaks: 200 WARNING @ Sat, 15 Jan 2022 19:26:08: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:08: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:08: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:08: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:08: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:08: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:26:08: #2 alternative fragment length(s) may be 0,16,33,57,79,88,116,141,143,153,188,252,289,362,563,571,577 bps INFO @ Sat, 15 Jan 2022 19:26:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781046/SRX11781046.10_model.r WARNING @ Sat, 15 Jan 2022 19:26:08: #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 19:26:08: #2 You may need to consider one of the other alternative d(s): 0,16,33,57,79,88,116,141,143,153,188,252,289,362,563,571,577 WARNING @ Sat, 15 Jan 2022 19:26:08: #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 19:26:08: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at154/job_scripts/14520482: line 297: 14429 Terminated MACS $i /var/spool/uge/at154/job_scripts/14520482: line 297: 14605 Terminated MACS $i /var/spool/uge/at154/job_scripts/14520482: line 297: 14750 Terminated MACS $i ls: cannot access SRX11781046.05.bed: No such file or directory mv: cannot stat ‘SRX11781046.05.bed’: No such file or directory mv: cannot stat ‘SRX11781046.05.bb’: No such file or directory ls: cannot access SRX11781046.10.bed: No such file or directory mv: cannot stat ‘SRX11781046.10.bed’: No such file or directory mv: cannot stat ‘SRX11781046.10.bb’: No such file or directory ls: cannot access SRX11781046.20.bed: No such file or directory mv: cannot stat ‘SRX11781046.20.bed’: No such file or directory mv: cannot stat ‘SRX11781046.20.bb’: No such file or directory