Job ID = 14520880 SRX = SRX8245318 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16327053 spots for SRR11684513/SRR11684513.sra Written 16327053 spots for SRR11684513/SRR11684513.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: 00:08:26 16327053 reads; of these: 16327053 (100.00%) were paired; of these: 8413423 (51.53%) aligned concordantly 0 times 6961936 (42.64%) aligned concordantly exactly 1 time 951694 (5.83%) aligned concordantly >1 times ---- 8413423 pairs aligned concordantly 0 times; of these: 219324 (2.61%) aligned discordantly 1 time ---- 8194099 pairs aligned 0 times concordantly or discordantly; of these: 16388198 mates make up the pairs; of these: 9749175 (59.49%) aligned 0 times 5690275 (34.72%) aligned exactly 1 time 948748 (5.79%) aligned >1 times 70.14% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 787185 / 8131878 = 0.0968 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 20:19:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.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 20:19:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:19:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:19:29: 1000000 INFO @ Sat, 15 Jan 2022 20:19:35: 2000000 INFO @ Sat, 15 Jan 2022 20:19:40: 3000000 INFO @ Sat, 15 Jan 2022 20:19:45: 4000000 INFO @ Sat, 15 Jan 2022 20:19:51: 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 20:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.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 20:19:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:19:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:19:57: 6000000 INFO @ Sat, 15 Jan 2022 20:20:00: 1000000 INFO @ Sat, 15 Jan 2022 20:20:03: 7000000 INFO @ Sat, 15 Jan 2022 20:20:06: 2000000 INFO @ Sat, 15 Jan 2022 20:20:10: 8000000 INFO @ Sat, 15 Jan 2022 20:20:12: 3000000 INFO @ Sat, 15 Jan 2022 20:20:16: 9000000 INFO @ Sat, 15 Jan 2022 20:20:19: 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 20:20:23: 10000000 INFO @ Sat, 15 Jan 2022 20:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.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 20:20:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:20:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:20:25: 5000000 INFO @ Sat, 15 Jan 2022 20:20:30: 11000000 INFO @ Sat, 15 Jan 2022 20:20:30: 1000000 INFO @ Sat, 15 Jan 2022 20:20:30: 6000000 INFO @ Sat, 15 Jan 2022 20:20:36: 2000000 INFO @ Sat, 15 Jan 2022 20:20:36: 7000000 INFO @ Sat, 15 Jan 2022 20:20:36: 12000000 INFO @ Sat, 15 Jan 2022 20:20:42: 8000000 INFO @ Sat, 15 Jan 2022 20:20:42: 3000000 INFO @ Sat, 15 Jan 2022 20:20:43: 13000000 INFO @ Sat, 15 Jan 2022 20:20:47: 9000000 INFO @ Sat, 15 Jan 2022 20:20:48: 4000000 INFO @ Sat, 15 Jan 2022 20:20:50: 14000000 INFO @ Sat, 15 Jan 2022 20:20:53: 10000000 INFO @ Sat, 15 Jan 2022 20:20:54: 5000000 INFO @ Sat, 15 Jan 2022 20:20:56: 15000000 INFO @ Sat, 15 Jan 2022 20:20:59: 11000000 INFO @ Sat, 15 Jan 2022 20:21:00: 6000000 INFO @ Sat, 15 Jan 2022 20:21:03: 16000000 INFO @ Sat, 15 Jan 2022 20:21:05: 12000000 INFO @ Sat, 15 Jan 2022 20:21:05: 7000000 INFO @ Sat, 15 Jan 2022 20:21:10: 17000000 INFO @ Sat, 15 Jan 2022 20:21:11: 13000000 INFO @ Sat, 15 Jan 2022 20:21:11: 8000000 INFO @ Sat, 15 Jan 2022 20:21:16: 18000000 INFO @ Sat, 15 Jan 2022 20:21:17: 14000000 INFO @ Sat, 15 Jan 2022 20:21:17: 9000000 INFO @ Sat, 15 Jan 2022 20:21:23: 10000000 INFO @ Sat, 15 Jan 2022 20:21:23: 15000000 INFO @ Sat, 15 Jan 2022 20:21:23: 19000000 INFO @ Sat, 15 Jan 2022 20:21:28: 11000000 INFO @ Sat, 15 Jan 2022 20:21:29: 16000000 INFO @ Sat, 15 Jan 2022 20:21:29: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:21:34: 12000000 INFO @ Sat, 15 Jan 2022 20:21:35: 17000000 INFO @ Sat, 15 Jan 2022 20:21:36: 21000000 INFO @ Sat, 15 Jan 2022 20:21:38: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:21:38: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:21:38: #1 total tags in treatment: 7135635 INFO @ Sat, 15 Jan 2022 20:21:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:21:38: #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 20:21:38: #1 tags after filtering in treatment: 4601388 INFO @ Sat, 15 Jan 2022 20:21:38: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 20:21:38: #1 finished! INFO @ Sat, 15 Jan 2022 20:21:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:21:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:21:38: #2 number of paired peaks: 134 WARNING @ Sat, 15 Jan 2022 20:21:38: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Jan 2022 20:21:38: start model_add_line... INFO @ Sat, 15 Jan 2022 20:21:38: start X-correlation... INFO @ Sat, 15 Jan 2022 20:21:38: end of X-cor INFO @ Sat, 15 Jan 2022 20:21:38: #2 finished! INFO @ Sat, 15 Jan 2022 20:21:38: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:21:38: #2 alternative fragment length(s) may be 0,41,59,72,126,163,174,209,239,269,286,300,313,320,327,340,355,385,406,417,445,467,491,512,542,556,592 bps INFO @ Sat, 15 Jan 2022 20:21:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245318/SRX8245318.05_model.r WARNING @ Sat, 15 Jan 2022 20:21:38: #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 20:21:38: #2 You may need to consider one of the other alternative d(s): 0,41,59,72,126,163,174,209,239,269,286,300,313,320,327,340,355,385,406,417,445,467,491,512,542,556,592 WARNING @ Sat, 15 Jan 2022 20:21:38: #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 20:21:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:21:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:21:40: 13000000 INFO @ Sat, 15 Jan 2022 20:21:41: 18000000 BigWig に変換しました。 /var/spool/uge/at156/job_scripts/14520880: line 297: 118462 Terminated MACS $i /var/spool/uge/at156/job_scripts/14520880: line 297: 118562 Terminated MACS $i /var/spool/uge/at156/job_scripts/14520880: line 297: 119810 Terminated MACS $i ls: cannot access SRX8245318.05.bed: No such file or directory mv: cannot stat ‘SRX8245318.05.bed’: No such file or directory mv: cannot stat ‘SRX8245318.05.bb’: No such file or directory ls: cannot access SRX8245318.10.bed: No such file or directory mv: cannot stat ‘SRX8245318.10.bed’: No such file or directory mv: cannot stat ‘SRX8245318.10.bb’: No such file or directory ls: cannot access SRX8245318.20.bed: No such file or directory mv: cannot stat ‘SRX8245318.20.bed’: No such file or directory mv: cannot stat ‘SRX8245318.20.bb’: No such file or directory