Job ID = 14520979 SRX = SRX8245457 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14125909 spots for SRR11684668/SRR11684668.sra Written 14125909 spots for SRR11684668/SRR11684668.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: 00:14:04 14125909 reads; of these: 14125909 (100.00%) were paired; of these: 3046765 (21.57%) aligned concordantly 0 times 10374358 (73.44%) aligned concordantly exactly 1 time 704786 (4.99%) aligned concordantly >1 times ---- 3046765 pairs aligned concordantly 0 times; of these: 77569 (2.55%) aligned discordantly 1 time ---- 2969196 pairs aligned 0 times concordantly or discordantly; of these: 5938392 mates make up the pairs; of these: 4565246 (76.88%) aligned 0 times 1246660 (20.99%) aligned exactly 1 time 126486 (2.13%) aligned >1 times 83.84% overall alignment rate Time searching: 00:14:04 Overall time: 00:14:04 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] 1731177 / 11155332 = 0.1552 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 20:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.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 20:36:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:36:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:01: 1000000 INFO @ Sat, 15 Jan 2022 20:37:09: 2000000 INFO @ Sat, 15 Jan 2022 20:37:17: 3000000 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 20:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.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 20:37:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:37:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:25: 4000000 INFO @ Sat, 15 Jan 2022 20:37:32: 1000000 INFO @ Sat, 15 Jan 2022 20:37:34: 5000000 INFO @ Sat, 15 Jan 2022 20:37:42: 2000000 INFO @ Sat, 15 Jan 2022 20:37:42: 6000000 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 20:37:51: 7000000 INFO @ Sat, 15 Jan 2022 20:37:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.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 20:37:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:37:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:52: 3000000 INFO @ Sat, 15 Jan 2022 20:37:59: 8000000 INFO @ Sat, 15 Jan 2022 20:38:03: 4000000 INFO @ Sat, 15 Jan 2022 20:38:03: 1000000 INFO @ Sat, 15 Jan 2022 20:38:08: 9000000 INFO @ Sat, 15 Jan 2022 20:38:13: 5000000 INFO @ Sat, 15 Jan 2022 20:38:15: 2000000 INFO @ Sat, 15 Jan 2022 20:38:16: 10000000 INFO @ Sat, 15 Jan 2022 20:38:23: 6000000 INFO @ Sat, 15 Jan 2022 20:38:25: 11000000 INFO @ Sat, 15 Jan 2022 20:38:27: 3000000 INFO @ Sat, 15 Jan 2022 20:38:33: 7000000 INFO @ Sat, 15 Jan 2022 20:38:33: 12000000 INFO @ Sat, 15 Jan 2022 20:38:38: 4000000 INFO @ Sat, 15 Jan 2022 20:38:42: 13000000 INFO @ Sat, 15 Jan 2022 20:38:42: 8000000 INFO @ Sat, 15 Jan 2022 20:38:48: 5000000 INFO @ Sat, 15 Jan 2022 20:38:51: 14000000 INFO @ Sat, 15 Jan 2022 20:38:52: 9000000 INFO @ Sat, 15 Jan 2022 20:38:58: 6000000 INFO @ Sat, 15 Jan 2022 20:39:00: 15000000 INFO @ Sat, 15 Jan 2022 20:39:02: 10000000 INFO @ Sat, 15 Jan 2022 20:39:08: 7000000 INFO @ Sat, 15 Jan 2022 20:39:09: 16000000 INFO @ Sat, 15 Jan 2022 20:39:12: 11000000 INFO @ Sat, 15 Jan 2022 20:39:18: 17000000 INFO @ Sat, 15 Jan 2022 20:39:19: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:39:22: 12000000 INFO @ Sat, 15 Jan 2022 20:39:26: 18000000 INFO @ Sat, 15 Jan 2022 20:39:29: 9000000 INFO @ Sat, 15 Jan 2022 20:39:31: 13000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:39:35: 19000000 INFO @ Sat, 15 Jan 2022 20:39:39: 10000000 INFO @ Sat, 15 Jan 2022 20:39:41: 14000000 INFO @ Sat, 15 Jan 2022 20:39:44: 20000000 INFO @ Sat, 15 Jan 2022 20:39:46: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:39:46: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:39:46: #1 total tags in treatment: 9353063 INFO @ Sat, 15 Jan 2022 20:39:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:39:46: #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 20:39:46: #1 tags after filtering in treatment: 4058426 INFO @ Sat, 15 Jan 2022 20:39:46: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 15 Jan 2022 20:39:46: #1 finished! INFO @ Sat, 15 Jan 2022 20:39:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:39:47: #2 number of paired peaks: 163 WARNING @ Sat, 15 Jan 2022 20:39:47: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 15 Jan 2022 20:39:47: start model_add_line... INFO @ Sat, 15 Jan 2022 20:39:47: start X-correlation... INFO @ Sat, 15 Jan 2022 20:39:47: end of X-cor INFO @ Sat, 15 Jan 2022 20:39:47: #2 finished! INFO @ Sat, 15 Jan 2022 20:39:47: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:39:47: #2 alternative fragment length(s) may be 0,17,35,54,131,150,189,212,236,262,324,374,425,431,499,513,549,589 bps INFO @ Sat, 15 Jan 2022 20:39:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245457/SRX8245457.05_model.r WARNING @ Sat, 15 Jan 2022 20:39:47: #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 20:39:47: #2 You may need to consider one of the other alternative d(s): 0,17,35,54,131,150,189,212,236,262,324,374,425,431,499,513,549,589 WARNING @ Sat, 15 Jan 2022 20:39:47: #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 20:39:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:39:47: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at085/job_scripts/14520979: line 297: 58255 Terminated MACS $i /var/spool/uge/at085/job_scripts/14520979: line 297: 64744 Terminated MACS $i /var/spool/uge/at085/job_scripts/14520979: line 297: 8207 Terminated MACS $i ls: cannot access SRX8245457.05.bed: No such file or directory mv: cannot stat ‘SRX8245457.05.bed’: No such file or directory mv: cannot stat ‘SRX8245457.05.bb’: No such file or directory ls: cannot access SRX8245457.10.bed: No such file or directory mv: cannot stat ‘SRX8245457.10.bed’: No such file or directory mv: cannot stat ‘SRX8245457.10.bb’: No such file or directory ls: cannot access SRX8245457.20.bed: No such file or directory mv: cannot stat ‘SRX8245457.20.bed’: No such file or directory mv: cannot stat ‘SRX8245457.20.bb’: No such file or directory