Job ID = 14520832 SRX = SRX8245539 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8698111 spots for SRR11684750/SRR11684750.sra Written 8698111 spots for SRR11684750/SRR11684750.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: 00:09:22 8698111 reads; of these: 8698111 (100.00%) were paired; of these: 4295270 (49.38%) aligned concordantly 0 times 3880463 (44.61%) aligned concordantly exactly 1 time 522378 (6.01%) aligned concordantly >1 times ---- 4295270 pairs aligned concordantly 0 times; of these: 51081 (1.19%) aligned discordantly 1 time ---- 4244189 pairs aligned 0 times concordantly or discordantly; of these: 8488378 mates make up the pairs; of these: 5124755 (60.37%) aligned 0 times 2913166 (34.32%) aligned exactly 1 time 450457 (5.31%) aligned >1 times 70.54% overall alignment rate Time searching: 00:09:22 Overall time: 00:09:22 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] 270758 / 4453248 = 0.0608 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 20:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.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 20:13:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:13:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:13:42: 1000000 INFO @ Sat, 15 Jan 2022 20:13:48: 2000000 INFO @ Sat, 15 Jan 2022 20:13:53: 3000000 INFO @ Sat, 15 Jan 2022 20:13:58: 4000000 INFO @ Sat, 15 Jan 2022 20:14:03: 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 20:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.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 20:14:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:09: 6000000 INFO @ Sat, 15 Jan 2022 20:14:12: 1000000 INFO @ Sat, 15 Jan 2022 20:14:14: 7000000 INFO @ Sat, 15 Jan 2022 20:14:18: 2000000 INFO @ Sat, 15 Jan 2022 20:14:20: 8000000 INFO @ Sat, 15 Jan 2022 20:14:23: 3000000 INFO @ Sat, 15 Jan 2022 20:14:25: 9000000 INFO @ Sat, 15 Jan 2022 20:14:28: 4000000 INFO @ Sat, 15 Jan 2022 20:14:30: 10000000 INFO @ Sat, 15 Jan 2022 20:14:34: 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 20:14:36: 11000000 INFO @ Sat, 15 Jan 2022 20:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.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 20:14:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:39: 6000000 INFO @ Sat, 15 Jan 2022 20:14:39: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:14:39: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:14:39: #1 total tags in treatment: 4133245 INFO @ Sat, 15 Jan 2022 20:14:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:14:39: #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 20:14:40: #1 tags after filtering in treatment: 2739337 INFO @ Sat, 15 Jan 2022 20:14:40: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 20:14:40: #1 finished! INFO @ Sat, 15 Jan 2022 20:14:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:14:40: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:14:40: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:14:40: start model_add_line... INFO @ Sat, 15 Jan 2022 20:14:40: start X-correlation... INFO @ Sat, 15 Jan 2022 20:14:40: end of X-cor INFO @ Sat, 15 Jan 2022 20:14:40: #2 finished! INFO @ Sat, 15 Jan 2022 20:14:40: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:14:40: #2 alternative fragment length(s) may be 0,14,21,46,97,131,163,202,229,247,264,296,331,372,397,415,421,427,452,471,489,537,553,585 bps INFO @ Sat, 15 Jan 2022 20:14:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.05_model.r WARNING @ Sat, 15 Jan 2022 20:14:40: #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 20:14:40: #2 You may need to consider one of the other alternative d(s): 0,14,21,46,97,131,163,202,229,247,264,296,331,372,397,415,421,427,452,471,489,537,553,585 WARNING @ Sat, 15 Jan 2022 20:14:40: #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 20:14:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:14:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:14:42: 1000000 INFO @ Sat, 15 Jan 2022 20:14:45: 7000000 INFO @ Sat, 15 Jan 2022 20:14:48: 2000000 INFO @ Sat, 15 Jan 2022 20:14:50: 8000000 INFO @ Sat, 15 Jan 2022 20:14:53: 3000000 INFO @ Sat, 15 Jan 2022 20:14:56: 9000000 INFO @ Sat, 15 Jan 2022 20:14:59: 4000000 INFO @ Sat, 15 Jan 2022 20:15:01: 10000000 INFO @ Sat, 15 Jan 2022 20:15:04: 5000000 INFO @ Sat, 15 Jan 2022 20:15:06: 11000000 INFO @ Sat, 15 Jan 2022 20:15:09: 6000000 INFO @ Sat, 15 Jan 2022 20:15:10: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:10: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:10: #1 total tags in treatment: 4133245 INFO @ Sat, 15 Jan 2022 20:15:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:10: #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 20:15:10: #1 tags after filtering in treatment: 2739337 INFO @ Sat, 15 Jan 2022 20:15:10: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 20:15:10: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:10: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:15:10: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:10: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:11: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:11: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:11: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:11: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:15:11: #2 alternative fragment length(s) may be 0,14,21,46,97,131,163,202,229,247,264,296,331,372,397,415,421,427,452,471,489,537,553,585 bps INFO @ Sat, 15 Jan 2022 20:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245539/SRX8245539.10_model.r WARNING @ Sat, 15 Jan 2022 20:15:11: #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 20:15:11: #2 You may need to consider one of the other alternative d(s): 0,14,21,46,97,131,163,202,229,247,264,296,331,372,397,415,421,427,452,471,489,537,553,585 WARNING @ Sat, 15 Jan 2022 20:15:11: #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 20:15:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:15:14: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:15:20: 8000000 INFO @ Sat, 15 Jan 2022 20:15:25: 9000000 BigWig に変換しました。 /var/spool/uge/at158/job_scripts/14520832: line 297: 115738 Terminated MACS $i /var/spool/uge/at158/job_scripts/14520832: line 297: 118166 Terminated MACS $i /var/spool/uge/at158/job_scripts/14520832: line 297: 120926 Terminated MACS $i ls: cannot access SRX8245539.05.bed: No such file or directory mv: cannot stat ‘SRX8245539.05.bed’: No such file or directory mv: cannot stat ‘SRX8245539.05.bb’: No such file or directory ls: cannot access SRX8245539.10.bed: No such file or directory mv: cannot stat ‘SRX8245539.10.bed’: No such file or directory mv: cannot stat ‘SRX8245539.10.bb’: No such file or directory ls: cannot access SRX8245539.20.bed: No such file or directory mv: cannot stat ‘SRX8245539.20.bed’: No such file or directory mv: cannot stat ‘SRX8245539.20.bb’: No such file or directory