Job ID = 14520830 SRX = SRX8245537 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10309376 spots for SRR11684748/SRR11684748.sra Written 10309376 spots for SRR11684748/SRR11684748.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: 00:06:58 10309376 reads; of these: 10309376 (100.00%) were paired; of these: 5214977 (50.58%) aligned concordantly 0 times 4386938 (42.55%) aligned concordantly exactly 1 time 707461 (6.86%) aligned concordantly >1 times ---- 5214977 pairs aligned concordantly 0 times; of these: 52991 (1.02%) aligned discordantly 1 time ---- 5161986 pairs aligned 0 times concordantly or discordantly; of these: 10323972 mates make up the pairs; of these: 5653266 (54.76%) aligned 0 times 3970915 (38.46%) aligned exactly 1 time 699791 (6.78%) aligned >1 times 72.58% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 121303 / 5146593 = 0.0236 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 20:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.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 20:14:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:15: 1000000 INFO @ Sat, 15 Jan 2022 20:14:20: 2000000 INFO @ Sat, 15 Jan 2022 20:14:25: 3000000 INFO @ Sat, 15 Jan 2022 20:14:29: 4000000 INFO @ Sat, 15 Jan 2022 20:14:34: 5000000 INFO @ Sat, 15 Jan 2022 20:14:38: 6000000 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 20:14:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.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 20:14:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:43: 7000000 INFO @ Sat, 15 Jan 2022 20:14:45: 1000000 INFO @ Sat, 15 Jan 2022 20:14:48: 8000000 INFO @ Sat, 15 Jan 2022 20:14:50: 2000000 INFO @ Sat, 15 Jan 2022 20:14:53: 9000000 INFO @ Sat, 15 Jan 2022 20:14:55: 3000000 INFO @ Sat, 15 Jan 2022 20:14:58: 10000000 INFO @ Sat, 15 Jan 2022 20:15:00: 4000000 INFO @ Sat, 15 Jan 2022 20:15:03: 11000000 INFO @ Sat, 15 Jan 2022 20:15:05: 5000000 INFO @ Sat, 15 Jan 2022 20:15:08: 12000000 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 20:15:10: 6000000 INFO @ Sat, 15 Jan 2022 20:15:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.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 20:15:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:13: 13000000 INFO @ Sat, 15 Jan 2022 20:15:15: 7000000 INFO @ Sat, 15 Jan 2022 20:15:15: 1000000 INFO @ Sat, 15 Jan 2022 20:15:18: 14000000 INFO @ Sat, 15 Jan 2022 20:15:20: 8000000 INFO @ Sat, 15 Jan 2022 20:15:20: 2000000 INFO @ Sat, 15 Jan 2022 20:15:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:22: #1 total tags in treatment: 4973367 INFO @ Sat, 15 Jan 2022 20:15:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:22: #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 20:15:22: #1 tags after filtering in treatment: 3402306 INFO @ Sat, 15 Jan 2022 20:15:22: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 20:15:22: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:22: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 20:15:22: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:22: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:22: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:22: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:22: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:22: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:15:22: #2 alternative fragment length(s) may be 0,24,53,90,144,197,218,236,257,279,312,333,359,381,405,463,491,509,550,583 bps INFO @ Sat, 15 Jan 2022 20:15:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.05_model.r WARNING @ Sat, 15 Jan 2022 20:15:22: #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 20:15:22: #2 You may need to consider one of the other alternative d(s): 0,24,53,90,144,197,218,236,257,279,312,333,359,381,405,463,491,509,550,583 WARNING @ Sat, 15 Jan 2022 20:15:22: #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 20:15:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:15:25: 9000000 INFO @ Sat, 15 Jan 2022 20:15:26: 3000000 INFO @ Sat, 15 Jan 2022 20:15:30: 10000000 INFO @ Sat, 15 Jan 2022 20:15:31: 4000000 INFO @ Sat, 15 Jan 2022 20:15:35: 11000000 INFO @ Sat, 15 Jan 2022 20:15:35: 5000000 INFO @ Sat, 15 Jan 2022 20:15:40: 6000000 INFO @ Sat, 15 Jan 2022 20:15:40: 12000000 INFO @ Sat, 15 Jan 2022 20:15:45: 7000000 INFO @ Sat, 15 Jan 2022 20:15:46: 13000000 INFO @ Sat, 15 Jan 2022 20:15:50: 8000000 INFO @ Sat, 15 Jan 2022 20:15:51: 14000000 INFO @ Sat, 15 Jan 2022 20:15:54: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:54: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:54: #1 total tags in treatment: 4973367 INFO @ Sat, 15 Jan 2022 20:15:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:54: #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 20:15:54: #1 tags after filtering in treatment: 3402306 INFO @ Sat, 15 Jan 2022 20:15:54: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 20:15:54: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:55: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 20:15:55: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:55: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:15:55: #2 alternative fragment length(s) may be 0,24,53,90,144,197,218,236,257,279,312,333,359,381,405,463,491,509,550,583 bps INFO @ Sat, 15 Jan 2022 20:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245537/SRX8245537.10_model.r WARNING @ Sat, 15 Jan 2022 20:15:55: #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 20:15:55: #2 You may need to consider one of the other alternative d(s): 0,24,53,90,144,197,218,236,257,279,312,333,359,381,405,463,491,509,550,583 WARNING @ Sat, 15 Jan 2022 20:15:55: #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 20:15:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:15:55: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:16:00: 10000000 INFO @ Sat, 15 Jan 2022 20:16:05: 11000000 BigWig に変換しました。 /var/spool/uge/at160/job_scripts/14520830: line 297: 130995 Terminated MACS $i /var/spool/uge/at160/job_scripts/14520830: line 297: 788 Terminated MACS $i /var/spool/uge/at160/job_scripts/14520830: line 297: 1042 Terminated MACS $i ls: cannot access SRX8245537.05.bed: No such file or directory mv: cannot stat ‘SRX8245537.05.bed’: No such file or directory mv: cannot stat ‘SRX8245537.05.bb’: No such file or directory ls: cannot access SRX8245537.10.bed: No such file or directory mv: cannot stat ‘SRX8245537.10.bed’: No such file or directory mv: cannot stat ‘SRX8245537.10.bb’: No such file or directory ls: cannot access SRX8245537.20.bed: No such file or directory mv: cannot stat ‘SRX8245537.20.bed’: No such file or directory mv: cannot stat ‘SRX8245537.20.bb’: No such file or directory