Job ID = 14521154 SRX = SRX8245486 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10717013 spots for SRR11684697/SRR11684697.sra Written 10717013 spots for SRR11684697/SRR11684697.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: 00:05:12 10717013 reads; of these: 10717013 (100.00%) were paired; of these: 6308665 (58.87%) aligned concordantly 0 times 3940009 (36.76%) aligned concordantly exactly 1 time 468339 (4.37%) aligned concordantly >1 times ---- 6308665 pairs aligned concordantly 0 times; of these: 116761 (1.85%) aligned discordantly 1 time ---- 6191904 pairs aligned 0 times concordantly or discordantly; of these: 12383808 mates make up the pairs; of these: 7577349 (61.19%) aligned 0 times 4183263 (33.78%) aligned exactly 1 time 623196 (5.03%) aligned >1 times 64.65% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 446180 / 4524342 = 0.0986 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 20:41:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.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 20:41:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:45: 1000000 INFO @ Sat, 15 Jan 2022 20:41:49: 2000000 INFO @ Sat, 15 Jan 2022 20:41:53: 3000000 INFO @ Sat, 15 Jan 2022 20:41:57: 4000000 INFO @ Sat, 15 Jan 2022 20:42:02: 5000000 INFO @ Sat, 15 Jan 2022 20:42:06: 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 20:42:10: 7000000 INFO @ Sat, 15 Jan 2022 20:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.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 20:42:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:14: 8000000 INFO @ Sat, 15 Jan 2022 20:42:16: 1000000 INFO @ Sat, 15 Jan 2022 20:42:19: 9000000 INFO @ Sat, 15 Jan 2022 20:42:22: 2000000 INFO @ Sat, 15 Jan 2022 20:42:23: 10000000 INFO @ Sat, 15 Jan 2022 20:42:28: 3000000 INFO @ Sat, 15 Jan 2022 20:42:28: 11000000 INFO @ Sat, 15 Jan 2022 20:42:33: 12000000 INFO @ Sat, 15 Jan 2022 20:42:33: 4000000 INFO @ Sat, 15 Jan 2022 20:42:37: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:42:37: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:42:37: #1 total tags in treatment: 3968164 INFO @ Sat, 15 Jan 2022 20:42:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:42:37: #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 20:42:37: #1 tags after filtering in treatment: 2669648 INFO @ Sat, 15 Jan 2022 20:42:37: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:42:37: #1 finished! INFO @ Sat, 15 Jan 2022 20:42:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:42:37: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:42:37: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:42:37: start model_add_line... INFO @ Sat, 15 Jan 2022 20:42:37: start X-correlation... INFO @ Sat, 15 Jan 2022 20:42:37: end of X-cor INFO @ Sat, 15 Jan 2022 20:42:37: #2 finished! INFO @ Sat, 15 Jan 2022 20:42:37: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:42:37: #2 alternative fragment length(s) may be 0,39,56,81,103,124,161,186,193,207,224,254,266,303,325,359,366,377,399,428,440,462,498,520,544 bps INFO @ Sat, 15 Jan 2022 20:42:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.05_model.r WARNING @ Sat, 15 Jan 2022 20:42:37: #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 20:42:37: #2 You may need to consider one of the other alternative d(s): 0,39,56,81,103,124,161,186,193,207,224,254,266,303,325,359,366,377,399,428,440,462,498,520,544 WARNING @ Sat, 15 Jan 2022 20:42:37: #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 20:42:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:42:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:42:38: 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 20:42:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.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 20:42:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:43: 6000000 INFO @ Sat, 15 Jan 2022 20:42:46: 1000000 INFO @ Sat, 15 Jan 2022 20:42:49: 7000000 INFO @ Sat, 15 Jan 2022 20:42:50: 2000000 INFO @ Sat, 15 Jan 2022 20:42:55: 8000000 INFO @ Sat, 15 Jan 2022 20:42:55: 3000000 INFO @ Sat, 15 Jan 2022 20:42:59: 4000000 INFO @ Sat, 15 Jan 2022 20:43:00: 9000000 INFO @ Sat, 15 Jan 2022 20:43:04: 5000000 INFO @ Sat, 15 Jan 2022 20:43:06: 10000000 INFO @ Sat, 15 Jan 2022 20:43:08: 6000000 INFO @ Sat, 15 Jan 2022 20:43:11: 11000000 INFO @ Sat, 15 Jan 2022 20:43:13: 7000000 INFO @ Sat, 15 Jan 2022 20:43:17: 12000000 INFO @ Sat, 15 Jan 2022 20:43:18: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:43:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:22: #1 total tags in treatment: 3968164 INFO @ Sat, 15 Jan 2022 20:43:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:22: #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 20:43:22: #1 tags after filtering in treatment: 2669648 INFO @ Sat, 15 Jan 2022 20:43:22: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:43:22: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:22: 9000000 INFO @ Sat, 15 Jan 2022 20:43:22: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:43:22: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:22: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:22: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:22: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:22: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:22: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:43:22: #2 alternative fragment length(s) may be 0,39,56,81,103,124,161,186,193,207,224,254,266,303,325,359,366,377,399,428,440,462,498,520,544 bps INFO @ Sat, 15 Jan 2022 20:43:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245486/SRX8245486.10_model.r WARNING @ Sat, 15 Jan 2022 20:43:22: #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 20:43:22: #2 You may need to consider one of the other alternative d(s): 0,39,56,81,103,124,161,186,193,207,224,254,266,303,325,359,366,377,399,428,440,462,498,520,544 WARNING @ Sat, 15 Jan 2022 20:43:22: #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 20:43:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:27: 10000000 INFO @ Sat, 15 Jan 2022 20:43:31: 11000000 BigWig に変換しました。 /var/spool/uge/at145/job_scripts/14521154: line 297: 73029 Terminated MACS $i /var/spool/uge/at145/job_scripts/14521154: line 297: 74375 Terminated MACS $i /var/spool/uge/at145/job_scripts/14521154: line 297: 74636 Terminated MACS $i ls: cannot access SRX8245486.05.bed: No such file or directory mv: cannot stat ‘SRX8245486.05.bed’: No such file or directory mv: cannot stat ‘SRX8245486.05.bb’: No such file or directory ls: cannot access SRX8245486.10.bed: No such file or directory mv: cannot stat ‘SRX8245486.10.bed’: No such file or directory mv: cannot stat ‘SRX8245486.10.bb’: No such file or directory ls: cannot access SRX8245486.20.bed: No such file or directory mv: cannot stat ‘SRX8245486.20.bed’: No such file or directory mv: cannot stat ‘SRX8245486.20.bb’: No such file or directory