Job ID = 14521094 SRX = SRX8245354 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13372559 spots for SRR11684565/SRR11684565.sra Written 13372559 spots for SRR11684565/SRR11684565.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: 00:06:13 13372559 reads; of these: 13372559 (100.00%) were paired; of these: 7012689 (52.44%) aligned concordantly 0 times 5626247 (42.07%) aligned concordantly exactly 1 time 733623 (5.49%) aligned concordantly >1 times ---- 7012689 pairs aligned concordantly 0 times; of these: 211912 (3.02%) aligned discordantly 1 time ---- 6800777 pairs aligned 0 times concordantly or discordantly; of these: 13601554 mates make up the pairs; of these: 9856633 (72.47%) aligned 0 times 3187259 (23.43%) aligned exactly 1 time 557662 (4.10%) aligned >1 times 63.15% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 1302702 / 6570828 = 0.1983 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 20:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.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 20:37:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:37:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:05: 1000000 INFO @ Sat, 15 Jan 2022 20:37:10: 2000000 INFO @ Sat, 15 Jan 2022 20:37:16: 3000000 INFO @ Sat, 15 Jan 2022 20:37:21: 4000000 INFO @ Sat, 15 Jan 2022 20:37:26: 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 20:37:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.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 20:37:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:37:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:31: 6000000 INFO @ Sat, 15 Jan 2022 20:37:34: 1000000 INFO @ Sat, 15 Jan 2022 20:37:36: 7000000 INFO @ Sat, 15 Jan 2022 20:37:39: 2000000 INFO @ Sat, 15 Jan 2022 20:37:41: 8000000 INFO @ Sat, 15 Jan 2022 20:37:43: 3000000 INFO @ Sat, 15 Jan 2022 20:37:46: 9000000 INFO @ Sat, 15 Jan 2022 20:37:47: 4000000 INFO @ Sat, 15 Jan 2022 20:37:52: 5000000 INFO @ Sat, 15 Jan 2022 20:37:52: 10000000 INFO @ Sat, 15 Jan 2022 20:37:56: 6000000 INFO @ Sat, 15 Jan 2022 20:37:57: 11000000 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 20:38:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.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 20:38:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:38:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:38:00: 7000000 INFO @ Sat, 15 Jan 2022 20:38:02: 12000000 INFO @ Sat, 15 Jan 2022 20:38:04: 1000000 INFO @ Sat, 15 Jan 2022 20:38:05: 8000000 INFO @ Sat, 15 Jan 2022 20:38:08: 13000000 INFO @ Sat, 15 Jan 2022 20:38:09: 2000000 INFO @ Sat, 15 Jan 2022 20:38:09: 9000000 INFO @ Sat, 15 Jan 2022 20:38:13: 14000000 INFO @ Sat, 15 Jan 2022 20:38:13: 3000000 INFO @ Sat, 15 Jan 2022 20:38:13: 10000000 INFO @ Sat, 15 Jan 2022 20:38:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:38:14: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:38:14: #1 total tags in treatment: 5080901 INFO @ Sat, 15 Jan 2022 20:38:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:38:14: #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 20:38:14: #1 tags after filtering in treatment: 3078542 INFO @ Sat, 15 Jan 2022 20:38:14: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:38:14: #1 finished! INFO @ Sat, 15 Jan 2022 20:38:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:38:15: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:38:15: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:38:15: start model_add_line... INFO @ Sat, 15 Jan 2022 20:38:15: start X-correlation... INFO @ Sat, 15 Jan 2022 20:38:15: end of X-cor INFO @ Sat, 15 Jan 2022 20:38:15: #2 finished! INFO @ Sat, 15 Jan 2022 20:38:15: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:38:15: #2 alternative fragment length(s) may be 0,23,51,79,115,132,176,195,214,253,275,301,307,330,348,366,384,413,420,453,487,501,545,570,591 bps INFO @ Sat, 15 Jan 2022 20:38:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.05_model.r WARNING @ Sat, 15 Jan 2022 20:38:15: #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 20:38:15: #2 You may need to consider one of the other alternative d(s): 0,23,51,79,115,132,176,195,214,253,275,301,307,330,348,366,384,413,420,453,487,501,545,570,591 WARNING @ Sat, 15 Jan 2022 20:38:15: #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 20:38:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:38:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:38:17: 4000000 INFO @ Sat, 15 Jan 2022 20:38:18: 11000000 INFO @ Sat, 15 Jan 2022 20:38:22: 5000000 INFO @ Sat, 15 Jan 2022 20:38:22: 12000000 INFO @ Sat, 15 Jan 2022 20:38:26: 6000000 INFO @ Sat, 15 Jan 2022 20:38:26: 13000000 INFO @ Sat, 15 Jan 2022 20:38:30: 7000000 INFO @ Sat, 15 Jan 2022 20:38:31: 14000000 INFO @ Sat, 15 Jan 2022 20:38:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:38:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:38:32: #1 total tags in treatment: 5080901 INFO @ Sat, 15 Jan 2022 20:38:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:38:32: #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 20:38:32: #1 tags after filtering in treatment: 3078542 INFO @ Sat, 15 Jan 2022 20:38:32: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:38:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:38:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:38:32: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:38:32: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:38:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:38:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:38:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:38:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:38:32: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:38:32: #2 alternative fragment length(s) may be 0,23,51,79,115,132,176,195,214,253,275,301,307,330,348,366,384,413,420,453,487,501,545,570,591 bps INFO @ Sat, 15 Jan 2022 20:38:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245354/SRX8245354.10_model.r WARNING @ Sat, 15 Jan 2022 20:38:32: #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 20:38:32: #2 You may need to consider one of the other alternative d(s): 0,23,51,79,115,132,176,195,214,253,275,301,307,330,348,366,384,413,420,453,487,501,545,570,591 WARNING @ Sat, 15 Jan 2022 20:38:32: #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 20:38:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:38:34: 8000000 INFO @ Sat, 15 Jan 2022 20:38:39: 9000000 INFO @ Sat, 15 Jan 2022 20:38:43: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:38:47: 11000000 INFO @ Sat, 15 Jan 2022 20:38:51: 12000000 BigWig に変換しました。 /var/spool/uge/at164/job_scripts/14521094: line 297: 89265 Terminated MACS $i /var/spool/uge/at164/job_scripts/14521094: line 297: 90789 Terminated MACS $i /var/spool/uge/at164/job_scripts/14521094: line 297: 101663 Terminated MACS $i ls: cannot access SRX8245354.05.bed: No such file or directory mv: cannot stat ‘SRX8245354.05.bed’: No such file or directory mv: cannot stat ‘SRX8245354.05.bb’: No such file or directory ls: cannot access SRX8245354.10.bed: No such file or directory mv: cannot stat ‘SRX8245354.10.bed’: No such file or directory mv: cannot stat ‘SRX8245354.10.bb’: No such file or directory ls: cannot access SRX8245354.20.bed: No such file or directory mv: cannot stat ‘SRX8245354.20.bed’: No such file or directory mv: cannot stat ‘SRX8245354.20.bb’: No such file or directory