Job ID = 7108107 SRX = SRX750574 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 33638679 spots for SRR1604810/SRR1604810.sra Written 33638679 spots for SRR1604810/SRR1604810.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: 00:04:11 33638679 reads; of these: 33638679 (100.00%) were unpaired; of these: 12254924 (36.43%) aligned 0 times 15576057 (46.30%) aligned exactly 1 time 5807698 (17.26%) aligned >1 times 63.57% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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_rmdupse_core] 18502964 / 21383755 = 0.8653 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.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 @ Wed, 22 Jul 2020 13:37:42: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:37:42: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:37:48: 1000000 INFO @ Wed, 22 Jul 2020 13:37:55: 2000000 INFO @ Wed, 22 Jul 2020 13:38:01: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 13:38:01: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 13:38:01: #1 total tags in treatment: 2880791 INFO @ Wed, 22 Jul 2020 13:38:01: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:38:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:38:01: #1 tags after filtering in treatment: 2880791 INFO @ Wed, 22 Jul 2020 13:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:38:01: #1 finished! INFO @ Wed, 22 Jul 2020 13:38:01: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:38:01: #2 number of paired peaks: 346 WARNING @ Wed, 22 Jul 2020 13:38:01: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 22 Jul 2020 13:38:01: start model_add_line... INFO @ Wed, 22 Jul 2020 13:38:01: start X-correlation... INFO @ Wed, 22 Jul 2020 13:38:01: end of X-cor INFO @ Wed, 22 Jul 2020 13:38:01: #2 finished! INFO @ Wed, 22 Jul 2020 13:38:01: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 13:38:01: #2 alternative fragment length(s) may be 0,11,506,555,573,586 bps INFO @ Wed, 22 Jul 2020 13:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.05_model.r WARNING @ Wed, 22 Jul 2020 13:38:01: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:38:01: #2 You may need to consider one of the other alternative d(s): 0,11,506,555,573,586 WARNING @ Wed, 22 Jul 2020 13:38:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:38:01: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:38:01: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:38:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.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 @ Wed, 22 Jul 2020 13:38:12: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:38:12: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:38:17: 1000000 INFO @ Wed, 22 Jul 2020 13:38:23: 2000000 INFO @ Wed, 22 Jul 2020 13:38:28: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 13:38:28: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 13:38:28: #1 total tags in treatment: 2880791 INFO @ Wed, 22 Jul 2020 13:38:28: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:38:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:38:28: #1 tags after filtering in treatment: 2880791 INFO @ Wed, 22 Jul 2020 13:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:38:28: #1 finished! INFO @ Wed, 22 Jul 2020 13:38:28: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:38:28: #2 number of paired peaks: 346 WARNING @ Wed, 22 Jul 2020 13:38:28: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 22 Jul 2020 13:38:28: start model_add_line... INFO @ Wed, 22 Jul 2020 13:38:28: start X-correlation... INFO @ Wed, 22 Jul 2020 13:38:28: end of X-cor INFO @ Wed, 22 Jul 2020 13:38:28: #2 finished! INFO @ Wed, 22 Jul 2020 13:38:28: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 13:38:28: #2 alternative fragment length(s) may be 0,11,506,555,573,586 bps INFO @ Wed, 22 Jul 2020 13:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.10_model.r WARNING @ Wed, 22 Jul 2020 13:38:28: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:38:28: #2 You may need to consider one of the other alternative d(s): 0,11,506,555,573,586 WARNING @ Wed, 22 Jul 2020 13:38:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:38:28: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:38:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:38:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.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 @ Wed, 22 Jul 2020 13:38:42: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:38:42: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:38:47: 1000000 INFO @ Wed, 22 Jul 2020 13:38:53: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:38:58: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 13:38:58: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 13:38:58: #1 total tags in treatment: 2880791 INFO @ Wed, 22 Jul 2020 13:38:58: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:38:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:38:58: #1 tags after filtering in treatment: 2880791 INFO @ Wed, 22 Jul 2020 13:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:38:58: #1 finished! INFO @ Wed, 22 Jul 2020 13:38:58: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:38:58: #2 number of paired peaks: 346 WARNING @ Wed, 22 Jul 2020 13:38:58: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 22 Jul 2020 13:38:58: start model_add_line... INFO @ Wed, 22 Jul 2020 13:38:58: start X-correlation... INFO @ Wed, 22 Jul 2020 13:38:58: end of X-cor INFO @ Wed, 22 Jul 2020 13:38:58: #2 finished! INFO @ Wed, 22 Jul 2020 13:38:58: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 13:38:58: #2 alternative fragment length(s) may be 0,11,506,555,573,586 bps INFO @ Wed, 22 Jul 2020 13:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX750574/SRX750574.20_model.r WARNING @ Wed, 22 Jul 2020 13:38:58: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:38:58: #2 You may need to consider one of the other alternative d(s): 0,11,506,555,573,586 WARNING @ Wed, 22 Jul 2020 13:38:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:38:58: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:38:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at142/job_scripts/7108107: line 297: 112146 Terminated MACS $i /var/spool/uge/at142/job_scripts/7108107: line 297: 112805 Terminated MACS $i /var/spool/uge/at142/job_scripts/7108107: line 297: 113059 Terminated MACS $i ls: cannot access SRX750574.05.bed: No such file or directory mv: cannot stat ‘SRX750574.05.bed’: No such file or directory mv: cannot stat ‘SRX750574.05.bb’: No such file or directory ls: cannot access SRX750574.10.bed: No such file or directory mv: cannot stat ‘SRX750574.10.bed’: No such file or directory mv: cannot stat ‘SRX750574.10.bb’: No such file or directory ls: cannot access SRX750574.20.bed: No such file or directory mv: cannot stat ‘SRX750574.20.bed’: No such file or directory mv: cannot stat ‘SRX750574.20.bb’: No such file or directory