Job ID = 14520986 SRX = ERX4123664 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6752745 spots for ERR4157919/ERR4157919.sra Written 6752745 spots for ERR4157919/ERR4157919.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: 00:00:58 6752745 reads; of these: 6752745 (100.00%) were unpaired; of these: 1110617 (16.45%) aligned 0 times 4778471 (70.76%) aligned exactly 1 time 863657 (12.79%) aligned >1 times 83.55% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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_rmdupse_core] 2202323 / 5642128 = 0.3903 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 20:15:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.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 20:15:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:11: 1000000 INFO @ Sat, 15 Jan 2022 20:15:16: 2000000 INFO @ Sat, 15 Jan 2022 20:15:20: 3000000 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: 3439805 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: 3439805 INFO @ Sat, 15 Jan 2022 20:15:22: #1 Redundant rate of treatment: 0.00 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: 173 WARNING @ Sat, 15 Jan 2022 20:15:22: 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 20:15:22: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:22: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:23: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:15:23: #2 alternative fragment length(s) may be 0,12,49,62,92,104,120,175,186,229,260,273,312,375,398,423,463,478,514,598 bps INFO @ Sat, 15 Jan 2022 20:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.05_model.r WARNING @ Sat, 15 Jan 2022 20:15:23: #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 20:15:23: #2 You may need to consider one of the other alternative d(s): 0,12,49,62,92,104,120,175,186,229,260,273,312,375,398,423,463,478,514,598 WARNING @ Sat, 15 Jan 2022 20:15:23: #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 20:15:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:23: #3 Pre-compute pvalue-qvalue table... 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 20:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.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 20:15:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:41: 1000000 INFO @ Sat, 15 Jan 2022 20:15:46: 2000000 INFO @ Sat, 15 Jan 2022 20:15:51: 3000000 INFO @ Sat, 15 Jan 2022 20:15:53: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:53: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:53: #1 total tags in treatment: 3439805 INFO @ Sat, 15 Jan 2022 20:15:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:53: #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 20:15:53: #1 tags after filtering in treatment: 3439805 INFO @ Sat, 15 Jan 2022 20:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:15:53: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:53: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:15:53: 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 20:15:53: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:53: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:53: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:53: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:53: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:15:53: #2 alternative fragment length(s) may be 0,12,49,62,92,104,120,175,186,229,260,273,312,375,398,423,463,478,514,598 bps INFO @ Sat, 15 Jan 2022 20:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.10_model.r WARNING @ Sat, 15 Jan 2022 20:15:53: #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 20:15:53: #2 You may need to consider one of the other alternative d(s): 0,12,49,62,92,104,120,175,186,229,260,273,312,375,398,423,463,478,514,598 WARNING @ Sat, 15 Jan 2022 20:15:53: #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 20:15:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:53: #3 Pre-compute pvalue-qvalue table... 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 20:16:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.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 20:16:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:16:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:16:11: 1000000 INFO @ Sat, 15 Jan 2022 20:16:16: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:16:20: 3000000 INFO @ Sat, 15 Jan 2022 20:16:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:16:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:16:22: #1 total tags in treatment: 3439805 INFO @ Sat, 15 Jan 2022 20:16:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:16:22: #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 20:16:22: #1 tags after filtering in treatment: 3439805 INFO @ Sat, 15 Jan 2022 20:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:16:22: #1 finished! INFO @ Sat, 15 Jan 2022 20:16:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:16:23: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:16:23: 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 20:16:23: start model_add_line... INFO @ Sat, 15 Jan 2022 20:16:23: start X-correlation... INFO @ Sat, 15 Jan 2022 20:16:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:16:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:16:23: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:16:23: #2 alternative fragment length(s) may be 0,12,49,62,92,104,120,175,186,229,260,273,312,375,398,423,463,478,514,598 bps INFO @ Sat, 15 Jan 2022 20:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123664/ERX4123664.20_model.r WARNING @ Sat, 15 Jan 2022 20:16:23: #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 20:16:23: #2 You may need to consider one of the other alternative d(s): 0,12,49,62,92,104,120,175,186,229,260,273,312,375,398,423,463,478,514,598 WARNING @ Sat, 15 Jan 2022 20:16:23: #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 20:16:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:16:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at145/job_scripts/14520986: line 297: 99679 Terminated MACS $i /var/spool/uge/at145/job_scripts/14520986: line 297: 99836 Terminated MACS $i /var/spool/uge/at145/job_scripts/14520986: line 297: 108739 Terminated MACS $i ls: cannot access ERX4123664.05.bed: No such file or directory mv: cannot stat ‘ERX4123664.05.bed’: No such file or directory mv: cannot stat ‘ERX4123664.05.bb’: No such file or directory ls: cannot access ERX4123664.10.bed: No such file or directory mv: cannot stat ‘ERX4123664.10.bed’: No such file or directory mv: cannot stat ‘ERX4123664.10.bb’: No such file or directory ls: cannot access ERX4123664.20.bed: No such file or directory mv: cannot stat ‘ERX4123664.20.bed’: No such file or directory mv: cannot stat ‘ERX4123664.20.bb’: No such file or directory