Job ID = 14520940 SRX = ERX4123659 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6110937 spots for ERR4157914/ERR4157914.sra Written 6110937 spots for ERR4157914/ERR4157914.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: 00:00:57 6110937 reads; of these: 6110937 (100.00%) were unpaired; of these: 1010460 (16.54%) aligned 0 times 4423683 (72.39%) aligned exactly 1 time 676794 (11.08%) aligned >1 times 83.46% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 1866361 / 5100477 = 0.3659 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 20:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.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 20:14:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:29: 1000000 INFO @ Sat, 15 Jan 2022 20:14:34: 2000000 INFO @ Sat, 15 Jan 2022 20:14:39: 3000000 INFO @ Sat, 15 Jan 2022 20:14:40: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:14:40: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:14:40: #1 total tags in treatment: 3234116 INFO @ Sat, 15 Jan 2022 20:14:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:14:40: #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 20:14:40: #1 tags after filtering in treatment: 3234116 INFO @ Sat, 15 Jan 2022 20:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:14:40: #1 finished! INFO @ Sat, 15 Jan 2022 20:14:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:14:40: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:14:40: 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 20:14:40: start model_add_line... INFO @ Sat, 15 Jan 2022 20:14:40: start X-correlation... INFO @ Sat, 15 Jan 2022 20:14:40: end of X-cor INFO @ Sat, 15 Jan 2022 20:14:40: #2 finished! INFO @ Sat, 15 Jan 2022 20:14:40: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:14:40: #2 alternative fragment length(s) may be 0,18,52,89,108,132,144,175,196,225,248,263,306,370,441,477,485,524,551 bps INFO @ Sat, 15 Jan 2022 20:14:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.05_model.r WARNING @ Sat, 15 Jan 2022 20:14:40: #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 20:14:40: #2 You may need to consider one of the other alternative d(s): 0,18,52,89,108,132,144,175,196,225,248,263,306,370,441,477,485,524,551 WARNING @ Sat, 15 Jan 2022 20:14:40: #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 20:14:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:14:40: #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 20:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.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 20:14:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:00: 1000000 INFO @ Sat, 15 Jan 2022 20:15:06: 2000000 INFO @ Sat, 15 Jan 2022 20:15:11: 3000000 INFO @ Sat, 15 Jan 2022 20:15:12: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:12: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:12: #1 total tags in treatment: 3234116 INFO @ Sat, 15 Jan 2022 20:15:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:12: #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 20:15:12: #1 tags after filtering in treatment: 3234116 INFO @ Sat, 15 Jan 2022 20:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:15:12: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:13: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:15:13: 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 20:15:13: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:13: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:13: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:13: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:13: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:15:13: #2 alternative fragment length(s) may be 0,18,52,89,108,132,144,175,196,225,248,263,306,370,441,477,485,524,551 bps INFO @ Sat, 15 Jan 2022 20:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.10_model.r WARNING @ Sat, 15 Jan 2022 20:15:13: #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 20:15:13: #2 You may need to consider one of the other alternative d(s): 0,18,52,89,108,132,144,175,196,225,248,263,306,370,441,477,485,524,551 WARNING @ Sat, 15 Jan 2022 20:15:13: #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 20:15:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:13: #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 20:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.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 20:15:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:29: 1000000 INFO @ Sat, 15 Jan 2022 20:15:34: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:15:39: 3000000 INFO @ Sat, 15 Jan 2022 20:15:40: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:40: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:40: #1 total tags in treatment: 3234116 INFO @ Sat, 15 Jan 2022 20:15:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:40: #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 20:15:40: #1 tags after filtering in treatment: 3234116 INFO @ Sat, 15 Jan 2022 20:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:15:40: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:40: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:15:40: 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 20:15:40: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:40: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:40: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:40: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:40: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:15:40: #2 alternative fragment length(s) may be 0,18,52,89,108,132,144,175,196,225,248,263,306,370,441,477,485,524,551 bps INFO @ Sat, 15 Jan 2022 20:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123659/ERX4123659.20_model.r WARNING @ Sat, 15 Jan 2022 20:15:40: #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 20:15:40: #2 You may need to consider one of the other alternative d(s): 0,18,52,89,108,132,144,175,196,225,248,263,306,370,441,477,485,524,551 WARNING @ Sat, 15 Jan 2022 20:15:40: #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 20:15:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at163/job_scripts/14520940: line 297: 111869 Terminated MACS $i /var/spool/uge/at163/job_scripts/14520940: line 297: 115132 Terminated MACS $i /var/spool/uge/at163/job_scripts/14520940: line 297: 117564 Terminated MACS $i ls: cannot access ERX4123659.05.bed: No such file or directory mv: cannot stat ‘ERX4123659.05.bed’: No such file or directory mv: cannot stat ‘ERX4123659.05.bb’: No such file or directory ls: cannot access ERX4123659.10.bed: No such file or directory mv: cannot stat ‘ERX4123659.10.bed’: No such file or directory mv: cannot stat ‘ERX4123659.10.bb’: No such file or directory ls: cannot access ERX4123659.20.bed: No such file or directory mv: cannot stat ‘ERX4123659.20.bed’: No such file or directory mv: cannot stat ‘ERX4123659.20.bb’: No such file or directory