Job ID = 6366328 SRX = SRX113602 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:07 prefetch.2.10.7: 1) Downloading 'SRR393702'... 2020-06-15T22:43:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:54 prefetch.2.10.7: 'SRR393702' is valid 2020-06-15T22:43:54 prefetch.2.10.7: 1) 'SRR393702' was downloaded successfully Read 12375428 spots for SRR393702/SRR393702.sra Written 12375428 spots for SRR393702/SRR393702.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: 00:02:25 12375428 reads; of these: 12375428 (100.00%) were unpaired; of these: 500100 (4.04%) aligned 0 times 9582879 (77.43%) aligned exactly 1 time 2292449 (18.52%) aligned >1 times 95.96% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2622847 / 11875328 = 0.2209 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 @ Tue, 16 Jun 2020 07:49:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 07:49:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:58: 1000000 INFO @ Tue, 16 Jun 2020 07:50:03: 2000000 INFO @ Tue, 16 Jun 2020 07:50:07: 3000000 INFO @ Tue, 16 Jun 2020 07:50:12: 4000000 INFO @ Tue, 16 Jun 2020 07:50:16: 5000000 INFO @ Tue, 16 Jun 2020 07:50:21: 6000000 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 @ Tue, 16 Jun 2020 07:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 07:50:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:26: 7000000 INFO @ Tue, 16 Jun 2020 07:50:28: 1000000 INFO @ Tue, 16 Jun 2020 07:50:30: 8000000 INFO @ Tue, 16 Jun 2020 07:50:33: 2000000 INFO @ Tue, 16 Jun 2020 07:50:35: 9000000 INFO @ Tue, 16 Jun 2020 07:50:36: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:50:36: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:50:36: #1 total tags in treatment: 9252481 INFO @ Tue, 16 Jun 2020 07:50:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:50:36: #1 tags after filtering in treatment: 9252481 INFO @ Tue, 16 Jun 2020 07:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:37: #2 number of paired peaks: 133 WARNING @ Tue, 16 Jun 2020 07:50:37: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:37: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:50:37: #2 alternative fragment length(s) may be 0,15,37,91,135,142,193,197,253,280,294,342,374,404,424,450,455,527,568,578,592 bps INFO @ Tue, 16 Jun 2020 07:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.05_model.r WARNING @ Tue, 16 Jun 2020 07:50:37: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:37: #2 You may need to consider one of the other alternative d(s): 0,15,37,91,135,142,193,197,253,280,294,342,374,404,424,450,455,527,568,578,592 WARNING @ Tue, 16 Jun 2020 07:50:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:50:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:37: 3000000 INFO @ Tue, 16 Jun 2020 07:50:42: 4000000 INFO @ Tue, 16 Jun 2020 07:50:47: 5000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 07:50:51: 6000000 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 @ Tue, 16 Jun 2020 07:50:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 07:50:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:56: 7000000 INFO @ Tue, 16 Jun 2020 07:50:58: 1000000 INFO @ Tue, 16 Jun 2020 07:51:01: 8000000 INFO @ Tue, 16 Jun 2020 07:51:03: 2000000 INFO @ Tue, 16 Jun 2020 07:51:06: 9000000 INFO @ Tue, 16 Jun 2020 07:51:07: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:51:07: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:51:07: #1 total tags in treatment: 9252481 INFO @ Tue, 16 Jun 2020 07:51:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:51:07: #1 tags after filtering in treatment: 9252481 INFO @ Tue, 16 Jun 2020 07:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:08: 3000000 INFO @ Tue, 16 Jun 2020 07:51:08: #2 number of paired peaks: 133 WARNING @ Tue, 16 Jun 2020 07:51:08: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:08: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:51:08: #2 alternative fragment length(s) may be 0,15,37,91,135,142,193,197,253,280,294,342,374,404,424,450,455,527,568,578,592 bps INFO @ Tue, 16 Jun 2020 07:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.10_model.r WARNING @ Tue, 16 Jun 2020 07:51:08: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:08: #2 You may need to consider one of the other alternative d(s): 0,15,37,91,135,142,193,197,253,280,294,342,374,404,424,450,455,527,568,578,592 WARNING @ Tue, 16 Jun 2020 07:51:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:51:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:51:12: 4000000 INFO @ Tue, 16 Jun 2020 07:51:17: 5000000 INFO @ Tue, 16 Jun 2020 07:51:22: 6000000 INFO @ Tue, 16 Jun 2020 07:51:27: 7000000 INFO @ Tue, 16 Jun 2020 07:51:32: 8000000 INFO @ Tue, 16 Jun 2020 07:51:36: 9000000 INFO @ Tue, 16 Jun 2020 07:51:38: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:51:38: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:51:38: #1 total tags in treatment: 9252481 INFO @ Tue, 16 Jun 2020 07:51:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:51:38: #1 tags after filtering in treatment: 9252481 INFO @ Tue, 16 Jun 2020 07:51:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:38: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:38: #2 number of paired peaks: 133 WARNING @ Tue, 16 Jun 2020 07:51:38: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:38: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:38: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:51:38: #2 alternative fragment length(s) may be 0,15,37,91,135,142,193,197,253,280,294,342,374,404,424,450,455,527,568,578,592 bps INFO @ Tue, 16 Jun 2020 07:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113602/SRX113602.20_model.r WARNING @ Tue, 16 Jun 2020 07:51:38: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:38: #2 You may need to consider one of the other alternative d(s): 0,15,37,91,135,142,193,197,253,280,294,342,374,404,424,450,455,527,568,578,592 WARNING @ Tue, 16 Jun 2020 07:51:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:51:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/at160/job_scripts/6366328: line 271: 83791 Terminated MACS $i /var/spool/uge/at160/job_scripts/6366328: line 271: 87971 Terminated MACS $i /var/spool/uge/at160/job_scripts/6366328: line 271: 102477 Terminated MACS $i ls: cannot access SRX113602.05.bed: No such file or directory mv: cannot stat ‘SRX113602.05.bed’: No such file or directory mv: cannot stat ‘SRX113602.05.bb’: No such file or directory ls: cannot access SRX113602.10.bed: No such file or directory mv: cannot stat ‘SRX113602.10.bed’: No such file or directory mv: cannot stat ‘SRX113602.10.bb’: No such file or directory ls: cannot access SRX113602.20.bed: No such file or directory mv: cannot stat ‘SRX113602.20.bed’: No such file or directory mv: cannot stat ‘SRX113602.20.bb’: No such file or directory