Job ID = 6368168 SRX = SRX494852 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:59:50 prefetch.2.10.7: 1) Downloading 'SRR1198384'... 2020-06-15T23:59:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:44 prefetch.2.10.7: 1) 'SRR1198384' was downloaded successfully Read 30788149 spots for SRR1198384/SRR1198384.sra Written 30788149 spots for SRR1198384/SRR1198384.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: 00:05:36 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169806 (0.55%) aligned 0 times 25275361 (82.09%) aligned exactly 1 time 5342982 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4711434 / 30618343 = 0.1539 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 09:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.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 09:15:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:25: 1000000 INFO @ Tue, 16 Jun 2020 09:15:31: 2000000 INFO @ Tue, 16 Jun 2020 09:15:36: 3000000 INFO @ Tue, 16 Jun 2020 09:15:42: 4000000 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 09:15:48: 5000000 INFO @ Tue, 16 Jun 2020 09:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.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 09:15:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:54: 6000000 INFO @ Tue, 16 Jun 2020 09:15:55: 1000000 INFO @ Tue, 16 Jun 2020 09:16:00: 7000000 INFO @ Tue, 16 Jun 2020 09:16:01: 2000000 INFO @ Tue, 16 Jun 2020 09:16:06: 8000000 INFO @ Tue, 16 Jun 2020 09:16:08: 3000000 INFO @ Tue, 16 Jun 2020 09:16:12: 9000000 INFO @ Tue, 16 Jun 2020 09:16:14: 4000000 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 @ Tue, 16 Jun 2020 09:16:18: 10000000 INFO @ Tue, 16 Jun 2020 09:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.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 09:16:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:20: 5000000 INFO @ Tue, 16 Jun 2020 09:16:25: 11000000 INFO @ Tue, 16 Jun 2020 09:16:25: 1000000 INFO @ Tue, 16 Jun 2020 09:16:27: 6000000 INFO @ Tue, 16 Jun 2020 09:16:31: 2000000 INFO @ Tue, 16 Jun 2020 09:16:31: 12000000 INFO @ Tue, 16 Jun 2020 09:16:33: 7000000 INFO @ Tue, 16 Jun 2020 09:16:37: 3000000 INFO @ Tue, 16 Jun 2020 09:16:37: 13000000 INFO @ Tue, 16 Jun 2020 09:16:40: 8000000 INFO @ Tue, 16 Jun 2020 09:16:43: 4000000 INFO @ Tue, 16 Jun 2020 09:16:44: 14000000 INFO @ Tue, 16 Jun 2020 09:16:46: 9000000 INFO @ Tue, 16 Jun 2020 09:16:49: 5000000 INFO @ Tue, 16 Jun 2020 09:16:50: 15000000 INFO @ Tue, 16 Jun 2020 09:16:53: 10000000 INFO @ Tue, 16 Jun 2020 09:16:55: 6000000 INFO @ Tue, 16 Jun 2020 09:16:57: 16000000 INFO @ Tue, 16 Jun 2020 09:16:59: 11000000 INFO @ Tue, 16 Jun 2020 09:17:01: 7000000 INFO @ Tue, 16 Jun 2020 09:17:03: 17000000 INFO @ Tue, 16 Jun 2020 09:17:06: 12000000 INFO @ Tue, 16 Jun 2020 09:17:08: 8000000 INFO @ Tue, 16 Jun 2020 09:17:10: 18000000 INFO @ Tue, 16 Jun 2020 09:17:12: 13000000 INFO @ Tue, 16 Jun 2020 09:17:14: 9000000 INFO @ Tue, 16 Jun 2020 09:17:16: 19000000 INFO @ Tue, 16 Jun 2020 09:17:19: 14000000 INFO @ Tue, 16 Jun 2020 09:17:20: 10000000 INFO @ Tue, 16 Jun 2020 09:17:23: 20000000 INFO @ Tue, 16 Jun 2020 09:17:26: 15000000 INFO @ Tue, 16 Jun 2020 09:17:26: 11000000 INFO @ Tue, 16 Jun 2020 09:17:30: 21000000 INFO @ Tue, 16 Jun 2020 09:17:33: 12000000 INFO @ Tue, 16 Jun 2020 09:17:33: 16000000 INFO @ Tue, 16 Jun 2020 09:17:36: 22000000 INFO @ Tue, 16 Jun 2020 09:17:39: 13000000 INFO @ Tue, 16 Jun 2020 09:17:40: 17000000 INFO @ Tue, 16 Jun 2020 09:17:43: 23000000 INFO @ Tue, 16 Jun 2020 09:17:45: 14000000 INFO @ Tue, 16 Jun 2020 09:17:47: 18000000 INFO @ Tue, 16 Jun 2020 09:17:50: 24000000 INFO @ Tue, 16 Jun 2020 09:17:52: 15000000 INFO @ Tue, 16 Jun 2020 09:17:53: 19000000 INFO @ Tue, 16 Jun 2020 09:17:57: 25000000 INFO @ Tue, 16 Jun 2020 09:17:58: 16000000 INFO @ Tue, 16 Jun 2020 09:18:00: 20000000 INFO @ Tue, 16 Jun 2020 09:18:03: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:18:03: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:18:03: #1 total tags in treatment: 25906909 INFO @ Tue, 16 Jun 2020 09:18:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:03: #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 09:18:03: #1 tags after filtering in treatment: 25906909 INFO @ Tue, 16 Jun 2020 09:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:05: #2 number of paired peaks: 142 WARNING @ Tue, 16 Jun 2020 09:18:05: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:05: 17000000 INFO @ Tue, 16 Jun 2020 09:18:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:05: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:18:05: #2 alternative fragment length(s) may be 0,32,83,131,307,352,421,507,554,571 bps INFO @ Tue, 16 Jun 2020 09:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.05_model.r WARNING @ Tue, 16 Jun 2020 09:18:05: #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 09:18:05: #2 You may need to consider one of the other alternative d(s): 0,32,83,131,307,352,421,507,554,571 WARNING @ Tue, 16 Jun 2020 09:18:05: #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 09:18:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:07: 21000000 INFO @ Tue, 16 Jun 2020 09:18:12: 18000000 INFO @ Tue, 16 Jun 2020 09:18:14: 22000000 INFO @ Tue, 16 Jun 2020 09:18:18: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:18:20: 23000000 INFO @ Tue, 16 Jun 2020 09:18:24: 20000000 INFO @ Tue, 16 Jun 2020 09:18:27: 24000000 INFO @ Tue, 16 Jun 2020 09:18:31: 21000000 INFO @ Tue, 16 Jun 2020 09:18:33: 25000000 INFO @ Tue, 16 Jun 2020 09:18:37: 22000000 INFO @ Tue, 16 Jun 2020 09:18:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:18:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:18:39: #1 total tags in treatment: 25906909 INFO @ Tue, 16 Jun 2020 09:18:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:39: #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 09:18:40: #1 tags after filtering in treatment: 25906909 INFO @ Tue, 16 Jun 2020 09:18:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:42: #2 number of paired peaks: 142 WARNING @ Tue, 16 Jun 2020 09:18:42: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:42: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:18:42: #2 alternative fragment length(s) may be 0,32,83,131,307,352,421,507,554,571 bps INFO @ Tue, 16 Jun 2020 09:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.10_model.r WARNING @ Tue, 16 Jun 2020 09:18:42: #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 09:18:42: #2 You may need to consider one of the other alternative d(s): 0,32,83,131,307,352,421,507,554,571 WARNING @ Tue, 16 Jun 2020 09:18:42: #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 09:18:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:43: 23000000 INFO @ Tue, 16 Jun 2020 09:18:49: 24000000 INFO @ Tue, 16 Jun 2020 09:18:54: 25000000 INFO @ Tue, 16 Jun 2020 09:18:59: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:18:59: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:18:59: #1 total tags in treatment: 25906909 INFO @ Tue, 16 Jun 2020 09:18:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:59: #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 09:19:00: #1 tags after filtering in treatment: 25906909 INFO @ Tue, 16 Jun 2020 09:19:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:01: #2 number of paired peaks: 142 WARNING @ Tue, 16 Jun 2020 09:19:01: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:02: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:19:02: #2 alternative fragment length(s) may be 0,32,83,131,307,352,421,507,554,571 bps INFO @ Tue, 16 Jun 2020 09:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494852/SRX494852.20_model.r WARNING @ Tue, 16 Jun 2020 09:19:02: #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 09:19:02: #2 You may need to consider one of the other alternative d(s): 0,32,83,131,307,352,421,507,554,571 WARNING @ Tue, 16 Jun 2020 09:19:02: #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 09:19:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at159/job_scripts/6368168: line 271: 20093 Terminated MACS $i /var/spool/uge/at159/job_scripts/6368168: line 271: 21089 Terminated MACS $i /var/spool/uge/at159/job_scripts/6368168: line 271: 21864 Terminated MACS $i ls: cannot access SRX494852.05.bed: No such file or directory mv: cannot stat ‘SRX494852.05.bed’: No such file or directory mv: cannot stat ‘SRX494852.05.bb’: No such file or directory ls: cannot access SRX494852.10.bed: No such file or directory mv: cannot stat ‘SRX494852.10.bed’: No such file or directory mv: cannot stat ‘SRX494852.10.bb’: No such file or directory ls: cannot access SRX494852.20.bed: No such file or directory mv: cannot stat ‘SRX494852.20.bed’: No such file or directory mv: cannot stat ‘SRX494852.20.bb’: No such file or directory