Job ID = 6497524 SRX = SRX495114 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:48:58 prefetch.2.10.7: 1) Downloading 'SRR1198646'... 2020-06-25T22:48:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:53:12 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:53:12 prefetch.2.10.7: 1) 'SRR1198646' was downloaded successfully Read 32932978 spots for SRR1198646/SRR1198646.sra Written 32932978 spots for SRR1198646/SRR1198646.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: 00:00:01 Multiseed full-index search: 00:05:53 32932978 reads; of these: 32932978 (100.00%) were unpaired; of these: 434431 (1.32%) aligned 0 times 27124012 (82.36%) aligned exactly 1 time 5374535 (16.32%) aligned >1 times 98.68% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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 12 files... [bam_rmdupse_core] 6590908 / 32498547 = 0.2028 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 @ Fri, 26 Jun 2020 08:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.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 @ Fri, 26 Jun 2020 08:09:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:09:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:09:56: 1000000 INFO @ Fri, 26 Jun 2020 08:10:01: 2000000 INFO @ Fri, 26 Jun 2020 08:10:06: 3000000 INFO @ Fri, 26 Jun 2020 08:10:11: 4000000 INFO @ Fri, 26 Jun 2020 08:10:17: 5000000 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 @ Fri, 26 Jun 2020 08:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.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 @ Fri, 26 Jun 2020 08:10:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:10:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:10:22: 6000000 INFO @ Fri, 26 Jun 2020 08:10:26: 1000000 INFO @ Fri, 26 Jun 2020 08:10:28: 7000000 INFO @ Fri, 26 Jun 2020 08:10:32: 2000000 INFO @ Fri, 26 Jun 2020 08:10:33: 8000000 INFO @ Fri, 26 Jun 2020 08:10:38: 3000000 INFO @ Fri, 26 Jun 2020 08:10:40: 9000000 INFO @ Fri, 26 Jun 2020 08:10:44: 4000000 INFO @ Fri, 26 Jun 2020 08:10:46: 10000000 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 @ Fri, 26 Jun 2020 08:10:50: 5000000 INFO @ Fri, 26 Jun 2020 08:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.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 @ Fri, 26 Jun 2020 08:10:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:10:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:10:52: 11000000 INFO @ Fri, 26 Jun 2020 08:10:56: 1000000 INFO @ Fri, 26 Jun 2020 08:10:56: 6000000 INFO @ Fri, 26 Jun 2020 08:10:58: 12000000 INFO @ Fri, 26 Jun 2020 08:11:01: 2000000 INFO @ Fri, 26 Jun 2020 08:11:03: 7000000 INFO @ Fri, 26 Jun 2020 08:11:04: 13000000 INFO @ Fri, 26 Jun 2020 08:11:07: 3000000 INFO @ Fri, 26 Jun 2020 08:11:09: 8000000 INFO @ Fri, 26 Jun 2020 08:11:11: 14000000 INFO @ Fri, 26 Jun 2020 08:11:13: 4000000 INFO @ Fri, 26 Jun 2020 08:11:16: 9000000 INFO @ Fri, 26 Jun 2020 08:11:17: 15000000 INFO @ Fri, 26 Jun 2020 08:11:18: 5000000 INFO @ Fri, 26 Jun 2020 08:11:22: 10000000 INFO @ Fri, 26 Jun 2020 08:11:24: 16000000 INFO @ Fri, 26 Jun 2020 08:11:24: 6000000 INFO @ Fri, 26 Jun 2020 08:11:28: 11000000 INFO @ Fri, 26 Jun 2020 08:11:29: 7000000 INFO @ Fri, 26 Jun 2020 08:11:30: 17000000 INFO @ Fri, 26 Jun 2020 08:11:35: 12000000 INFO @ Fri, 26 Jun 2020 08:11:35: 8000000 INFO @ Fri, 26 Jun 2020 08:11:37: 18000000 INFO @ Fri, 26 Jun 2020 08:11:42: 13000000 INFO @ Fri, 26 Jun 2020 08:11:42: 9000000 INFO @ Fri, 26 Jun 2020 08:11:43: 19000000 INFO @ Fri, 26 Jun 2020 08:11:47: 10000000 INFO @ Fri, 26 Jun 2020 08:11:48: 14000000 INFO @ Fri, 26 Jun 2020 08:11:50: 20000000 INFO @ Fri, 26 Jun 2020 08:11:53: 11000000 INFO @ Fri, 26 Jun 2020 08:11:55: 15000000 INFO @ Fri, 26 Jun 2020 08:11:57: 21000000 INFO @ Fri, 26 Jun 2020 08:11:59: 12000000 INFO @ Fri, 26 Jun 2020 08:12:01: 16000000 INFO @ Fri, 26 Jun 2020 08:12:03: 22000000 INFO @ Fri, 26 Jun 2020 08:12:05: 13000000 INFO @ Fri, 26 Jun 2020 08:12:08: 17000000 INFO @ Fri, 26 Jun 2020 08:12:10: 23000000 INFO @ Fri, 26 Jun 2020 08:12:11: 14000000 INFO @ Fri, 26 Jun 2020 08:12:15: 18000000 INFO @ Fri, 26 Jun 2020 08:12:16: 15000000 INFO @ Fri, 26 Jun 2020 08:12:17: 24000000 INFO @ Fri, 26 Jun 2020 08:12:21: 19000000 INFO @ Fri, 26 Jun 2020 08:12:22: 16000000 INFO @ Fri, 26 Jun 2020 08:12:23: 25000000 INFO @ Fri, 26 Jun 2020 08:12:28: 20000000 INFO @ Fri, 26 Jun 2020 08:12:28: 17000000 INFO @ Fri, 26 Jun 2020 08:12:29: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:12:29: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:12:29: #1 total tags in treatment: 25907639 INFO @ Fri, 26 Jun 2020 08:12:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:12:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:12:30: #1 tags after filtering in treatment: 25907639 INFO @ Fri, 26 Jun 2020 08:12:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:12:30: #1 finished! INFO @ Fri, 26 Jun 2020 08:12:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:12:31: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 08:12:31: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 08:12:31: start model_add_line... INFO @ Fri, 26 Jun 2020 08:12:32: start X-correlation... INFO @ Fri, 26 Jun 2020 08:12:32: end of X-cor INFO @ Fri, 26 Jun 2020 08:12:32: #2 finished! INFO @ Fri, 26 Jun 2020 08:12:32: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 08:12:32: #2 alternative fragment length(s) may be 0,10,37,92,144,199,363,414,540,560,583 bps INFO @ Fri, 26 Jun 2020 08:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.05_model.r WARNING @ Fri, 26 Jun 2020 08:12:32: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:12:32: #2 You may need to consider one of the other alternative d(s): 0,10,37,92,144,199,363,414,540,560,583 WARNING @ Fri, 26 Jun 2020 08:12:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:12:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:12:34: 18000000 INFO @ Fri, 26 Jun 2020 08:12:34: 21000000 INFO @ Fri, 26 Jun 2020 08:12:39: 19000000 INFO @ Fri, 26 Jun 2020 08:12:41: 22000000 INFO @ Fri, 26 Jun 2020 08:12:45: 20000000 INFO @ Fri, 26 Jun 2020 08:12:47: 23000000 INFO @ Fri, 26 Jun 2020 08:12:51: 21000000 INFO @ Fri, 26 Jun 2020 08:12:54: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:12:57: 22000000 INFO @ Fri, 26 Jun 2020 08:13:00: 25000000 INFO @ Fri, 26 Jun 2020 08:13:02: 23000000 INFO @ Fri, 26 Jun 2020 08:13:06: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:13:06: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:13:06: #1 total tags in treatment: 25907639 INFO @ Fri, 26 Jun 2020 08:13:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:13:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:13:07: #1 tags after filtering in treatment: 25907639 INFO @ Fri, 26 Jun 2020 08:13:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:13:07: #1 finished! INFO @ Fri, 26 Jun 2020 08:13:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:13:08: 24000000 INFO @ Fri, 26 Jun 2020 08:13:08: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 08:13:08: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 08:13:08: start model_add_line... INFO @ Fri, 26 Jun 2020 08:13:09: start X-correlation... INFO @ Fri, 26 Jun 2020 08:13:09: end of X-cor INFO @ Fri, 26 Jun 2020 08:13:09: #2 finished! INFO @ Fri, 26 Jun 2020 08:13:09: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 08:13:09: #2 alternative fragment length(s) may be 0,10,37,92,144,199,363,414,540,560,583 bps INFO @ Fri, 26 Jun 2020 08:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.10_model.r WARNING @ Fri, 26 Jun 2020 08:13:09: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:13:09: #2 You may need to consider one of the other alternative d(s): 0,10,37,92,144,199,363,414,540,560,583 WARNING @ Fri, 26 Jun 2020 08:13:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:13:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:13:13: 25000000 INFO @ Fri, 26 Jun 2020 08:13:19: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:13:19: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:13:19: #1 total tags in treatment: 25907639 INFO @ Fri, 26 Jun 2020 08:13:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:13:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:13:19: #1 tags after filtering in treatment: 25907639 INFO @ Fri, 26 Jun 2020 08:13:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:13:19: #1 finished! INFO @ Fri, 26 Jun 2020 08:13:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:13:21: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 08:13:21: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 08:13:21: start model_add_line... INFO @ Fri, 26 Jun 2020 08:13:21: start X-correlation... INFO @ Fri, 26 Jun 2020 08:13:21: end of X-cor INFO @ Fri, 26 Jun 2020 08:13:21: #2 finished! INFO @ Fri, 26 Jun 2020 08:13:21: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 08:13:21: #2 alternative fragment length(s) may be 0,10,37,92,144,199,363,414,540,560,583 bps INFO @ Fri, 26 Jun 2020 08:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495114/SRX495114.20_model.r WARNING @ Fri, 26 Jun 2020 08:13:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:13:21: #2 You may need to consider one of the other alternative d(s): 0,10,37,92,144,199,363,414,540,560,583 WARNING @ Fri, 26 Jun 2020 08:13:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:13:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:13:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it007/job_scripts/6497524: line 274: 27928 Terminated MACS $i /var/spool/uge/it007/job_scripts/6497524: line 274: 28203 Terminated MACS $i /var/spool/uge/it007/job_scripts/6497524: line 274: 28336 Terminated MACS $i ls: cannot access SRX495114.05.bed: No such file or directory mv: cannot stat ‘SRX495114.05.bed’: No such file or directory mv: cannot stat ‘SRX495114.05.bb’: No such file or directory ls: cannot access SRX495114.10.bed: No such file or directory mv: cannot stat ‘SRX495114.10.bed’: No such file or directory mv: cannot stat ‘SRX495114.10.bb’: No such file or directory ls: cannot access SRX495114.20.bed: No such file or directory mv: cannot stat ‘SRX495114.20.bed’: No such file or directory mv: cannot stat ‘SRX495114.20.bb’: No such file or directory