Job ID = 6507974 SRX = SRX514730 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:16:49 prefetch.2.10.7: 1) Downloading 'SRR1231451'... 2020-06-26T13:16:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:21:30 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:21:30 prefetch.2.10.7: 1) 'SRR1231451' was downloaded successfully Read 32932978 spots for SRR1231451/SRR1231451.sra Written 32932978 spots for SRR1231451/SRR1231451.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: 00:06:29 32932978 reads; of these: 32932978 (100.00%) were unpaired; of these: 421364 (1.28%) aligned 0 times 26714470 (81.12%) aligned exactly 1 time 5797144 (17.60%) aligned >1 times 98.72% overall alignment rate Time searching: 00:06:29 Overall time: 00:06:29 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] 6594413 / 32511614 = 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 22:36:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.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 22:36:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:29: 1000000 INFO @ Fri, 26 Jun 2020 22:36:34: 2000000 INFO @ Fri, 26 Jun 2020 22:36:39: 3000000 INFO @ Fri, 26 Jun 2020 22:36:44: 4000000 INFO @ Fri, 26 Jun 2020 22:36:50: 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 22:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.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 22:36:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:56: 6000000 INFO @ Fri, 26 Jun 2020 22:37:00: 1000000 INFO @ Fri, 26 Jun 2020 22:37:02: 7000000 INFO @ Fri, 26 Jun 2020 22:37:05: 2000000 INFO @ Fri, 26 Jun 2020 22:37:08: 8000000 INFO @ Fri, 26 Jun 2020 22:37:11: 3000000 INFO @ Fri, 26 Jun 2020 22:37:13: 9000000 INFO @ Fri, 26 Jun 2020 22:37:16: 4000000 INFO @ Fri, 26 Jun 2020 22:37:19: 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 22:37:23: 5000000 INFO @ Fri, 26 Jun 2020 22:37:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.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 22:37:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:24: 11000000 INFO @ Fri, 26 Jun 2020 22:37:29: 6000000 INFO @ Fri, 26 Jun 2020 22:37:30: 12000000 INFO @ Fri, 26 Jun 2020 22:37:30: 1000000 INFO @ Fri, 26 Jun 2020 22:37:36: 7000000 INFO @ Fri, 26 Jun 2020 22:37:36: 13000000 INFO @ Fri, 26 Jun 2020 22:37:36: 2000000 INFO @ Fri, 26 Jun 2020 22:37:42: 8000000 INFO @ Fri, 26 Jun 2020 22:37:42: 3000000 INFO @ Fri, 26 Jun 2020 22:37:42: 14000000 INFO @ Fri, 26 Jun 2020 22:37:47: 9000000 INFO @ Fri, 26 Jun 2020 22:37:48: 4000000 INFO @ Fri, 26 Jun 2020 22:37:48: 15000000 INFO @ Fri, 26 Jun 2020 22:37:53: 10000000 INFO @ Fri, 26 Jun 2020 22:37:54: 16000000 INFO @ Fri, 26 Jun 2020 22:37:54: 5000000 INFO @ Fri, 26 Jun 2020 22:37:59: 11000000 INFO @ Fri, 26 Jun 2020 22:38:00: 17000000 INFO @ Fri, 26 Jun 2020 22:38:01: 6000000 INFO @ Fri, 26 Jun 2020 22:38:06: 12000000 INFO @ Fri, 26 Jun 2020 22:38:06: 18000000 INFO @ Fri, 26 Jun 2020 22:38:07: 7000000 INFO @ Fri, 26 Jun 2020 22:38:12: 13000000 INFO @ Fri, 26 Jun 2020 22:38:12: 19000000 INFO @ Fri, 26 Jun 2020 22:38:14: 8000000 INFO @ Fri, 26 Jun 2020 22:38:18: 14000000 INFO @ Fri, 26 Jun 2020 22:38:18: 20000000 INFO @ Fri, 26 Jun 2020 22:38:21: 9000000 INFO @ Fri, 26 Jun 2020 22:38:24: 15000000 INFO @ Fri, 26 Jun 2020 22:38:25: 21000000 INFO @ Fri, 26 Jun 2020 22:38:28: 10000000 INFO @ Fri, 26 Jun 2020 22:38:30: 16000000 INFO @ Fri, 26 Jun 2020 22:38:31: 22000000 INFO @ Fri, 26 Jun 2020 22:38:35: 11000000 INFO @ Fri, 26 Jun 2020 22:38:36: 17000000 INFO @ Fri, 26 Jun 2020 22:38:37: 23000000 INFO @ Fri, 26 Jun 2020 22:38:41: 12000000 INFO @ Fri, 26 Jun 2020 22:38:42: 18000000 INFO @ Fri, 26 Jun 2020 22:38:43: 24000000 INFO @ Fri, 26 Jun 2020 22:38:48: 13000000 INFO @ Fri, 26 Jun 2020 22:38:49: 19000000 INFO @ Fri, 26 Jun 2020 22:38:49: 25000000 INFO @ Fri, 26 Jun 2020 22:38:55: 20000000 INFO @ Fri, 26 Jun 2020 22:38:55: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:38:55: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:38:55: #1 total tags in treatment: 25917201 INFO @ Fri, 26 Jun 2020 22:38:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:55: #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 22:38:55: 14000000 INFO @ Fri, 26 Jun 2020 22:38:55: #1 tags after filtering in treatment: 25917201 INFO @ Fri, 26 Jun 2020 22:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:55: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:57: #2 number of paired peaks: 123 WARNING @ Fri, 26 Jun 2020 22:38:57: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:57: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:57: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:57: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:57: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:57: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:38:57: #2 alternative fragment length(s) may be 0,38,132,293,306,419,482,503,593 bps INFO @ Fri, 26 Jun 2020 22:38:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.05_model.r WARNING @ Fri, 26 Jun 2020 22:38:57: #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 22:38:57: #2 You may need to consider one of the other alternative d(s): 0,38,132,293,306,419,482,503,593 WARNING @ Fri, 26 Jun 2020 22:38:57: #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 22:38:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:01: 21000000 INFO @ Fri, 26 Jun 2020 22:39:02: 15000000 INFO @ Fri, 26 Jun 2020 22:39:08: 22000000 INFO @ Fri, 26 Jun 2020 22:39:09: 16000000 INFO @ Fri, 26 Jun 2020 22:39:14: 23000000 INFO @ Fri, 26 Jun 2020 22:39:16: 17000000 INFO @ Fri, 26 Jun 2020 22:39:20: 24000000 INFO @ Fri, 26 Jun 2020 22:39:22: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:39:26: 25000000 INFO @ Fri, 26 Jun 2020 22:39:29: 19000000 INFO @ Fri, 26 Jun 2020 22:39:32: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:39:32: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:39:32: #1 total tags in treatment: 25917201 INFO @ Fri, 26 Jun 2020 22:39:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:32: #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 22:39:32: #1 tags after filtering in treatment: 25917201 INFO @ Fri, 26 Jun 2020 22:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:32: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:34: #2 number of paired peaks: 123 WARNING @ Fri, 26 Jun 2020 22:39:34: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:34: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:34: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:34: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:34: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:34: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:39:34: #2 alternative fragment length(s) may be 0,38,132,293,306,419,482,503,593 bps INFO @ Fri, 26 Jun 2020 22:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.10_model.r WARNING @ Fri, 26 Jun 2020 22:39:34: #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 22:39:34: #2 You may need to consider one of the other alternative d(s): 0,38,132,293,306,419,482,503,593 WARNING @ Fri, 26 Jun 2020 22:39:34: #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 22:39:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:35: 20000000 INFO @ Fri, 26 Jun 2020 22:39:42: 21000000 INFO @ Fri, 26 Jun 2020 22:39:48: 22000000 INFO @ Fri, 26 Jun 2020 22:39:55: 23000000 INFO @ Fri, 26 Jun 2020 22:40:01: 24000000 INFO @ Fri, 26 Jun 2020 22:40:07: 25000000 INFO @ Fri, 26 Jun 2020 22:40:13: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:40:13: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:40:13: #1 total tags in treatment: 25917201 INFO @ Fri, 26 Jun 2020 22:40:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:40:13: #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 22:40:14: #1 tags after filtering in treatment: 25917201 INFO @ Fri, 26 Jun 2020 22:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:40:14: #1 finished! INFO @ Fri, 26 Jun 2020 22:40:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:40:15: #2 number of paired peaks: 123 WARNING @ Fri, 26 Jun 2020 22:40:15: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Fri, 26 Jun 2020 22:40:15: start model_add_line... BigWig に変換しました。 /var/spool/uge/at160/job_scripts/6507974: line 274: 35014 Terminated MACS $i /var/spool/uge/at160/job_scripts/6507974: line 274: 35334 Terminated MACS $i /var/spool/uge/at160/job_scripts/6507974: line 274: 38014 Terminated MACS $i ls: cannot access SRX514730.05.bed: No such file or directory mv: cannot stat ‘SRX514730.05.bed’: No such file or directory mv: cannot stat ‘SRX514730.05.bb’: No such file or directory ls: cannot access SRX514730.10.bed: No such file or directory mv: cannot stat ‘SRX514730.10.bed’: No such file or directory mv: cannot stat ‘SRX514730.10.bb’: No such file or directory ls: cannot access SRX514730.20.bed: No such file or directory mv: cannot stat ‘SRX514730.20.bed’: No such file or directory mv: cannot stat ‘SRX514730.20.bb’: No such file or directory INFO @ Fri, 26 Jun 2020 22:40:15: start X-correlation... INFO @ Fri, 26 Jun 2020 22:40:15: end of X-cor INFO @ Fri, 26 Jun 2020 22:40:15: #2 finished! INFO @ Fri, 26 Jun 2020 22:40:15: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:40:15: #2 alternative fragment length(s) may be 0,38,132,293,306,419,482,503,593 bps INFO @ Fri, 26 Jun 2020 22:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514730/SRX514730.20_model.r WARNING @ Fri, 26 Jun 2020 22:40:15: #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 22:40:15: #2 You may need to consider one of the other alternative d(s): 0,38,132,293,306,419,482,503,593 WARNING @ Fri, 26 Jun 2020 22:40:15: #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 22:40:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:40:15: #3 Pre-compute pvalue-qvalue table...