Job ID = 6507954 SRX = SRX495114 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:30:58 prefetch.2.10.7: 1) Downloading 'SRR1198646'... 2020-06-26T13:30:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:35:04 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:35:04 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: 00:00:00 Multiseed full-index search: 00:05:38 32932978 reads; of these: 32932978 (100.00%) were unpaired; of these: 432691 (1.31%) aligned 0 times 27125517 (82.37%) aligned exactly 1 time 5374770 (16.32%) aligned >1 times 98.69% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 6591455 / 32500287 = 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 22:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:49:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:49:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:49:21: 1000000 INFO @ Fri, 26 Jun 2020 22:49:27: 2000000 INFO @ Fri, 26 Jun 2020 22:49:32: 3000000 INFO @ Fri, 26 Jun 2020 22:49:37: 4000000 INFO @ Fri, 26 Jun 2020 22:49:43: 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 22:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:49:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:49:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:49:48: 6000000 INFO @ Fri, 26 Jun 2020 22:49:51: 1000000 INFO @ Fri, 26 Jun 2020 22:49:54: 7000000 INFO @ Fri, 26 Jun 2020 22:49:56: 2000000 INFO @ Fri, 26 Jun 2020 22:49:59: 8000000 INFO @ Fri, 26 Jun 2020 22:50:02: 3000000 INFO @ Fri, 26 Jun 2020 22:50:05: 9000000 INFO @ Fri, 26 Jun 2020 22:50:07: 4000000 INFO @ Fri, 26 Jun 2020 22:50:11: 10000000 INFO @ Fri, 26 Jun 2020 22:50:12: 5000000 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 22:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:50:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:50:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:17: 11000000 INFO @ Fri, 26 Jun 2020 22:50:17: 6000000 INFO @ Fri, 26 Jun 2020 22:50:22: 1000000 INFO @ Fri, 26 Jun 2020 22:50:22: 7000000 INFO @ Fri, 26 Jun 2020 22:50:22: 12000000 INFO @ Fri, 26 Jun 2020 22:50:27: 8000000 INFO @ Fri, 26 Jun 2020 22:50:27: 2000000 INFO @ Fri, 26 Jun 2020 22:50:28: 13000000 INFO @ Fri, 26 Jun 2020 22:50:32: 9000000 INFO @ Fri, 26 Jun 2020 22:50:33: 3000000 INFO @ Fri, 26 Jun 2020 22:50:33: 14000000 INFO @ Fri, 26 Jun 2020 22:50:38: 10000000 INFO @ Fri, 26 Jun 2020 22:50:39: 4000000 INFO @ Fri, 26 Jun 2020 22:50:39: 15000000 INFO @ Fri, 26 Jun 2020 22:50:43: 11000000 INFO @ Fri, 26 Jun 2020 22:50:44: 5000000 INFO @ Fri, 26 Jun 2020 22:50:45: 16000000 INFO @ Fri, 26 Jun 2020 22:50:48: 12000000 INFO @ Fri, 26 Jun 2020 22:50:50: 6000000 INFO @ Fri, 26 Jun 2020 22:50:50: 17000000 INFO @ Fri, 26 Jun 2020 22:50:53: 13000000 INFO @ Fri, 26 Jun 2020 22:50:55: 7000000 INFO @ Fri, 26 Jun 2020 22:50:56: 18000000 INFO @ Fri, 26 Jun 2020 22:50:58: 14000000 INFO @ Fri, 26 Jun 2020 22:51:01: 8000000 INFO @ Fri, 26 Jun 2020 22:51:02: 19000000 INFO @ Fri, 26 Jun 2020 22:51:03: 15000000 INFO @ Fri, 26 Jun 2020 22:51:07: 9000000 INFO @ Fri, 26 Jun 2020 22:51:08: 20000000 INFO @ Fri, 26 Jun 2020 22:51:08: 16000000 INFO @ Fri, 26 Jun 2020 22:51:12: 10000000 INFO @ Fri, 26 Jun 2020 22:51:13: 17000000 INFO @ Fri, 26 Jun 2020 22:51:14: 21000000 INFO @ Fri, 26 Jun 2020 22:51:18: 11000000 INFO @ Fri, 26 Jun 2020 22:51:18: 18000000 INFO @ Fri, 26 Jun 2020 22:51:20: 22000000 INFO @ Fri, 26 Jun 2020 22:51:23: 12000000 INFO @ Fri, 26 Jun 2020 22:51:24: 19000000 INFO @ Fri, 26 Jun 2020 22:51:25: 23000000 INFO @ Fri, 26 Jun 2020 22:51:29: 20000000 INFO @ Fri, 26 Jun 2020 22:51:29: 13000000 INFO @ Fri, 26 Jun 2020 22:51:31: 24000000 INFO @ Fri, 26 Jun 2020 22:51:34: 21000000 INFO @ Fri, 26 Jun 2020 22:51:34: 14000000 INFO @ Fri, 26 Jun 2020 22:51:37: 25000000 INFO @ Fri, 26 Jun 2020 22:51:39: 22000000 INFO @ Fri, 26 Jun 2020 22:51:40: 15000000 INFO @ Fri, 26 Jun 2020 22:51:42: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:51:42: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:51:42: #1 total tags in treatment: 25908832 INFO @ Fri, 26 Jun 2020 22:51:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:51:42: #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 22:51:43: #1 tags after filtering in treatment: 25908832 INFO @ Fri, 26 Jun 2020 22:51:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:51:43: #1 finished! INFO @ Fri, 26 Jun 2020 22:51:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:51:44: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 22:51:44: 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 22:51:44: start model_add_line... INFO @ Fri, 26 Jun 2020 22:51:44: start X-correlation... INFO @ Fri, 26 Jun 2020 22:51:44: 23000000 INFO @ Fri, 26 Jun 2020 22:51:44: end of X-cor INFO @ Fri, 26 Jun 2020 22:51:44: #2 finished! INFO @ Fri, 26 Jun 2020 22:51:44: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:51:44: #2 alternative fragment length(s) may be 0,10,15,37,96,156,200,365,415,506,525,560,584 bps INFO @ Fri, 26 Jun 2020 22:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.05_model.r WARNING @ Fri, 26 Jun 2020 22:51:44: #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 22:51:44: #2 You may need to consider one of the other alternative d(s): 0,10,15,37,96,156,200,365,415,506,525,560,584 WARNING @ Fri, 26 Jun 2020 22:51:44: #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 22:51:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:51:46: 16000000 INFO @ Fri, 26 Jun 2020 22:51:50: 24000000 INFO @ Fri, 26 Jun 2020 22:51:51: 17000000 INFO @ Fri, 26 Jun 2020 22:51:55: 25000000 INFO @ Fri, 26 Jun 2020 22:51:57: 18000000 INFO @ Fri, 26 Jun 2020 22:52:00: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:52:00: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:52:00: #1 total tags in treatment: 25908832 INFO @ Fri, 26 Jun 2020 22:52:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:52:00: #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 22:52:00: #1 tags after filtering in treatment: 25908832 INFO @ Fri, 26 Jun 2020 22:52:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:52:00: #1 finished! INFO @ Fri, 26 Jun 2020 22:52:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:52:00: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:52:02: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 22:52:02: 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 22:52:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:52:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:52:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:52:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:52:02: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:52:02: #2 alternative fragment length(s) may be 0,10,15,37,96,156,200,365,415,506,525,560,584 bps INFO @ Fri, 26 Jun 2020 22:52:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.10_model.r WARNING @ Fri, 26 Jun 2020 22:52:02: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:52:02: #2 You may need to consider one of the other alternative d(s): 0,10,15,37,96,156,200,365,415,506,525,560,584 WARNING @ Fri, 26 Jun 2020 22:52:02: #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 22:52:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:52:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:52:03: 19000000 INFO @ Fri, 26 Jun 2020 22:52:08: 20000000 INFO @ Fri, 26 Jun 2020 22:52:14: 21000000 INFO @ Fri, 26 Jun 2020 22:52:19: 22000000 INFO @ Fri, 26 Jun 2020 22:52:25: 23000000 INFO @ Fri, 26 Jun 2020 22:52:31: 24000000 INFO @ Fri, 26 Jun 2020 22:52:36: 25000000 INFO @ Fri, 26 Jun 2020 22:52:41: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:52:41: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:52:41: #1 total tags in treatment: 25908832 INFO @ Fri, 26 Jun 2020 22:52:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:52:41: #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 22:52:41: #1 tags after filtering in treatment: 25908832 INFO @ Fri, 26 Jun 2020 22:52:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:52:41: #1 finished! INFO @ Fri, 26 Jun 2020 22:52:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:52:43: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 22:52:43: 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 22:52:43: start model_add_line... INFO @ Fri, 26 Jun 2020 22:52:43: start X-correlation... INFO @ Fri, 26 Jun 2020 22:52:43: end of X-cor INFO @ Fri, 26 Jun 2020 22:52:43: #2 finished! INFO @ Fri, 26 Jun 2020 22:52:43: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:52:43: #2 alternative fragment length(s) may be 0,10,15,37,96,156,200,365,415,506,525,560,584 bps INFO @ Fri, 26 Jun 2020 22:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495114/SRX495114.20_model.r WARNING @ Fri, 26 Jun 2020 22:52:43: #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 22:52:43: #2 You may need to consider one of the other alternative d(s): 0,10,15,37,96,156,200,365,415,506,525,560,584 WARNING @ Fri, 26 Jun 2020 22:52:43: #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 22:52:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:52:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at154/job_scripts/6507954: line 274: 24200 Terminated MACS $i /var/spool/uge/at154/job_scripts/6507954: line 274: 48524 Terminated MACS $i /var/spool/uge/at154/job_scripts/6507954: line 274: 69911 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