Job ID = 6366296 SRX = SRX1078720 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:52 prefetch.2.10.7: 1) Downloading 'SRR2084327'... 2020-06-15T22:48:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:52:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:52:42 prefetch.2.10.7: 1) 'SRR2084327' was downloaded successfully Read 31268796 spots for SRR2084327/SRR2084327.sra Written 31268796 spots for SRR2084327/SRR2084327.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: 00:07:25 31268796 reads; of these: 31268796 (100.00%) were unpaired; of these: 358359 (1.15%) aligned 0 times 26000144 (83.15%) aligned exactly 1 time 4910293 (15.70%) aligned >1 times 98.85% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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_sort_core] merging from 16 files... [bam_rmdupse_core] 4887846 / 30910437 = 0.1581 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 08:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.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 08:09:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:43: 1000000 INFO @ Tue, 16 Jun 2020 08:09:49: 2000000 INFO @ Tue, 16 Jun 2020 08:09:55: 3000000 INFO @ Tue, 16 Jun 2020 08:10:01: 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 08:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.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 08:10:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:07: 5000000 INFO @ Tue, 16 Jun 2020 08:10:14: 6000000 INFO @ Tue, 16 Jun 2020 08:10:14: 1000000 INFO @ Tue, 16 Jun 2020 08:10:21: 7000000 INFO @ Tue, 16 Jun 2020 08:10:21: 2000000 INFO @ Tue, 16 Jun 2020 08:10:28: 8000000 INFO @ Tue, 16 Jun 2020 08:10:29: 3000000 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 08:10:36: 9000000 INFO @ Tue, 16 Jun 2020 08:10:36: 4000000 INFO @ Tue, 16 Jun 2020 08:10:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.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 08:10:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:43: 10000000 INFO @ Tue, 16 Jun 2020 08:10:44: 5000000 INFO @ Tue, 16 Jun 2020 08:10:44: 1000000 INFO @ Tue, 16 Jun 2020 08:10:50: 11000000 INFO @ Tue, 16 Jun 2020 08:10:51: 2000000 INFO @ Tue, 16 Jun 2020 08:10:51: 6000000 INFO @ Tue, 16 Jun 2020 08:10:57: 12000000 INFO @ Tue, 16 Jun 2020 08:10:58: 3000000 INFO @ Tue, 16 Jun 2020 08:10:59: 7000000 INFO @ Tue, 16 Jun 2020 08:11:04: 13000000 INFO @ Tue, 16 Jun 2020 08:11:05: 4000000 INFO @ Tue, 16 Jun 2020 08:11:07: 8000000 INFO @ Tue, 16 Jun 2020 08:11:11: 14000000 INFO @ Tue, 16 Jun 2020 08:11:12: 5000000 INFO @ Tue, 16 Jun 2020 08:11:14: 9000000 INFO @ Tue, 16 Jun 2020 08:11:19: 15000000 INFO @ Tue, 16 Jun 2020 08:11:19: 6000000 INFO @ Tue, 16 Jun 2020 08:11:22: 10000000 INFO @ Tue, 16 Jun 2020 08:11:26: 16000000 INFO @ Tue, 16 Jun 2020 08:11:26: 7000000 INFO @ Tue, 16 Jun 2020 08:11:29: 11000000 INFO @ Tue, 16 Jun 2020 08:11:33: 17000000 INFO @ Tue, 16 Jun 2020 08:11:33: 8000000 INFO @ Tue, 16 Jun 2020 08:11:37: 12000000 INFO @ Tue, 16 Jun 2020 08:11:40: 9000000 INFO @ Tue, 16 Jun 2020 08:11:40: 18000000 INFO @ Tue, 16 Jun 2020 08:11:44: 13000000 INFO @ Tue, 16 Jun 2020 08:11:47: 10000000 INFO @ Tue, 16 Jun 2020 08:11:47: 19000000 INFO @ Tue, 16 Jun 2020 08:11:52: 14000000 INFO @ Tue, 16 Jun 2020 08:11:54: 11000000 INFO @ Tue, 16 Jun 2020 08:11:54: 20000000 INFO @ Tue, 16 Jun 2020 08:12:00: 15000000 INFO @ Tue, 16 Jun 2020 08:12:01: 12000000 INFO @ Tue, 16 Jun 2020 08:12:01: 21000000 INFO @ Tue, 16 Jun 2020 08:12:07: 16000000 INFO @ Tue, 16 Jun 2020 08:12:08: 13000000 INFO @ Tue, 16 Jun 2020 08:12:08: 22000000 INFO @ Tue, 16 Jun 2020 08:12:15: 14000000 INFO @ Tue, 16 Jun 2020 08:12:15: 17000000 INFO @ Tue, 16 Jun 2020 08:12:15: 23000000 INFO @ Tue, 16 Jun 2020 08:12:22: 15000000 INFO @ Tue, 16 Jun 2020 08:12:22: 24000000 INFO @ Tue, 16 Jun 2020 08:12:23: 18000000 INFO @ Tue, 16 Jun 2020 08:12:29: 16000000 INFO @ Tue, 16 Jun 2020 08:12:30: 25000000 INFO @ Tue, 16 Jun 2020 08:12:30: 19000000 INFO @ Tue, 16 Jun 2020 08:12:36: 17000000 INFO @ Tue, 16 Jun 2020 08:12:37: 26000000 INFO @ Tue, 16 Jun 2020 08:12:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:37: #1 total tags in treatment: 26022591 INFO @ Tue, 16 Jun 2020 08:12:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:37: #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 08:12:38: #1 tags after filtering in treatment: 26022591 INFO @ Tue, 16 Jun 2020 08:12:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:38: 20000000 INFO @ Tue, 16 Jun 2020 08:12:39: #2 number of paired peaks: 114 WARNING @ Tue, 16 Jun 2020 08:12:39: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:39: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:12:39: #2 alternative fragment length(s) may be 0,22,47,124,270,430,493,543,572 bps INFO @ Tue, 16 Jun 2020 08:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.05_model.r WARNING @ Tue, 16 Jun 2020 08:12:39: #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 08:12:39: #2 You may need to consider one of the other alternative d(s): 0,22,47,124,270,430,493,543,572 WARNING @ Tue, 16 Jun 2020 08:12:39: #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 08:12:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:43: 18000000 INFO @ Tue, 16 Jun 2020 08:12:45: 21000000 INFO @ Tue, 16 Jun 2020 08:12:50: 19000000 INFO @ Tue, 16 Jun 2020 08:12:53: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:12:57: 20000000 INFO @ Tue, 16 Jun 2020 08:13:00: 23000000 INFO @ Tue, 16 Jun 2020 08:13:04: 21000000 INFO @ Tue, 16 Jun 2020 08:13:08: 24000000 INFO @ Tue, 16 Jun 2020 08:13:11: 22000000 INFO @ Tue, 16 Jun 2020 08:13:15: 25000000 INFO @ Tue, 16 Jun 2020 08:13:18: 23000000 INFO @ Tue, 16 Jun 2020 08:13:22: 26000000 INFO @ Tue, 16 Jun 2020 08:13:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:23: #1 total tags in treatment: 26022591 INFO @ Tue, 16 Jun 2020 08:13:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:23: #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 08:13:23: #1 tags after filtering in treatment: 26022591 INFO @ Tue, 16 Jun 2020 08:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:25: #2 number of paired peaks: 114 WARNING @ Tue, 16 Jun 2020 08:13:25: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:25: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:13:25: #2 alternative fragment length(s) may be 0,22,47,124,270,430,493,543,572 bps INFO @ Tue, 16 Jun 2020 08:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.10_model.r WARNING @ Tue, 16 Jun 2020 08:13:25: #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 08:13:25: #2 You may need to consider one of the other alternative d(s): 0,22,47,124,270,430,493,543,572 WARNING @ Tue, 16 Jun 2020 08:13:25: #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 08:13:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:25: 24000000 INFO @ Tue, 16 Jun 2020 08:13:32: 25000000 INFO @ Tue, 16 Jun 2020 08:13:38: 26000000 INFO @ Tue, 16 Jun 2020 08:13:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:39: #1 total tags in treatment: 26022591 INFO @ Tue, 16 Jun 2020 08:13:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:39: #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 08:13:39: #1 tags after filtering in treatment: 26022591 INFO @ Tue, 16 Jun 2020 08:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:41: #2 number of paired peaks: 114 WARNING @ Tue, 16 Jun 2020 08:13:41: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:41: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:13:41: #2 alternative fragment length(s) may be 0,22,47,124,270,430,493,543,572 bps INFO @ Tue, 16 Jun 2020 08:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078720/SRX1078720.20_model.r WARNING @ Tue, 16 Jun 2020 08:13:41: #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 08:13:41: #2 You may need to consider one of the other alternative d(s): 0,22,47,124,270,430,493,543,572 WARNING @ Tue, 16 Jun 2020 08:13:41: #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 08:13:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at147/job_scripts/6366296: line 271: 63118 Terminated MACS $i /var/spool/uge/at147/job_scripts/6366296: line 271: 83549 Terminated MACS $i /var/spool/uge/at147/job_scripts/6366296: line 271: 97773 Terminated MACS $i ls: cannot access SRX1078720.05.bed: No such file or directory mv: cannot stat ‘SRX1078720.05.bed’: No such file or directory mv: cannot stat ‘SRX1078720.05.bb’: No such file or directory ls: cannot access SRX1078720.10.bed: No such file or directory mv: cannot stat ‘SRX1078720.10.bed’: No such file or directory mv: cannot stat ‘SRX1078720.10.bb’: No such file or directory ls: cannot access SRX1078720.20.bed: No such file or directory mv: cannot stat ‘SRX1078720.20.bed’: No such file or directory mv: cannot stat ‘SRX1078720.20.bb’: No such file or directory