Job ID = 6507959 SRX = SRX495118 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:10:27 prefetch.2.10.7: 1) Downloading 'SRR1198650'... 2020-06-26T14:10:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:16:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:16:23 prefetch.2.10.7: 1) 'SRR1198650' was downloaded successfully Read 32932978 spots for SRR1198650/SRR1198650.sra Written 32932978 spots for SRR1198650/SRR1198650.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: 00:06:16 32932978 reads; of these: 32932978 (100.00%) were unpaired; of these: 432731 (1.31%) aligned 0 times 27125486 (82.37%) aligned exactly 1 time 5374761 (16.32%) aligned >1 times 98.69% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 6590765 / 32500247 = 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 23:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.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 23:31:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:31:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:31:24: 1000000 INFO @ Fri, 26 Jun 2020 23:31:29: 2000000 INFO @ Fri, 26 Jun 2020 23:31:35: 3000000 INFO @ Fri, 26 Jun 2020 23:31:41: 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 @ Fri, 26 Jun 2020 23:31:46: 5000000 INFO @ Fri, 26 Jun 2020 23:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.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 23:31:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:31:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:31:52: 6000000 INFO @ Fri, 26 Jun 2020 23:31:53: 1000000 INFO @ Fri, 26 Jun 2020 23:31:58: 7000000 INFO @ Fri, 26 Jun 2020 23:31:58: 2000000 INFO @ Fri, 26 Jun 2020 23:32:04: 8000000 INFO @ Fri, 26 Jun 2020 23:32:04: 3000000 INFO @ Fri, 26 Jun 2020 23:32:09: 4000000 INFO @ Fri, 26 Jun 2020 23:32:10: 9000000 INFO @ Fri, 26 Jun 2020 23:32:15: 5000000 INFO @ Fri, 26 Jun 2020 23:32:16: 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 23:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.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 23:32:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:32:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:32:20: 6000000 INFO @ Fri, 26 Jun 2020 23:32:21: 11000000 INFO @ Fri, 26 Jun 2020 23:32:24: 1000000 INFO @ Fri, 26 Jun 2020 23:32:25: 7000000 INFO @ Fri, 26 Jun 2020 23:32:27: 12000000 INFO @ Fri, 26 Jun 2020 23:32:30: 2000000 INFO @ Fri, 26 Jun 2020 23:32:31: 8000000 INFO @ Fri, 26 Jun 2020 23:32:34: 13000000 INFO @ Fri, 26 Jun 2020 23:32:36: 3000000 INFO @ Fri, 26 Jun 2020 23:32:36: 9000000 INFO @ Fri, 26 Jun 2020 23:32:40: 14000000 INFO @ Fri, 26 Jun 2020 23:32:42: 10000000 INFO @ Fri, 26 Jun 2020 23:32:42: 4000000 INFO @ Fri, 26 Jun 2020 23:32:46: 15000000 INFO @ Fri, 26 Jun 2020 23:32:47: 11000000 INFO @ Fri, 26 Jun 2020 23:32:48: 5000000 INFO @ Fri, 26 Jun 2020 23:32:51: 16000000 INFO @ Fri, 26 Jun 2020 23:32:53: 12000000 INFO @ Fri, 26 Jun 2020 23:32:54: 6000000 INFO @ Fri, 26 Jun 2020 23:32:57: 17000000 INFO @ Fri, 26 Jun 2020 23:32:58: 13000000 INFO @ Fri, 26 Jun 2020 23:33:00: 7000000 INFO @ Fri, 26 Jun 2020 23:33:03: 18000000 INFO @ Fri, 26 Jun 2020 23:33:04: 14000000 INFO @ Fri, 26 Jun 2020 23:33:07: 8000000 INFO @ Fri, 26 Jun 2020 23:33:09: 15000000 INFO @ Fri, 26 Jun 2020 23:33:09: 19000000 INFO @ Fri, 26 Jun 2020 23:33:13: 9000000 INFO @ Fri, 26 Jun 2020 23:33:15: 16000000 INFO @ Fri, 26 Jun 2020 23:33:15: 20000000 INFO @ Fri, 26 Jun 2020 23:33:19: 10000000 INFO @ Fri, 26 Jun 2020 23:33:20: 17000000 INFO @ Fri, 26 Jun 2020 23:33:21: 21000000 INFO @ Fri, 26 Jun 2020 23:33:25: 11000000 INFO @ Fri, 26 Jun 2020 23:33:26: 18000000 INFO @ Fri, 26 Jun 2020 23:33:27: 22000000 INFO @ Fri, 26 Jun 2020 23:33:31: 12000000 INFO @ Fri, 26 Jun 2020 23:33:31: 19000000 INFO @ Fri, 26 Jun 2020 23:33:33: 23000000 INFO @ Fri, 26 Jun 2020 23:33:37: 20000000 INFO @ Fri, 26 Jun 2020 23:33:37: 13000000 INFO @ Fri, 26 Jun 2020 23:33:40: 24000000 INFO @ Fri, 26 Jun 2020 23:33:42: 21000000 INFO @ Fri, 26 Jun 2020 23:33:44: 14000000 INFO @ Fri, 26 Jun 2020 23:33:46: 25000000 INFO @ Fri, 26 Jun 2020 23:33:48: 22000000 INFO @ Fri, 26 Jun 2020 23:33:50: 15000000 INFO @ Fri, 26 Jun 2020 23:33:52: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:33:52: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:33:52: #1 total tags in treatment: 25909482 INFO @ Fri, 26 Jun 2020 23:33:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:33:52: #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 23:33:52: #1 tags after filtering in treatment: 25909482 INFO @ Fri, 26 Jun 2020 23:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:33:52: #1 finished! INFO @ Fri, 26 Jun 2020 23:33:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:33:54: 23000000 INFO @ Fri, 26 Jun 2020 23:33:54: #2 number of paired peaks: 134 WARNING @ Fri, 26 Jun 2020 23:33:54: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 26 Jun 2020 23:33:54: start model_add_line... INFO @ Fri, 26 Jun 2020 23:33:54: start X-correlation... INFO @ Fri, 26 Jun 2020 23:33:54: end of X-cor INFO @ Fri, 26 Jun 2020 23:33:54: #2 finished! INFO @ Fri, 26 Jun 2020 23:33:54: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 23:33:54: #2 alternative fragment length(s) may be 0,15,36,121,252,343,392,492,496,592 bps INFO @ Fri, 26 Jun 2020 23:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.05_model.r WARNING @ Fri, 26 Jun 2020 23:33:54: #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 23:33:54: #2 You may need to consider one of the other alternative d(s): 0,15,36,121,252,343,392,492,496,592 WARNING @ Fri, 26 Jun 2020 23:33:54: #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 23:33:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:33:56: 16000000 INFO @ Fri, 26 Jun 2020 23:33:59: 24000000 INFO @ Fri, 26 Jun 2020 23:34:02: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:34:05: 25000000 INFO @ Fri, 26 Jun 2020 23:34:08: 18000000 INFO @ Fri, 26 Jun 2020 23:34:10: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:34:10: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:34:10: #1 total tags in treatment: 25909482 INFO @ Fri, 26 Jun 2020 23:34:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:34:10: #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 23:34:11: #1 tags after filtering in treatment: 25909482 INFO @ Fri, 26 Jun 2020 23:34:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:34:11: #1 finished! INFO @ Fri, 26 Jun 2020 23:34:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:34:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:34:12: #2 number of paired peaks: 134 WARNING @ Fri, 26 Jun 2020 23:34:12: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 26 Jun 2020 23:34:12: start model_add_line... INFO @ Fri, 26 Jun 2020 23:34:12: start X-correlation... INFO @ Fri, 26 Jun 2020 23:34:12: end of X-cor INFO @ Fri, 26 Jun 2020 23:34:12: #2 finished! INFO @ Fri, 26 Jun 2020 23:34:12: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 23:34:12: #2 alternative fragment length(s) may be 0,15,36,121,252,343,392,492,496,592 bps INFO @ Fri, 26 Jun 2020 23:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.10_model.r WARNING @ Fri, 26 Jun 2020 23:34:12: #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 23:34:12: #2 You may need to consider one of the other alternative d(s): 0,15,36,121,252,343,392,492,496,592 WARNING @ Fri, 26 Jun 2020 23:34:12: #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 23:34:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:34:14: 19000000 INFO @ Fri, 26 Jun 2020 23:34:20: 20000000 INFO @ Fri, 26 Jun 2020 23:34:25: 21000000 INFO @ Fri, 26 Jun 2020 23:34:31: 22000000 INFO @ Fri, 26 Jun 2020 23:34:37: 23000000 INFO @ Fri, 26 Jun 2020 23:34:43: 24000000 INFO @ Fri, 26 Jun 2020 23:34:49: 25000000 INFO @ Fri, 26 Jun 2020 23:34:54: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:34:54: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:34:54: #1 total tags in treatment: 25909482 INFO @ Fri, 26 Jun 2020 23:34:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:34:54: #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 23:34:54: #1 tags after filtering in treatment: 25909482 INFO @ Fri, 26 Jun 2020 23:34:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:34:54: #1 finished! INFO @ Fri, 26 Jun 2020 23:34:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:34:56: #2 number of paired peaks: 134 WARNING @ Fri, 26 Jun 2020 23:34:56: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 26 Jun 2020 23:34:56: start model_add_line... INFO @ Fri, 26 Jun 2020 23:34:56: start X-correlation... INFO @ Fri, 26 Jun 2020 23:34:56: end of X-cor INFO @ Fri, 26 Jun 2020 23:34:56: #2 finished! INFO @ Fri, 26 Jun 2020 23:34:56: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 23:34:56: #2 alternative fragment length(s) may be 0,15,36,121,252,343,392,492,496,592 bps INFO @ Fri, 26 Jun 2020 23:34:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495118/SRX495118.20_model.r WARNING @ Fri, 26 Jun 2020 23:34:56: #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 23:34:56: #2 You may need to consider one of the other alternative d(s): 0,15,36,121,252,343,392,492,496,592 WARNING @ Fri, 26 Jun 2020 23:34:56: #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 23:34:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:34:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at146/job_scripts/6507959: line 274: 56652 Terminated MACS $i /var/spool/uge/at146/job_scripts/6507959: line 274: 85482 Terminated MACS $i /var/spool/uge/at146/job_scripts/6507959: line 274: 106563 Terminated MACS $i ls: cannot access SRX495118.05.bed: No such file or directory mv: cannot stat ‘SRX495118.05.bed’: No such file or directory mv: cannot stat ‘SRX495118.05.bb’: No such file or directory ls: cannot access SRX495118.10.bed: No such file or directory mv: cannot stat ‘SRX495118.10.bed’: No such file or directory mv: cannot stat ‘SRX495118.10.bb’: No such file or directory ls: cannot access SRX495118.20.bed: No such file or directory mv: cannot stat ‘SRX495118.20.bed’: No such file or directory mv: cannot stat ‘SRX495118.20.bb’: No such file or directory