Job ID = 6507958 SRX = SRX495117 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:45:16 prefetch.2.10.7: 1) Downloading 'SRR1198649'... 2020-06-26T13:45:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:47:08 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:47:08 prefetch.2.10.7: 1) 'SRR1198649' was downloaded successfully Read 30788149 spots for SRR1198649/SRR1198649.sra Written 30788149 spots for SRR1198649/SRR1198649.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: 00:06:36 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169821 (0.55%) aligned 0 times 25275311 (82.09%) aligned exactly 1 time 5343017 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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 8 files... [bam_rmdupse_core] 4710966 / 30618328 = 0.1539 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 23:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.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 23:02:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:02:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:02:23: 1000000 INFO @ Fri, 26 Jun 2020 23:02:29: 2000000 INFO @ Fri, 26 Jun 2020 23:02:34: 3000000 INFO @ Fri, 26 Jun 2020 23:02:40: 4000000 INFO @ Fri, 26 Jun 2020 23:02:45: 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 23:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.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 23:02:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:02:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:02:51: 6000000 INFO @ Fri, 26 Jun 2020 23:02:53: 1000000 INFO @ Fri, 26 Jun 2020 23:02:57: 7000000 INFO @ Fri, 26 Jun 2020 23:02:59: 2000000 INFO @ Fri, 26 Jun 2020 23:03:03: 8000000 INFO @ Fri, 26 Jun 2020 23:03:05: 3000000 INFO @ Fri, 26 Jun 2020 23:03:09: 9000000 INFO @ Fri, 26 Jun 2020 23:03:11: 4000000 INFO @ Fri, 26 Jun 2020 23:03:15: 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 23:03:17: 5000000 INFO @ Fri, 26 Jun 2020 23:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.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 23:03:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:03:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:03:21: 11000000 INFO @ Fri, 26 Jun 2020 23:03:23: 6000000 INFO @ Fri, 26 Jun 2020 23:03:24: 1000000 INFO @ Fri, 26 Jun 2020 23:03:27: 12000000 INFO @ Fri, 26 Jun 2020 23:03:29: 7000000 INFO @ Fri, 26 Jun 2020 23:03:29: 2000000 INFO @ Fri, 26 Jun 2020 23:03:33: 13000000 INFO @ Fri, 26 Jun 2020 23:03:35: 8000000 INFO @ Fri, 26 Jun 2020 23:03:35: 3000000 INFO @ Fri, 26 Jun 2020 23:03:39: 14000000 INFO @ Fri, 26 Jun 2020 23:03:40: 9000000 INFO @ Fri, 26 Jun 2020 23:03:41: 4000000 INFO @ Fri, 26 Jun 2020 23:03:44: 15000000 INFO @ Fri, 26 Jun 2020 23:03:46: 10000000 INFO @ Fri, 26 Jun 2020 23:03:47: 5000000 INFO @ Fri, 26 Jun 2020 23:03:50: 16000000 INFO @ Fri, 26 Jun 2020 23:03:52: 11000000 INFO @ Fri, 26 Jun 2020 23:03:53: 6000000 INFO @ Fri, 26 Jun 2020 23:03:56: 17000000 INFO @ Fri, 26 Jun 2020 23:03:58: 12000000 INFO @ Fri, 26 Jun 2020 23:03:58: 7000000 INFO @ Fri, 26 Jun 2020 23:04:02: 18000000 INFO @ Fri, 26 Jun 2020 23:04:03: 13000000 INFO @ Fri, 26 Jun 2020 23:04:04: 8000000 INFO @ Fri, 26 Jun 2020 23:04:08: 19000000 INFO @ Fri, 26 Jun 2020 23:04:09: 14000000 INFO @ Fri, 26 Jun 2020 23:04:10: 9000000 INFO @ Fri, 26 Jun 2020 23:04:13: 20000000 INFO @ Fri, 26 Jun 2020 23:04:15: 15000000 INFO @ Fri, 26 Jun 2020 23:04:16: 10000000 INFO @ Fri, 26 Jun 2020 23:04:19: 21000000 INFO @ Fri, 26 Jun 2020 23:04:20: 16000000 INFO @ Fri, 26 Jun 2020 23:04:22: 11000000 INFO @ Fri, 26 Jun 2020 23:04:25: 22000000 INFO @ Fri, 26 Jun 2020 23:04:26: 17000000 INFO @ Fri, 26 Jun 2020 23:04:27: 12000000 INFO @ Fri, 26 Jun 2020 23:04:31: 23000000 INFO @ Fri, 26 Jun 2020 23:04:32: 18000000 INFO @ Fri, 26 Jun 2020 23:04:33: 13000000 INFO @ Fri, 26 Jun 2020 23:04:36: 24000000 INFO @ Fri, 26 Jun 2020 23:04:38: 19000000 INFO @ Fri, 26 Jun 2020 23:04:39: 14000000 INFO @ Fri, 26 Jun 2020 23:04:42: 25000000 INFO @ Fri, 26 Jun 2020 23:04:44: 20000000 INFO @ Fri, 26 Jun 2020 23:04:45: 15000000 INFO @ Fri, 26 Jun 2020 23:04:47: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:04:47: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:04:47: #1 total tags in treatment: 25907362 INFO @ Fri, 26 Jun 2020 23:04:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:04:47: #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 23:04:48: #1 tags after filtering in treatment: 25907362 INFO @ Fri, 26 Jun 2020 23:04:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:04:48: #1 finished! INFO @ Fri, 26 Jun 2020 23:04:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:04:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:04:49: 21000000 INFO @ Fri, 26 Jun 2020 23:04:49: #2 number of paired peaks: 146 WARNING @ Fri, 26 Jun 2020 23:04:49: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 26 Jun 2020 23:04:49: start model_add_line... INFO @ Fri, 26 Jun 2020 23:04:50: start X-correlation... INFO @ Fri, 26 Jun 2020 23:04:50: end of X-cor INFO @ Fri, 26 Jun 2020 23:04:50: #2 finished! INFO @ Fri, 26 Jun 2020 23:04:50: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 23:04:50: #2 alternative fragment length(s) may be 0,29,498,534,578 bps INFO @ Fri, 26 Jun 2020 23:04:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.05_model.r WARNING @ Fri, 26 Jun 2020 23:04:50: #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 23:04:50: #2 You may need to consider one of the other alternative d(s): 0,29,498,534,578 WARNING @ Fri, 26 Jun 2020 23:04:50: #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 23:04:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:04:50: 16000000 INFO @ Fri, 26 Jun 2020 23:04:55: 22000000 INFO @ Fri, 26 Jun 2020 23:04:56: 17000000 INFO @ Fri, 26 Jun 2020 23:05:01: 23000000 INFO @ Fri, 26 Jun 2020 23:05:02: 18000000 INFO @ Fri, 26 Jun 2020 23:05:06: 24000000 INFO @ Fri, 26 Jun 2020 23:05:07: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:05:12: 25000000 INFO @ Fri, 26 Jun 2020 23:05:13: 20000000 INFO @ Fri, 26 Jun 2020 23:05:17: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:05:17: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:05:17: #1 total tags in treatment: 25907362 INFO @ Fri, 26 Jun 2020 23:05:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:05:17: #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 23:05:18: #1 tags after filtering in treatment: 25907362 INFO @ Fri, 26 Jun 2020 23:05:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:05:18: #1 finished! INFO @ Fri, 26 Jun 2020 23:05:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:05:19: 21000000 INFO @ Fri, 26 Jun 2020 23:05:20: #2 number of paired peaks: 146 WARNING @ Fri, 26 Jun 2020 23:05:20: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 26 Jun 2020 23:05:20: start model_add_line... INFO @ Fri, 26 Jun 2020 23:05:20: start X-correlation... INFO @ Fri, 26 Jun 2020 23:05:20: end of X-cor INFO @ Fri, 26 Jun 2020 23:05:20: #2 finished! INFO @ Fri, 26 Jun 2020 23:05:20: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 23:05:20: #2 alternative fragment length(s) may be 0,29,498,534,578 bps INFO @ Fri, 26 Jun 2020 23:05:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.10_model.r WARNING @ Fri, 26 Jun 2020 23:05:20: #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 23:05:20: #2 You may need to consider one of the other alternative d(s): 0,29,498,534,578 WARNING @ Fri, 26 Jun 2020 23:05:20: #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 23:05:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:05:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:05:24: 22000000 INFO @ Fri, 26 Jun 2020 23:05:30: 23000000 INFO @ Fri, 26 Jun 2020 23:05:35: 24000000 INFO @ Fri, 26 Jun 2020 23:05:40: 25000000 INFO @ Fri, 26 Jun 2020 23:05:45: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:05:45: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:05:45: #1 total tags in treatment: 25907362 INFO @ Fri, 26 Jun 2020 23:05:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:05:45: #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 23:05:45: #1 tags after filtering in treatment: 25907362 INFO @ Fri, 26 Jun 2020 23:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:05:45: #1 finished! INFO @ Fri, 26 Jun 2020 23:05:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:05:47: #2 number of paired peaks: 146 WARNING @ Fri, 26 Jun 2020 23:05:47: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 26 Jun 2020 23:05:47: start model_add_line... INFO @ Fri, 26 Jun 2020 23:05:47: start X-correlation... INFO @ Fri, 26 Jun 2020 23:05:47: end of X-cor INFO @ Fri, 26 Jun 2020 23:05:47: #2 finished! INFO @ Fri, 26 Jun 2020 23:05:47: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 23:05:47: #2 alternative fragment length(s) may be 0,29,498,534,578 bps INFO @ Fri, 26 Jun 2020 23:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495117/SRX495117.20_model.r WARNING @ Fri, 26 Jun 2020 23:05:47: #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 23:05:47: #2 You may need to consider one of the other alternative d(s): 0,29,498,534,578 WARNING @ Fri, 26 Jun 2020 23:05:47: #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 23:05:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:05:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at150/job_scripts/6507958: line 274: 130462 Terminated MACS $i /var/spool/uge/at150/job_scripts/6507958: line 274: 130649 Terminated MACS $i /var/spool/uge/at150/job_scripts/6507958: line 274: 130844 Terminated MACS $i ls: cannot access SRX495117.05.bed: No such file or directory mv: cannot stat ‘SRX495117.05.bed’: No such file or directory mv: cannot stat ‘SRX495117.05.bb’: No such file or directory ls: cannot access SRX495117.10.bed: No such file or directory mv: cannot stat ‘SRX495117.10.bed’: No such file or directory mv: cannot stat ‘SRX495117.10.bb’: No such file or directory ls: cannot access SRX495117.20.bed: No such file or directory mv: cannot stat ‘SRX495117.20.bed’: No such file or directory mv: cannot stat ‘SRX495117.20.bb’: No such file or directory