Job ID = 6368160 SRX = SRX494844 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:03:15 prefetch.2.10.7: 1) Downloading 'SRR1198376'... 2020-06-16T00:03:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:35 prefetch.2.10.7: 1) 'SRR1198376' was downloaded successfully Read 30788149 spots for SRR1198376/SRR1198376.sra Written 30788149 spots for SRR1198376/SRR1198376.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: 00:05:50 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169817 (0.55%) aligned 0 times 25275410 (82.09%) aligned exactly 1 time 5342922 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 4711369 / 30618332 = 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 @ Tue, 16 Jun 2020 09:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.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 09:19:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:36: 1000000 INFO @ Tue, 16 Jun 2020 09:19:42: 2000000 INFO @ Tue, 16 Jun 2020 09:19:47: 3000000 INFO @ Tue, 16 Jun 2020 09:19:53: 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 09:19:59: 5000000 INFO @ Tue, 16 Jun 2020 09:20:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.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 09:20:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:05: 1000000 INFO @ Tue, 16 Jun 2020 09:20:06: 6000000 INFO @ Tue, 16 Jun 2020 09:20:11: 2000000 INFO @ Tue, 16 Jun 2020 09:20:12: 7000000 INFO @ Tue, 16 Jun 2020 09:20:17: 3000000 INFO @ Tue, 16 Jun 2020 09:20:18: 8000000 INFO @ Tue, 16 Jun 2020 09:20:23: 4000000 INFO @ Tue, 16 Jun 2020 09:20:24: 9000000 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 09:20:29: 5000000 INFO @ Tue, 16 Jun 2020 09:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.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 09:20:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:30: 10000000 INFO @ Tue, 16 Jun 2020 09:20:35: 6000000 INFO @ Tue, 16 Jun 2020 09:20:36: 1000000 INFO @ Tue, 16 Jun 2020 09:20:36: 11000000 INFO @ Tue, 16 Jun 2020 09:20:41: 7000000 INFO @ Tue, 16 Jun 2020 09:20:42: 2000000 INFO @ Tue, 16 Jun 2020 09:20:43: 12000000 INFO @ Tue, 16 Jun 2020 09:20:47: 8000000 INFO @ Tue, 16 Jun 2020 09:20:47: 3000000 INFO @ Tue, 16 Jun 2020 09:20:49: 13000000 INFO @ Tue, 16 Jun 2020 09:20:52: 9000000 INFO @ Tue, 16 Jun 2020 09:20:53: 4000000 INFO @ Tue, 16 Jun 2020 09:20:55: 14000000 INFO @ Tue, 16 Jun 2020 09:20:58: 10000000 INFO @ Tue, 16 Jun 2020 09:20:59: 5000000 INFO @ Tue, 16 Jun 2020 09:21:01: 15000000 INFO @ Tue, 16 Jun 2020 09:21:04: 11000000 INFO @ Tue, 16 Jun 2020 09:21:05: 6000000 INFO @ Tue, 16 Jun 2020 09:21:08: 16000000 INFO @ Tue, 16 Jun 2020 09:21:10: 12000000 INFO @ Tue, 16 Jun 2020 09:21:11: 7000000 INFO @ Tue, 16 Jun 2020 09:21:14: 17000000 INFO @ Tue, 16 Jun 2020 09:21:16: 13000000 INFO @ Tue, 16 Jun 2020 09:21:17: 8000000 INFO @ Tue, 16 Jun 2020 09:21:20: 18000000 INFO @ Tue, 16 Jun 2020 09:21:22: 14000000 INFO @ Tue, 16 Jun 2020 09:21:23: 9000000 INFO @ Tue, 16 Jun 2020 09:21:27: 19000000 INFO @ Tue, 16 Jun 2020 09:21:28: 15000000 INFO @ Tue, 16 Jun 2020 09:21:29: 10000000 INFO @ Tue, 16 Jun 2020 09:21:33: 20000000 INFO @ Tue, 16 Jun 2020 09:21:34: 16000000 INFO @ Tue, 16 Jun 2020 09:21:35: 11000000 INFO @ Tue, 16 Jun 2020 09:21:40: 21000000 INFO @ Tue, 16 Jun 2020 09:21:40: 17000000 INFO @ Tue, 16 Jun 2020 09:21:41: 12000000 INFO @ Tue, 16 Jun 2020 09:21:46: 18000000 INFO @ Tue, 16 Jun 2020 09:21:46: 22000000 INFO @ Tue, 16 Jun 2020 09:21:47: 13000000 INFO @ Tue, 16 Jun 2020 09:21:52: 19000000 INFO @ Tue, 16 Jun 2020 09:21:53: 14000000 INFO @ Tue, 16 Jun 2020 09:21:53: 23000000 INFO @ Tue, 16 Jun 2020 09:21:58: 20000000 INFO @ Tue, 16 Jun 2020 09:21:59: 15000000 INFO @ Tue, 16 Jun 2020 09:22:00: 24000000 INFO @ Tue, 16 Jun 2020 09:22:04: 21000000 INFO @ Tue, 16 Jun 2020 09:22:05: 16000000 INFO @ Tue, 16 Jun 2020 09:22:06: 25000000 INFO @ Tue, 16 Jun 2020 09:22:10: 22000000 INFO @ Tue, 16 Jun 2020 09:22:11: 17000000 INFO @ Tue, 16 Jun 2020 09:22:13: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:22:13: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:22:13: #1 total tags in treatment: 25906963 INFO @ Tue, 16 Jun 2020 09:22:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:13: #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 09:22:13: #1 tags after filtering in treatment: 25906963 INFO @ Tue, 16 Jun 2020 09:22:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:15: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 09:22:15: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:15: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:22:15: #2 alternative fragment length(s) may be 0,24,297,510,554,568 bps INFO @ Tue, 16 Jun 2020 09:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.05_model.r WARNING @ Tue, 16 Jun 2020 09:22:15: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:15: #2 You may need to consider one of the other alternative d(s): 0,24,297,510,554,568 WARNING @ Tue, 16 Jun 2020 09:22:15: #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 09:22:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:16: 23000000 INFO @ Tue, 16 Jun 2020 09:22:17: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:22:22: 24000000 INFO @ Tue, 16 Jun 2020 09:22:22: 19000000 INFO @ Tue, 16 Jun 2020 09:22:28: 25000000 INFO @ Tue, 16 Jun 2020 09:22:28: 20000000 INFO @ Tue, 16 Jun 2020 09:22:33: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:22:33: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:22:33: #1 total tags in treatment: 25906963 INFO @ Tue, 16 Jun 2020 09:22:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:33: #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 09:22:34: #1 tags after filtering in treatment: 25906963 INFO @ Tue, 16 Jun 2020 09:22:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:34: 21000000 INFO @ Tue, 16 Jun 2020 09:22:36: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 09:22:36: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:36: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:22:36: #2 alternative fragment length(s) may be 0,24,297,510,554,568 bps INFO @ Tue, 16 Jun 2020 09:22:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.10_model.r WARNING @ Tue, 16 Jun 2020 09:22:36: #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 09:22:36: #2 You may need to consider one of the other alternative d(s): 0,24,297,510,554,568 WARNING @ Tue, 16 Jun 2020 09:22:36: #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 09:22:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:40: 22000000 INFO @ Tue, 16 Jun 2020 09:22:45: 23000000 INFO @ Tue, 16 Jun 2020 09:22:51: 24000000 INFO @ Tue, 16 Jun 2020 09:22:56: 25000000 INFO @ Tue, 16 Jun 2020 09:23:01: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:23:01: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:23:01: #1 total tags in treatment: 25906963 INFO @ Tue, 16 Jun 2020 09:23:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:01: #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 09:23:02: #1 tags after filtering in treatment: 25906963 INFO @ Tue, 16 Jun 2020 09:23:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:04: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 09:23:04: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:04: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:23:04: #2 alternative fragment length(s) may be 0,24,297,510,554,568 bps INFO @ Tue, 16 Jun 2020 09:23:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494844/SRX494844.20_model.r WARNING @ Tue, 16 Jun 2020 09:23:04: #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 09:23:04: #2 You may need to consider one of the other alternative d(s): 0,24,297,510,554,568 WARNING @ Tue, 16 Jun 2020 09:23:04: #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 09:23:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at149/job_scripts/6368160: line 271: 56526 Terminated MACS $i /var/spool/uge/at149/job_scripts/6368160: line 271: 58143 Terminated MACS $i /var/spool/uge/at149/job_scripts/6368160: line 271: 58767 Terminated MACS $i ls: cannot access SRX494844.05.bed: No such file or directory mv: cannot stat ‘SRX494844.05.bed’: No such file or directory mv: cannot stat ‘SRX494844.05.bb’: No such file or directory ls: cannot access SRX494844.10.bed: No such file or directory mv: cannot stat ‘SRX494844.10.bed’: No such file or directory mv: cannot stat ‘SRX494844.10.bb’: No such file or directory ls: cannot access SRX494844.20.bed: No such file or directory mv: cannot stat ‘SRX494844.20.bed’: No such file or directory mv: cannot stat ‘SRX494844.20.bb’: No such file or directory