Job ID = 6507841 SRX = SRX494840 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:16:49 prefetch.2.10.7: 1) Downloading 'SRR1198372'... 2020-06-26T13:16:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:19:27 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:19:27 prefetch.2.10.7: 1) 'SRR1198372' was downloaded successfully Read 30788149 spots for SRR1198372/SRR1198372.sra Written 30788149 spots for SRR1198372/SRR1198372.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: 00:05:14 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169808 (0.55%) aligned 0 times 25275432 (82.09%) aligned exactly 1 time 5342909 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 4711367 / 30618341 = 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 22:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.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 22:32:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:32:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:32:46: 1000000 INFO @ Fri, 26 Jun 2020 22:32:53: 2000000 INFO @ Fri, 26 Jun 2020 22:33:00: 3000000 INFO @ Fri, 26 Jun 2020 22:33:06: 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 22:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.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 22:33:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:13: 5000000 INFO @ Fri, 26 Jun 2020 22:33:16: 1000000 INFO @ Fri, 26 Jun 2020 22:33:20: 6000000 INFO @ Fri, 26 Jun 2020 22:33:22: 2000000 INFO @ Fri, 26 Jun 2020 22:33:27: 7000000 INFO @ Fri, 26 Jun 2020 22:33:28: 3000000 INFO @ Fri, 26 Jun 2020 22:33:33: 8000000 INFO @ Fri, 26 Jun 2020 22:33:35: 4000000 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 22:33:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.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 22:33:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:40: 9000000 INFO @ Fri, 26 Jun 2020 22:33:41: 5000000 INFO @ Fri, 26 Jun 2020 22:33:46: 1000000 INFO @ Fri, 26 Jun 2020 22:33:47: 6000000 INFO @ Fri, 26 Jun 2020 22:33:47: 10000000 INFO @ Fri, 26 Jun 2020 22:33:53: 2000000 INFO @ Fri, 26 Jun 2020 22:33:54: 7000000 INFO @ Fri, 26 Jun 2020 22:33:54: 11000000 INFO @ Fri, 26 Jun 2020 22:33:59: 3000000 INFO @ Fri, 26 Jun 2020 22:34:00: 8000000 INFO @ Fri, 26 Jun 2020 22:34:01: 12000000 INFO @ Fri, 26 Jun 2020 22:34:06: 4000000 INFO @ Fri, 26 Jun 2020 22:34:06: 9000000 INFO @ Fri, 26 Jun 2020 22:34:08: 13000000 INFO @ Fri, 26 Jun 2020 22:34:12: 5000000 INFO @ Fri, 26 Jun 2020 22:34:13: 10000000 INFO @ Fri, 26 Jun 2020 22:34:15: 14000000 INFO @ Fri, 26 Jun 2020 22:34:19: 6000000 INFO @ Fri, 26 Jun 2020 22:34:19: 11000000 INFO @ Fri, 26 Jun 2020 22:34:22: 15000000 INFO @ Fri, 26 Jun 2020 22:34:25: 7000000 INFO @ Fri, 26 Jun 2020 22:34:25: 12000000 INFO @ Fri, 26 Jun 2020 22:34:29: 16000000 INFO @ Fri, 26 Jun 2020 22:34:32: 8000000 INFO @ Fri, 26 Jun 2020 22:34:32: 13000000 INFO @ Fri, 26 Jun 2020 22:34:36: 17000000 INFO @ Fri, 26 Jun 2020 22:34:38: 9000000 INFO @ Fri, 26 Jun 2020 22:34:38: 14000000 INFO @ Fri, 26 Jun 2020 22:34:44: 18000000 INFO @ Fri, 26 Jun 2020 22:34:44: 10000000 INFO @ Fri, 26 Jun 2020 22:34:45: 15000000 INFO @ Fri, 26 Jun 2020 22:34:51: 19000000 INFO @ Fri, 26 Jun 2020 22:34:51: 11000000 INFO @ Fri, 26 Jun 2020 22:34:51: 16000000 INFO @ Fri, 26 Jun 2020 22:34:57: 12000000 INFO @ Fri, 26 Jun 2020 22:34:57: 17000000 INFO @ Fri, 26 Jun 2020 22:34:58: 20000000 INFO @ Fri, 26 Jun 2020 22:35:04: 13000000 INFO @ Fri, 26 Jun 2020 22:35:04: 18000000 INFO @ Fri, 26 Jun 2020 22:35:05: 21000000 INFO @ Fri, 26 Jun 2020 22:35:10: 14000000 INFO @ Fri, 26 Jun 2020 22:35:10: 19000000 INFO @ Fri, 26 Jun 2020 22:35:12: 22000000 INFO @ Fri, 26 Jun 2020 22:35:17: 15000000 INFO @ Fri, 26 Jun 2020 22:35:17: 20000000 INFO @ Fri, 26 Jun 2020 22:35:19: 23000000 INFO @ Fri, 26 Jun 2020 22:35:23: 16000000 INFO @ Fri, 26 Jun 2020 22:35:23: 21000000 INFO @ Fri, 26 Jun 2020 22:35:27: 24000000 INFO @ Fri, 26 Jun 2020 22:35:30: 17000000 INFO @ Fri, 26 Jun 2020 22:35:30: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:35:34: 25000000 INFO @ Fri, 26 Jun 2020 22:35:36: 23000000 INFO @ Fri, 26 Jun 2020 22:35:36: 18000000 INFO @ Fri, 26 Jun 2020 22:35:40: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:35:40: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:35:40: #1 total tags in treatment: 25906974 INFO @ Fri, 26 Jun 2020 22:35:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:40: #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 22:35:41: #1 tags after filtering in treatment: 25906974 INFO @ Fri, 26 Jun 2020 22:35:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:35:41: #1 finished! INFO @ Fri, 26 Jun 2020 22:35:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:35:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:35:43: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 22:35:43: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 22:35:43: start model_add_line... INFO @ Fri, 26 Jun 2020 22:35:43: 24000000 INFO @ Fri, 26 Jun 2020 22:35:43: 19000000 INFO @ Fri, 26 Jun 2020 22:35:43: start X-correlation... INFO @ Fri, 26 Jun 2020 22:35:43: end of X-cor INFO @ Fri, 26 Jun 2020 22:35:43: #2 finished! INFO @ Fri, 26 Jun 2020 22:35:43: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:35:43: #2 alternative fragment length(s) may be 0,31,92,217,297,385,412,502,568,584,588 bps INFO @ Fri, 26 Jun 2020 22:35:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.05_model.r WARNING @ Fri, 26 Jun 2020 22:35:43: #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 22:35:43: #2 You may need to consider one of the other alternative d(s): 0,31,92,217,297,385,412,502,568,584,588 WARNING @ Fri, 26 Jun 2020 22:35:43: #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 22:35:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:35:49: 25000000 INFO @ Fri, 26 Jun 2020 22:35:49: 20000000 INFO @ Fri, 26 Jun 2020 22:35:55: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:35:55: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:35:55: #1 total tags in treatment: 25906974 INFO @ Fri, 26 Jun 2020 22:35:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:55: #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 22:35:55: 21000000 INFO @ Fri, 26 Jun 2020 22:35:55: #1 tags after filtering in treatment: 25906974 INFO @ Fri, 26 Jun 2020 22:35:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:35:55: #1 finished! INFO @ Fri, 26 Jun 2020 22:35:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:35:57: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 22:35:57: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 22:35:57: start model_add_line... INFO @ Fri, 26 Jun 2020 22:35:57: start X-correlation... INFO @ Fri, 26 Jun 2020 22:35:57: end of X-cor INFO @ Fri, 26 Jun 2020 22:35:57: #2 finished! INFO @ Fri, 26 Jun 2020 22:35:57: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:35:57: #2 alternative fragment length(s) may be 0,31,92,217,297,385,412,502,568,584,588 bps INFO @ Fri, 26 Jun 2020 22:35:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.10_model.r WARNING @ Fri, 26 Jun 2020 22:35:57: #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 22:35:57: #2 You may need to consider one of the other alternative d(s): 0,31,92,217,297,385,412,502,568,584,588 WARNING @ Fri, 26 Jun 2020 22:35:57: #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 22:35:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:35:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:36:01: 22000000 INFO @ Fri, 26 Jun 2020 22:36:07: 23000000 INFO @ Fri, 26 Jun 2020 22:36:13: 24000000 INFO @ Fri, 26 Jun 2020 22:36:19: 25000000 INFO @ Fri, 26 Jun 2020 22:36:24: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:36:24: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:36:24: #1 total tags in treatment: 25906974 INFO @ Fri, 26 Jun 2020 22:36:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:36:24: #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 22:36:25: #1 tags after filtering in treatment: 25906974 INFO @ Fri, 26 Jun 2020 22:36:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:36:25: #1 finished! INFO @ Fri, 26 Jun 2020 22:36:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:36:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:36:27: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 22:36:27: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 22:36:27: start model_add_line... INFO @ Fri, 26 Jun 2020 22:36:27: start X-correlation... INFO @ Fri, 26 Jun 2020 22:36:27: end of X-cor INFO @ Fri, 26 Jun 2020 22:36:27: #2 finished! INFO @ Fri, 26 Jun 2020 22:36:27: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:36:27: #2 alternative fragment length(s) may be 0,31,92,217,297,385,412,502,568,584,588 bps INFO @ Fri, 26 Jun 2020 22:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494840/SRX494840.20_model.r WARNING @ Fri, 26 Jun 2020 22:36:27: #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 22:36:27: #2 You may need to consider one of the other alternative d(s): 0,31,92,217,297,385,412,502,568,584,588 WARNING @ Fri, 26 Jun 2020 22:36:27: #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 22:36:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:36:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at161/job_scripts/6507841: line 274: 103667 Terminated MACS $i /var/spool/uge/at161/job_scripts/6507841: line 274: 106475 Terminated MACS $i /var/spool/uge/at161/job_scripts/6507841: line 274: 106747 Terminated MACS $i ls: cannot access SRX494840.05.bed: No such file or directory mv: cannot stat ‘SRX494840.05.bed’: No such file or directory mv: cannot stat ‘SRX494840.05.bb’: No such file or directory ls: cannot access SRX494840.10.bed: No such file or directory mv: cannot stat ‘SRX494840.10.bed’: No such file or directory mv: cannot stat ‘SRX494840.10.bb’: No such file or directory ls: cannot access SRX494840.20.bed: No such file or directory mv: cannot stat ‘SRX494840.20.bed’: No such file or directory mv: cannot stat ‘SRX494840.20.bb’: No such file or directory