Job ID = 10165632 SRX = SRX6799189 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 42139643 spots for SRR10065396/SRR10065396.sra Written 42139643 spots for SRR10065396/SRR10065396.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165939 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:02 42139643 reads; of these: 42139643 (100.00%) were unpaired; of these: 1695744 (4.02%) aligned 0 times 27801306 (65.97%) aligned exactly 1 time 12642593 (30.00%) aligned >1 times 95.98% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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 20 files... [bam_rmdupse_core] 14203508 / 40443899 = 0.3512 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 @ Thu, 08 Oct 2020 19:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.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 @ Thu, 08 Oct 2020 19:50:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:50:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:50:23: 1000000 INFO @ Thu, 08 Oct 2020 19:50:29: 2000000 INFO @ Thu, 08 Oct 2020 19:50:36: 3000000 INFO @ Thu, 08 Oct 2020 19:50:42: 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 @ Thu, 08 Oct 2020 19:50:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.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 @ Thu, 08 Oct 2020 19:50:46: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:50:46: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:50:49: 5000000 INFO @ Thu, 08 Oct 2020 19:50:53: 1000000 INFO @ Thu, 08 Oct 2020 19:50:56: 6000000 INFO @ Thu, 08 Oct 2020 19:51:00: 2000000 INFO @ Thu, 08 Oct 2020 19:51:03: 7000000 INFO @ Thu, 08 Oct 2020 19:51:07: 3000000 INFO @ Thu, 08 Oct 2020 19:51:10: 8000000 INFO @ Thu, 08 Oct 2020 19:51:13: 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 @ Thu, 08 Oct 2020 19:51:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.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 @ Thu, 08 Oct 2020 19:51:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:51:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:51:16: 9000000 INFO @ Thu, 08 Oct 2020 19:51:20: 5000000 INFO @ Thu, 08 Oct 2020 19:51:23: 1000000 INFO @ Thu, 08 Oct 2020 19:51:23: 10000000 INFO @ Thu, 08 Oct 2020 19:51:27: 6000000 INFO @ Thu, 08 Oct 2020 19:51:30: 11000000 INFO @ Thu, 08 Oct 2020 19:51:30: 2000000 INFO @ Thu, 08 Oct 2020 19:51:34: 7000000 INFO @ Thu, 08 Oct 2020 19:51:37: 12000000 INFO @ Thu, 08 Oct 2020 19:51:37: 3000000 INFO @ Thu, 08 Oct 2020 19:51:41: 8000000 INFO @ Thu, 08 Oct 2020 19:51:44: 13000000 INFO @ Thu, 08 Oct 2020 19:51:44: 4000000 INFO @ Thu, 08 Oct 2020 19:51:47: 9000000 INFO @ Thu, 08 Oct 2020 19:51:50: 14000000 INFO @ Thu, 08 Oct 2020 19:51:51: 5000000 INFO @ Thu, 08 Oct 2020 19:51:54: 10000000 INFO @ Thu, 08 Oct 2020 19:51:57: 15000000 INFO @ Thu, 08 Oct 2020 19:51:58: 6000000 INFO @ Thu, 08 Oct 2020 19:52:01: 11000000 INFO @ Thu, 08 Oct 2020 19:52:04: 16000000 INFO @ Thu, 08 Oct 2020 19:52:05: 7000000 INFO @ Thu, 08 Oct 2020 19:52:08: 12000000 INFO @ Thu, 08 Oct 2020 19:52:10: 17000000 INFO @ Thu, 08 Oct 2020 19:52:11: 8000000 INFO @ Thu, 08 Oct 2020 19:52:14: 13000000 INFO @ Thu, 08 Oct 2020 19:52:17: 18000000 INFO @ Thu, 08 Oct 2020 19:52:18: 9000000 INFO @ Thu, 08 Oct 2020 19:52:21: 14000000 INFO @ Thu, 08 Oct 2020 19:52:24: 19000000 INFO @ Thu, 08 Oct 2020 19:52:25: 10000000 INFO @ Thu, 08 Oct 2020 19:52:28: 15000000 INFO @ Thu, 08 Oct 2020 19:52:31: 20000000 INFO @ Thu, 08 Oct 2020 19:52:32: 11000000 INFO @ Thu, 08 Oct 2020 19:52:34: 16000000 INFO @ Thu, 08 Oct 2020 19:52:37: 21000000 INFO @ Thu, 08 Oct 2020 19:52:39: 12000000 INFO @ Thu, 08 Oct 2020 19:52:41: 17000000 INFO @ Thu, 08 Oct 2020 19:52:44: 22000000 INFO @ Thu, 08 Oct 2020 19:52:45: 13000000 INFO @ Thu, 08 Oct 2020 19:52:48: 18000000 INFO @ Thu, 08 Oct 2020 19:52:51: 23000000 INFO @ Thu, 08 Oct 2020 19:52:52: 14000000 INFO @ Thu, 08 Oct 2020 19:52:54: 19000000 INFO @ Thu, 08 Oct 2020 19:52:58: 24000000 INFO @ Thu, 08 Oct 2020 19:52:59: 15000000 INFO @ Thu, 08 Oct 2020 19:53:01: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:53:04: 25000000 INFO @ Thu, 08 Oct 2020 19:53:06: 16000000 INFO @ Thu, 08 Oct 2020 19:53:08: 21000000 INFO @ Thu, 08 Oct 2020 19:53:11: 26000000 INFO @ Thu, 08 Oct 2020 19:53:13: 17000000 INFO @ Thu, 08 Oct 2020 19:53:13: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:53:13: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:53:13: #1 total tags in treatment: 26240391 INFO @ Thu, 08 Oct 2020 19:53:13: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:53:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:53:13: #1 tags after filtering in treatment: 26240391 INFO @ Thu, 08 Oct 2020 19:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:53:13: #1 finished! INFO @ Thu, 08 Oct 2020 19:53:13: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:53:15: 22000000 INFO @ Thu, 08 Oct 2020 19:53:15: #2 number of paired peaks: 304 WARNING @ Thu, 08 Oct 2020 19:53:15: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Thu, 08 Oct 2020 19:53:15: start model_add_line... INFO @ Thu, 08 Oct 2020 19:53:15: start X-correlation... INFO @ Thu, 08 Oct 2020 19:53:15: end of X-cor INFO @ Thu, 08 Oct 2020 19:53:15: #2 finished! INFO @ Thu, 08 Oct 2020 19:53:15: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 19:53:15: #2 alternative fragment length(s) may be 0,13,50,483,561 bps INFO @ Thu, 08 Oct 2020 19:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.05_model.r WARNING @ Thu, 08 Oct 2020 19:53:15: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:53:15: #2 You may need to consider one of the other alternative d(s): 0,13,50,483,561 WARNING @ Thu, 08 Oct 2020 19:53:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:53:15: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:53:19: 18000000 INFO @ Thu, 08 Oct 2020 19:53:21: 23000000 INFO @ Thu, 08 Oct 2020 19:53:26: 19000000 INFO @ Thu, 08 Oct 2020 19:53:28: 24000000 INFO @ Thu, 08 Oct 2020 19:53:33: 20000000 INFO @ Thu, 08 Oct 2020 19:53:34: 25000000 INFO @ Thu, 08 Oct 2020 19:53:39: 21000000 INFO @ Thu, 08 Oct 2020 19:53:41: 26000000 INFO @ Thu, 08 Oct 2020 19:53:42: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:53:42: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:53:42: #1 total tags in treatment: 26240391 INFO @ Thu, 08 Oct 2020 19:53:42: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:53:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:53:43: #1 tags after filtering in treatment: 26240391 INFO @ Thu, 08 Oct 2020 19:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:53:43: #1 finished! INFO @ Thu, 08 Oct 2020 19:53:43: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:53:44: #2 number of paired peaks: 304 WARNING @ Thu, 08 Oct 2020 19:53:44: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Thu, 08 Oct 2020 19:53:44: start model_add_line... INFO @ Thu, 08 Oct 2020 19:53:45: start X-correlation... INFO @ Thu, 08 Oct 2020 19:53:45: end of X-cor INFO @ Thu, 08 Oct 2020 19:53:45: #2 finished! INFO @ Thu, 08 Oct 2020 19:53:45: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 19:53:45: #2 alternative fragment length(s) may be 0,13,50,483,561 bps INFO @ Thu, 08 Oct 2020 19:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799189/SRX6799189.10_model.r WARNING @ Thu, 08 Oct 2020 19:53:45: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:53:45: #2 You may need to consider one of the other alternative d(s): 0,13,50,483,561 WARNING @ Thu, 08 Oct 2020 19:53:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:53:45: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:53:46: 22000000 BigWig に変換しました。 /var/spool/uge/at145/job_scripts/10165632: line 297: 30416 Terminated MACS $i /var/spool/uge/at145/job_scripts/10165632: line 297: 52363 Terminated MACS $i /var/spool/uge/at145/job_scripts/10165632: line 297: 75064 Terminated MACS $i ls: cannot access SRX6799189.05.bed: No such file or directory mv: cannot stat ‘SRX6799189.05.bed’: No such file or directory mv: cannot stat ‘SRX6799189.05.bb’: No such file or directory ls: cannot access SRX6799189.10.bed: No such file or directory mv: cannot stat ‘SRX6799189.10.bed’: No such file or directory mv: cannot stat ‘SRX6799189.10.bb’: No such file or directory ls: cannot access SRX6799189.20.bed: No such file or directory mv: cannot stat ‘SRX6799189.20.bed’: No such file or directory mv: cannot stat ‘SRX6799189.20.bb’: No such file or directory