Job ID = 10165780 SRX = SRX9120614 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32219704 spots for SRR12638557/SRR12638557.sra Written 32219704 spots for SRR12638557/SRR12638557.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166097 ("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: 00:07:14 32219704 reads; of these: 32219704 (100.00%) were unpaired; of these: 95637 (0.30%) aligned 0 times 26908007 (83.51%) aligned exactly 1 time 5216060 (16.19%) aligned >1 times 99.70% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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 16 files... [bam_rmdupse_core] 5991543 / 32124067 = 0.1865 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 20:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.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 20:04:55: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:55: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:01: 1000000 INFO @ Thu, 08 Oct 2020 20:05:06: 2000000 INFO @ Thu, 08 Oct 2020 20:05:11: 3000000 INFO @ Thu, 08 Oct 2020 20:05:17: 4000000 INFO @ Thu, 08 Oct 2020 20:05:22: 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 @ Thu, 08 Oct 2020 20:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.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 20:05:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:28: 6000000 INFO @ Thu, 08 Oct 2020 20:05:32: 1000000 INFO @ Thu, 08 Oct 2020 20:05:34: 7000000 INFO @ Thu, 08 Oct 2020 20:05:38: 2000000 INFO @ Thu, 08 Oct 2020 20:05:40: 8000000 INFO @ Thu, 08 Oct 2020 20:05:45: 3000000 INFO @ Thu, 08 Oct 2020 20:05:47: 9000000 INFO @ Thu, 08 Oct 2020 20:05:52: 4000000 INFO @ Thu, 08 Oct 2020 20:05:53: 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 @ Thu, 08 Oct 2020 20:05:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.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 20:05:55: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:55: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:58: 5000000 INFO @ Thu, 08 Oct 2020 20:06:00: 11000000 INFO @ Thu, 08 Oct 2020 20:06:02: 1000000 INFO @ Thu, 08 Oct 2020 20:06:05: 6000000 INFO @ Thu, 08 Oct 2020 20:06:06: 12000000 INFO @ Thu, 08 Oct 2020 20:06:08: 2000000 INFO @ Thu, 08 Oct 2020 20:06:11: 7000000 INFO @ Thu, 08 Oct 2020 20:06:12: 13000000 INFO @ Thu, 08 Oct 2020 20:06:14: 3000000 INFO @ Thu, 08 Oct 2020 20:06:18: 8000000 INFO @ Thu, 08 Oct 2020 20:06:18: 14000000 INFO @ Thu, 08 Oct 2020 20:06:20: 4000000 INFO @ Thu, 08 Oct 2020 20:06:25: 15000000 INFO @ Thu, 08 Oct 2020 20:06:25: 9000000 INFO @ Thu, 08 Oct 2020 20:06:27: 5000000 INFO @ Thu, 08 Oct 2020 20:06:31: 16000000 INFO @ Thu, 08 Oct 2020 20:06:31: 10000000 INFO @ Thu, 08 Oct 2020 20:06:33: 6000000 INFO @ Thu, 08 Oct 2020 20:06:37: 17000000 INFO @ Thu, 08 Oct 2020 20:06:38: 11000000 INFO @ Thu, 08 Oct 2020 20:06:39: 7000000 INFO @ Thu, 08 Oct 2020 20:06:43: 18000000 INFO @ Thu, 08 Oct 2020 20:06:45: 12000000 INFO @ Thu, 08 Oct 2020 20:06:45: 8000000 INFO @ Thu, 08 Oct 2020 20:06:49: 19000000 INFO @ Thu, 08 Oct 2020 20:06:51: 9000000 INFO @ Thu, 08 Oct 2020 20:06:51: 13000000 INFO @ Thu, 08 Oct 2020 20:06:55: 20000000 INFO @ Thu, 08 Oct 2020 20:06:57: 10000000 INFO @ Thu, 08 Oct 2020 20:06:58: 14000000 INFO @ Thu, 08 Oct 2020 20:07:01: 21000000 INFO @ Thu, 08 Oct 2020 20:07:04: 11000000 INFO @ Thu, 08 Oct 2020 20:07:04: 15000000 INFO @ Thu, 08 Oct 2020 20:07:08: 22000000 INFO @ Thu, 08 Oct 2020 20:07:10: 12000000 INFO @ Thu, 08 Oct 2020 20:07:11: 16000000 INFO @ Thu, 08 Oct 2020 20:07:14: 23000000 INFO @ Thu, 08 Oct 2020 20:07:16: 13000000 INFO @ Thu, 08 Oct 2020 20:07:18: 17000000 INFO @ Thu, 08 Oct 2020 20:07:20: 24000000 INFO @ Thu, 08 Oct 2020 20:07:23: 14000000 INFO @ Thu, 08 Oct 2020 20:07:24: 18000000 INFO @ Thu, 08 Oct 2020 20:07:26: 25000000 INFO @ Thu, 08 Oct 2020 20:07:29: 15000000 INFO @ Thu, 08 Oct 2020 20:07:31: 19000000 INFO @ Thu, 08 Oct 2020 20:07:32: 26000000 INFO @ Thu, 08 Oct 2020 20:07:33: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:33: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:33: #1 total tags in treatment: 26132524 INFO @ Thu, 08 Oct 2020 20:07:33: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:33: #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 20:07:34: #1 tags after filtering in treatment: 26132524 INFO @ Thu, 08 Oct 2020 20:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:34: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:35: 16000000 INFO @ Thu, 08 Oct 2020 20:07:35: #2 number of paired peaks: 130 WARNING @ Thu, 08 Oct 2020 20:07:35: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Thu, 08 Oct 2020 20:07:35: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:36: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:36: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:36: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:36: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:07:36: #2 alternative fragment length(s) may be 0,44,400,507,525,552,582 bps INFO @ Thu, 08 Oct 2020 20:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.05_model.r WARNING @ Thu, 08 Oct 2020 20:07:36: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:07:36: #2 You may need to consider one of the other alternative d(s): 0,44,400,507,525,552,582 WARNING @ Thu, 08 Oct 2020 20:07:36: #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 20:07:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:37: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:07:41: 17000000 INFO @ Thu, 08 Oct 2020 20:07:44: 21000000 INFO @ Thu, 08 Oct 2020 20:07:47: 18000000 INFO @ Thu, 08 Oct 2020 20:07:50: 22000000 INFO @ Thu, 08 Oct 2020 20:07:53: 19000000 INFO @ Thu, 08 Oct 2020 20:07:57: 23000000 INFO @ Thu, 08 Oct 2020 20:07:59: 20000000 INFO @ Thu, 08 Oct 2020 20:08:03: 24000000 INFO @ Thu, 08 Oct 2020 20:08:06: 21000000 INFO @ Thu, 08 Oct 2020 20:08:10: 25000000 INFO @ Thu, 08 Oct 2020 20:08:12: 22000000 INFO @ Thu, 08 Oct 2020 20:08:16: 26000000 INFO @ Thu, 08 Oct 2020 20:08:17: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:08:17: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:08:17: #1 total tags in treatment: 26132524 INFO @ Thu, 08 Oct 2020 20:08:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:08:17: #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 20:08:18: #1 tags after filtering in treatment: 26132524 INFO @ Thu, 08 Oct 2020 20:08:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:08:18: #1 finished! INFO @ Thu, 08 Oct 2020 20:08:18: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:08:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:08:18: 23000000 INFO @ Thu, 08 Oct 2020 20:08:19: #2 number of paired peaks: 130 WARNING @ Thu, 08 Oct 2020 20:08:19: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Thu, 08 Oct 2020 20:08:19: start model_add_line... INFO @ Thu, 08 Oct 2020 20:08:19: start X-correlation... INFO @ Thu, 08 Oct 2020 20:08:19: end of X-cor INFO @ Thu, 08 Oct 2020 20:08:19: #2 finished! INFO @ Thu, 08 Oct 2020 20:08:19: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:08:19: #2 alternative fragment length(s) may be 0,44,400,507,525,552,582 bps INFO @ Thu, 08 Oct 2020 20:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.10_model.r WARNING @ Thu, 08 Oct 2020 20:08:19: #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 20:08:19: #2 You may need to consider one of the other alternative d(s): 0,44,400,507,525,552,582 WARNING @ Thu, 08 Oct 2020 20:08:19: #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 20:08:19: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:08:24: 24000000 INFO @ Thu, 08 Oct 2020 20:08:30: 25000000 BigWig に変換しました。 /var/spool/uge/at152/job_scripts/10165780: line 297: 90943 Terminated MACS $i /var/spool/uge/at152/job_scripts/10165780: line 297: 91705 Terminated MACS $i /var/spool/uge/at152/job_scripts/10165780: line 297: 92512 Terminated MACS $i ls: cannot access SRX9120614.05.bed: No such file or directory mv: cannot stat ‘SRX9120614.05.bed’: No such file or directory mv: cannot stat ‘SRX9120614.05.bb’: No such file or directory ls: cannot access SRX9120614.10.bed: No such file or directory mv: cannot stat ‘SRX9120614.10.bed’: No such file or directory mv: cannot stat ‘SRX9120614.10.bb’: No such file or directory ls: cannot access SRX9120614.20.bed: No such file or directory mv: cannot stat ‘SRX9120614.20.bed’: No such file or directory mv: cannot stat ‘SRX9120614.20.bb’: No such file or directory