Job ID = 14159155 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 14159418 ("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: 00:07:15 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: 00:07:15 Overall time: 00:07:15 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:12:45: # 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 @ Wed, 08 Dec 2021 20:12:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:12:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:12:52: 1000000 INFO @ Wed, 08 Dec 2021 20:12:57: 2000000 INFO @ Wed, 08 Dec 2021 20:13:03: 3000000 INFO @ Wed, 08 Dec 2021 20:13:08: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:13:13: 5000000 INFO @ Wed, 08 Dec 2021 20:13:15: # 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 @ Wed, 08 Dec 2021 20:13:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:13:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:13:18: 6000000 INFO @ Wed, 08 Dec 2021 20:13:20: 1000000 INFO @ Wed, 08 Dec 2021 20:13:24: 7000000 INFO @ Wed, 08 Dec 2021 20:13:25: 2000000 INFO @ Wed, 08 Dec 2021 20:13:29: 8000000 INFO @ Wed, 08 Dec 2021 20:13:31: 3000000 INFO @ Wed, 08 Dec 2021 20:13:34: 9000000 INFO @ Wed, 08 Dec 2021 20:13:36: 4000000 INFO @ Wed, 08 Dec 2021 20:13:39: 10000000 INFO @ Wed, 08 Dec 2021 20:13:41: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:13:44: 11000000 INFO @ Wed, 08 Dec 2021 20:13:45: # 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 @ Wed, 08 Dec 2021 20:13:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:13:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:13:46: 6000000 INFO @ Wed, 08 Dec 2021 20:13:50: 12000000 INFO @ Wed, 08 Dec 2021 20:13:51: 1000000 INFO @ Wed, 08 Dec 2021 20:13:52: 7000000 INFO @ Wed, 08 Dec 2021 20:13:56: 13000000 INFO @ Wed, 08 Dec 2021 20:13:58: 2000000 INFO @ Wed, 08 Dec 2021 20:13:58: 8000000 INFO @ Wed, 08 Dec 2021 20:14:02: 14000000 INFO @ Wed, 08 Dec 2021 20:14:04: 3000000 INFO @ Wed, 08 Dec 2021 20:14:04: 9000000 INFO @ Wed, 08 Dec 2021 20:14:08: 15000000 INFO @ Wed, 08 Dec 2021 20:14:10: 10000000 INFO @ Wed, 08 Dec 2021 20:14:10: 4000000 INFO @ Wed, 08 Dec 2021 20:14:14: 16000000 INFO @ Wed, 08 Dec 2021 20:14:16: 11000000 INFO @ Wed, 08 Dec 2021 20:14:17: 5000000 INFO @ Wed, 08 Dec 2021 20:14:20: 17000000 INFO @ Wed, 08 Dec 2021 20:14:22: 12000000 INFO @ Wed, 08 Dec 2021 20:14:23: 6000000 INFO @ Wed, 08 Dec 2021 20:14:26: 18000000 INFO @ Wed, 08 Dec 2021 20:14:28: 13000000 INFO @ Wed, 08 Dec 2021 20:14:29: 7000000 INFO @ Wed, 08 Dec 2021 20:14:32: 19000000 INFO @ Wed, 08 Dec 2021 20:14:34: 14000000 INFO @ Wed, 08 Dec 2021 20:14:36: 8000000 INFO @ Wed, 08 Dec 2021 20:14:38: 20000000 INFO @ Wed, 08 Dec 2021 20:14:40: 15000000 INFO @ Wed, 08 Dec 2021 20:14:42: 9000000 INFO @ Wed, 08 Dec 2021 20:14:44: 21000000 INFO @ Wed, 08 Dec 2021 20:14:46: 16000000 INFO @ Wed, 08 Dec 2021 20:14:49: 10000000 INFO @ Wed, 08 Dec 2021 20:14:50: 22000000 INFO @ Wed, 08 Dec 2021 20:14:52: 17000000 INFO @ Wed, 08 Dec 2021 20:14:55: 11000000 INFO @ Wed, 08 Dec 2021 20:14:56: 23000000 INFO @ Wed, 08 Dec 2021 20:14:58: 18000000 INFO @ Wed, 08 Dec 2021 20:15:02: 12000000 INFO @ Wed, 08 Dec 2021 20:15:02: 24000000 INFO @ Wed, 08 Dec 2021 20:15:04: 19000000 INFO @ Wed, 08 Dec 2021 20:15:08: 13000000 INFO @ Wed, 08 Dec 2021 20:15:09: 25000000 INFO @ Wed, 08 Dec 2021 20:15:10: 20000000 INFO @ Wed, 08 Dec 2021 20:15:14: 14000000 INFO @ Wed, 08 Dec 2021 20:15:15: 26000000 INFO @ Wed, 08 Dec 2021 20:15:15: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:15:15: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:15:15: #1 total tags in treatment: 26132524 INFO @ Wed, 08 Dec 2021 20:15:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:15:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:15:16: #1 tags after filtering in treatment: 26132524 INFO @ Wed, 08 Dec 2021 20:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:15:16: #1 finished! INFO @ Wed, 08 Dec 2021 20:15:16: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:15:16: 21000000 INFO @ Wed, 08 Dec 2021 20:15:17: #2 number of paired peaks: 130 WARNING @ Wed, 08 Dec 2021 20:15:17: 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 @ Wed, 08 Dec 2021 20:15:17: start model_add_line... INFO @ Wed, 08 Dec 2021 20:15:18: start X-correlation... INFO @ Wed, 08 Dec 2021 20:15:18: end of X-cor INFO @ Wed, 08 Dec 2021 20:15:18: #2 finished! INFO @ Wed, 08 Dec 2021 20:15:18: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 20:15:18: #2 alternative fragment length(s) may be 0,44,400,507,525,552,582 bps INFO @ Wed, 08 Dec 2021 20:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.05_model.r WARNING @ Wed, 08 Dec 2021 20:15:18: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:15:18: #2 You may need to consider one of the other alternative d(s): 0,44,400,507,525,552,582 WARNING @ Wed, 08 Dec 2021 20:15:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:15:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:15:21: 15000000 INFO @ Wed, 08 Dec 2021 20:15:22: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:15:27: 16000000 INFO @ Wed, 08 Dec 2021 20:15:28: 23000000 INFO @ Wed, 08 Dec 2021 20:15:33: 17000000 INFO @ Wed, 08 Dec 2021 20:15:34: 24000000 INFO @ Wed, 08 Dec 2021 20:15:40: 18000000 INFO @ Wed, 08 Dec 2021 20:15:40: 25000000 INFO @ Wed, 08 Dec 2021 20:15:46: 26000000 INFO @ Wed, 08 Dec 2021 20:15:46: 19000000 INFO @ Wed, 08 Dec 2021 20:15:47: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:15:47: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:15:47: #1 total tags in treatment: 26132524 INFO @ Wed, 08 Dec 2021 20:15:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:15:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:15:47: #1 tags after filtering in treatment: 26132524 INFO @ Wed, 08 Dec 2021 20:15:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:15:47: #1 finished! INFO @ Wed, 08 Dec 2021 20:15:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:15:49: #2 number of paired peaks: 130 WARNING @ Wed, 08 Dec 2021 20:15:49: 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 @ Wed, 08 Dec 2021 20:15:49: start model_add_line... INFO @ Wed, 08 Dec 2021 20:15:49: start X-correlation... INFO @ Wed, 08 Dec 2021 20:15:49: end of X-cor INFO @ Wed, 08 Dec 2021 20:15:49: #2 finished! INFO @ Wed, 08 Dec 2021 20:15:49: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 20:15:49: #2 alternative fragment length(s) may be 0,44,400,507,525,552,582 bps INFO @ Wed, 08 Dec 2021 20:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120614/SRX9120614.10_model.r WARNING @ Wed, 08 Dec 2021 20:15:49: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:15:49: #2 You may need to consider one of the other alternative d(s): 0,44,400,507,525,552,582 WARNING @ Wed, 08 Dec 2021 20:15:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:15:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:15:52: 20000000 INFO @ Wed, 08 Dec 2021 20:15:58: 21000000 INFO @ Wed, 08 Dec 2021 20:16:04: 22000000 INFO @ Wed, 08 Dec 2021 20:16:10: 23000000 INFO @ Wed, 08 Dec 2021 20:16:16: 24000000 BigWig に変換しました。 /var/spool/uge/at141/job_scripts/14159155: line 297: 100643 Terminated MACS $i /var/spool/uge/at141/job_scripts/14159155: line 297: 100848 Terminated MACS $i /var/spool/uge/at141/job_scripts/14159155: line 297: 100949 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 INFO @ Wed, 08 Dec 2021 20:16:22: 25000000