Job ID = 6367577 SRX = SRX331333 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:50 prefetch.2.10.7: 1) Downloading 'SRR947570'... 2020-06-15T23:29:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:42 prefetch.2.10.7: 1) 'SRR947570' was downloaded successfully Read 30788149 spots for SRR947570/SRR947570.sra Written 30788149 spots for SRR947570/SRR947570.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: 00:05:30 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169807 (0.55%) aligned 0 times 25275418 (82.09%) aligned exactly 1 time 5342924 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 4711694 / 30618342 = 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 08:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.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 08:45:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:55: 1000000 INFO @ Tue, 16 Jun 2020 08:46:01: 2000000 INFO @ Tue, 16 Jun 2020 08:46:07: 3000000 INFO @ Tue, 16 Jun 2020 08:46:13: 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 08:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.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 08:46:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:19: 5000000 INFO @ Tue, 16 Jun 2020 08:46:24: 1000000 INFO @ Tue, 16 Jun 2020 08:46:25: 6000000 INFO @ Tue, 16 Jun 2020 08:46:30: 2000000 INFO @ Tue, 16 Jun 2020 08:46:32: 7000000 INFO @ Tue, 16 Jun 2020 08:46:35: 3000000 INFO @ Tue, 16 Jun 2020 08:46:38: 8000000 INFO @ Tue, 16 Jun 2020 08:46:41: 4000000 INFO @ Tue, 16 Jun 2020 08:46:45: 9000000 INFO @ Tue, 16 Jun 2020 08:46:46: 5000000 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 08:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.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 08:46:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:51: 10000000 INFO @ Tue, 16 Jun 2020 08:46:52: 6000000 INFO @ Tue, 16 Jun 2020 08:46:55: 1000000 INFO @ Tue, 16 Jun 2020 08:46:57: 7000000 INFO @ Tue, 16 Jun 2020 08:46:58: 11000000 INFO @ Tue, 16 Jun 2020 08:47:00: 2000000 INFO @ Tue, 16 Jun 2020 08:47:03: 8000000 INFO @ Tue, 16 Jun 2020 08:47:04: 12000000 INFO @ Tue, 16 Jun 2020 08:47:06: 3000000 INFO @ Tue, 16 Jun 2020 08:47:08: 9000000 INFO @ Tue, 16 Jun 2020 08:47:11: 13000000 INFO @ Tue, 16 Jun 2020 08:47:11: 4000000 INFO @ Tue, 16 Jun 2020 08:47:14: 10000000 INFO @ Tue, 16 Jun 2020 08:47:17: 5000000 INFO @ Tue, 16 Jun 2020 08:47:17: 14000000 INFO @ Tue, 16 Jun 2020 08:47:19: 11000000 INFO @ Tue, 16 Jun 2020 08:47:22: 6000000 INFO @ Tue, 16 Jun 2020 08:47:23: 15000000 INFO @ Tue, 16 Jun 2020 08:47:25: 12000000 INFO @ Tue, 16 Jun 2020 08:47:28: 7000000 INFO @ Tue, 16 Jun 2020 08:47:30: 16000000 INFO @ Tue, 16 Jun 2020 08:47:31: 13000000 INFO @ Tue, 16 Jun 2020 08:47:33: 8000000 INFO @ Tue, 16 Jun 2020 08:47:36: 17000000 INFO @ Tue, 16 Jun 2020 08:47:36: 14000000 INFO @ Tue, 16 Jun 2020 08:47:39: 9000000 INFO @ Tue, 16 Jun 2020 08:47:42: 15000000 INFO @ Tue, 16 Jun 2020 08:47:42: 18000000 INFO @ Tue, 16 Jun 2020 08:47:44: 10000000 INFO @ Tue, 16 Jun 2020 08:47:47: 16000000 INFO @ Tue, 16 Jun 2020 08:47:49: 19000000 INFO @ Tue, 16 Jun 2020 08:47:50: 11000000 INFO @ Tue, 16 Jun 2020 08:47:53: 17000000 INFO @ Tue, 16 Jun 2020 08:47:55: 20000000 INFO @ Tue, 16 Jun 2020 08:47:55: 12000000 INFO @ Tue, 16 Jun 2020 08:47:58: 18000000 INFO @ Tue, 16 Jun 2020 08:48:01: 13000000 INFO @ Tue, 16 Jun 2020 08:48:01: 21000000 INFO @ Tue, 16 Jun 2020 08:48:04: 19000000 INFO @ Tue, 16 Jun 2020 08:48:06: 14000000 INFO @ Tue, 16 Jun 2020 08:48:08: 22000000 INFO @ Tue, 16 Jun 2020 08:48:09: 20000000 INFO @ Tue, 16 Jun 2020 08:48:12: 15000000 INFO @ Tue, 16 Jun 2020 08:48:14: 23000000 INFO @ Tue, 16 Jun 2020 08:48:15: 21000000 INFO @ Tue, 16 Jun 2020 08:48:17: 16000000 INFO @ Tue, 16 Jun 2020 08:48:20: 22000000 INFO @ Tue, 16 Jun 2020 08:48:20: 24000000 INFO @ Tue, 16 Jun 2020 08:48:23: 17000000 INFO @ Tue, 16 Jun 2020 08:48:26: 23000000 INFO @ Tue, 16 Jun 2020 08:48:27: 25000000 INFO @ Tue, 16 Jun 2020 08:48:29: 18000000 INFO @ Tue, 16 Jun 2020 08:48:31: 24000000 INFO @ Tue, 16 Jun 2020 08:48:33: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:48:33: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:48:33: #1 total tags in treatment: 25906648 INFO @ Tue, 16 Jun 2020 08:48:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:33: #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 08:48:33: #1 tags after filtering in treatment: 25906648 INFO @ Tue, 16 Jun 2020 08:48:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:34: 19000000 INFO @ Tue, 16 Jun 2020 08:48:35: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 08:48:35: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:35: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:48:35: #2 alternative fragment length(s) may be 0,32,149,438,510 bps INFO @ Tue, 16 Jun 2020 08:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.05_model.r WARNING @ Tue, 16 Jun 2020 08:48:35: #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 08:48:35: #2 You may need to consider one of the other alternative d(s): 0,32,149,438,510 WARNING @ Tue, 16 Jun 2020 08:48:35: #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 08:48:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:37: 25000000 INFO @ Tue, 16 Jun 2020 08:48:40: 20000000 INFO @ Tue, 16 Jun 2020 08:48:42: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:48:42: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:48:42: #1 total tags in treatment: 25906648 INFO @ Tue, 16 Jun 2020 08:48:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:42: #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 08:48:42: #1 tags after filtering in treatment: 25906648 INFO @ Tue, 16 Jun 2020 08:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:44: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 08:48:44: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:44: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:48:44: #2 alternative fragment length(s) may be 0,32,149,438,510 bps INFO @ Tue, 16 Jun 2020 08:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.10_model.r WARNING @ Tue, 16 Jun 2020 08:48:44: #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 08:48:44: #2 You may need to consider one of the other alternative d(s): 0,32,149,438,510 WARNING @ Tue, 16 Jun 2020 08:48:44: #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 08:48:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:45: 21000000 INFO @ Tue, 16 Jun 2020 08:48:49: 22000000 INFO @ Tue, 16 Jun 2020 08:48:54: 23000000 INFO @ Tue, 16 Jun 2020 08:48:59: 24000000 INFO @ Tue, 16 Jun 2020 08:49:04: 25000000 INFO @ Tue, 16 Jun 2020 08:49:08: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:49:08: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:49:08: #1 total tags in treatment: 25906648 INFO @ Tue, 16 Jun 2020 08:49:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:08: #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 08:49:09: #1 tags after filtering in treatment: 25906648 INFO @ Tue, 16 Jun 2020 08:49:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:10: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 08:49:10: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:11: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:49:11: #2 alternative fragment length(s) may be 0,32,149,438,510 bps INFO @ Tue, 16 Jun 2020 08:49:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331333/SRX331333.20_model.r WARNING @ Tue, 16 Jun 2020 08:49:11: #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 08:49:11: #2 You may need to consider one of the other alternative d(s): 0,32,149,438,510 WARNING @ Tue, 16 Jun 2020 08:49:11: #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 08:49:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at147/job_scripts/6367577: line 271: 52117 Terminated MACS $i /var/spool/uge/at147/job_scripts/6367577: line 271: 52974 Terminated MACS $i /var/spool/uge/at147/job_scripts/6367577: line 271: 53564 Terminated MACS $i ls: cannot access SRX331333.05.bed: No such file or directory mv: cannot stat ‘SRX331333.05.bed’: No such file or directory mv: cannot stat ‘SRX331333.05.bb’: No such file or directory ls: cannot access SRX331333.10.bed: No such file or directory mv: cannot stat ‘SRX331333.10.bed’: No such file or directory mv: cannot stat ‘SRX331333.10.bb’: No such file or directory ls: cannot access SRX331333.20.bed: No such file or directory mv: cannot stat ‘SRX331333.20.bed’: No such file or directory mv: cannot stat ‘SRX331333.20.bb’: No such file or directory