Job ID = 6368096 SRX = SRX466559 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:15:06 prefetch.2.10.7: 1) Downloading 'SRR1163625'... 2020-06-16T00:15:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:17:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:17:13 prefetch.2.10.7: 1) 'SRR1163625' was downloaded successfully Read 30788149 spots for SRR1163625/SRR1163625.sra Written 30788149 spots for SRR1163625/SRR1163625.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: 00:05:38 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169816 (0.55%) aligned 0 times 25275386 (82.09%) aligned exactly 1 time 5342947 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 4712171 / 30618333 = 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 09:30:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.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 09:30:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:05: 1000000 INFO @ Tue, 16 Jun 2020 09:31:10: 2000000 INFO @ Tue, 16 Jun 2020 09:31:15: 3000000 INFO @ Tue, 16 Jun 2020 09:31:21: 4000000 INFO @ Tue, 16 Jun 2020 09:31:26: 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 @ Tue, 16 Jun 2020 09:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.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 09:31:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:31: 6000000 INFO @ Tue, 16 Jun 2020 09:31:35: 1000000 INFO @ Tue, 16 Jun 2020 09:31:37: 7000000 INFO @ Tue, 16 Jun 2020 09:31:41: 2000000 INFO @ Tue, 16 Jun 2020 09:31:43: 8000000 INFO @ Tue, 16 Jun 2020 09:31:47: 3000000 INFO @ Tue, 16 Jun 2020 09:31:48: 9000000 INFO @ Tue, 16 Jun 2020 09:31:53: 4000000 INFO @ Tue, 16 Jun 2020 09:31:54: 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 @ Tue, 16 Jun 2020 09:31:59: 5000000 INFO @ Tue, 16 Jun 2020 09:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.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 09:31:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:00: 11000000 INFO @ Tue, 16 Jun 2020 09:32:05: 6000000 INFO @ Tue, 16 Jun 2020 09:32:06: 1000000 INFO @ Tue, 16 Jun 2020 09:32:06: 12000000 INFO @ Tue, 16 Jun 2020 09:32:11: 7000000 INFO @ Tue, 16 Jun 2020 09:32:12: 13000000 INFO @ Tue, 16 Jun 2020 09:32:13: 2000000 INFO @ Tue, 16 Jun 2020 09:32:17: 8000000 INFO @ Tue, 16 Jun 2020 09:32:19: 14000000 INFO @ Tue, 16 Jun 2020 09:32:20: 3000000 INFO @ Tue, 16 Jun 2020 09:32:24: 9000000 INFO @ Tue, 16 Jun 2020 09:32:25: 15000000 INFO @ Tue, 16 Jun 2020 09:32:26: 4000000 INFO @ Tue, 16 Jun 2020 09:32:30: 10000000 INFO @ Tue, 16 Jun 2020 09:32:31: 16000000 INFO @ Tue, 16 Jun 2020 09:32:33: 5000000 INFO @ Tue, 16 Jun 2020 09:32:36: 11000000 INFO @ Tue, 16 Jun 2020 09:32:37: 17000000 INFO @ Tue, 16 Jun 2020 09:32:40: 6000000 INFO @ Tue, 16 Jun 2020 09:32:42: 12000000 INFO @ Tue, 16 Jun 2020 09:32:43: 18000000 INFO @ Tue, 16 Jun 2020 09:32:46: 7000000 INFO @ Tue, 16 Jun 2020 09:32:49: 13000000 INFO @ Tue, 16 Jun 2020 09:32:49: 19000000 INFO @ Tue, 16 Jun 2020 09:32:53: 8000000 INFO @ Tue, 16 Jun 2020 09:32:55: 14000000 INFO @ Tue, 16 Jun 2020 09:32:55: 20000000 INFO @ Tue, 16 Jun 2020 09:33:01: 9000000 INFO @ Tue, 16 Jun 2020 09:33:01: 15000000 INFO @ Tue, 16 Jun 2020 09:33:02: 21000000 INFO @ Tue, 16 Jun 2020 09:33:07: 16000000 INFO @ Tue, 16 Jun 2020 09:33:07: 10000000 INFO @ Tue, 16 Jun 2020 09:33:08: 22000000 INFO @ Tue, 16 Jun 2020 09:33:14: 17000000 INFO @ Tue, 16 Jun 2020 09:33:14: 11000000 INFO @ Tue, 16 Jun 2020 09:33:14: 23000000 INFO @ Tue, 16 Jun 2020 09:33:20: 18000000 INFO @ Tue, 16 Jun 2020 09:33:21: 12000000 INFO @ Tue, 16 Jun 2020 09:33:21: 24000000 INFO @ Tue, 16 Jun 2020 09:33:26: 19000000 INFO @ Tue, 16 Jun 2020 09:33:27: 25000000 INFO @ Tue, 16 Jun 2020 09:33:27: 13000000 INFO @ Tue, 16 Jun 2020 09:33:32: 20000000 INFO @ Tue, 16 Jun 2020 09:33:33: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:33:33: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:33:33: #1 total tags in treatment: 25906162 INFO @ Tue, 16 Jun 2020 09:33:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:33: #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 09:33:33: #1 tags after filtering in treatment: 25906162 INFO @ Tue, 16 Jun 2020 09:33:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:34: 14000000 INFO @ Tue, 16 Jun 2020 09:33:35: #2 number of paired peaks: 144 WARNING @ Tue, 16 Jun 2020 09:33:35: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:35: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:33:35: #2 alternative fragment length(s) may be 0,34,128,412,425,550,579 bps INFO @ Tue, 16 Jun 2020 09:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:35: #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 09:33:35: #2 You may need to consider one of the other alternative d(s): 0,34,128,412,425,550,579 WARNING @ Tue, 16 Jun 2020 09:33:35: #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 09:33:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:39: 21000000 INFO @ Tue, 16 Jun 2020 09:33:40: 15000000 INFO @ Tue, 16 Jun 2020 09:33:45: 22000000 INFO @ Tue, 16 Jun 2020 09:33:47: 16000000 INFO @ Tue, 16 Jun 2020 09:33:52: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:54: 17000000 INFO @ Tue, 16 Jun 2020 09:33:58: 24000000 INFO @ Tue, 16 Jun 2020 09:34:01: 18000000 INFO @ Tue, 16 Jun 2020 09:34:05: 25000000 INFO @ Tue, 16 Jun 2020 09:34:08: 19000000 INFO @ Tue, 16 Jun 2020 09:34:11: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:34:11: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:34:11: #1 total tags in treatment: 25906162 INFO @ Tue, 16 Jun 2020 09:34:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:11: #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 09:34:12: #1 tags after filtering in treatment: 25906162 INFO @ Tue, 16 Jun 2020 09:34:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:13: #2 number of paired peaks: 144 WARNING @ Tue, 16 Jun 2020 09:34:13: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:14: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:34:14: #2 alternative fragment length(s) may be 0,34,128,412,425,550,579 bps INFO @ Tue, 16 Jun 2020 09:34:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466559/SRX466559.10_model.r WARNING @ Tue, 16 Jun 2020 09:34:14: #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 09:34:14: #2 You may need to consider one of the other alternative d(s): 0,34,128,412,425,550,579 WARNING @ Tue, 16 Jun 2020 09:34:14: #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 09:34:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:14: 20000000 INFO @ Tue, 16 Jun 2020 09:34:21: 21000000 INFO @ Tue, 16 Jun 2020 09:34:27: 22000000 INFO @ Tue, 16 Jun 2020 09:34:34: 23000000 INFO @ Tue, 16 Jun 2020 09:34:40: 24000000 INFO @ Tue, 16 Jun 2020 09:34:47: 25000000 BigWig に変換しました。 /var/spool/uge/at154/job_scripts/6368096: line 271: 112769 Terminated MACS $i /var/spool/uge/at154/job_scripts/6368096: line 271: 113383 Terminated MACS $i /var/spool/uge/at154/job_scripts/6368096: line 271: 123246 Terminated MACS $i ls: cannot access SRX466559.05.bed: No such file or directory mv: cannot stat ‘SRX466559.05.bed’: No such file or directory mv: cannot stat ‘SRX466559.05.bb’: No such file or directory ls: cannot access SRX466559.10.bed: No such file or directory mv: cannot stat ‘SRX466559.10.bed’: No such file or directory mv: cannot stat ‘SRX466559.10.bb’: No such file or directory ls: cannot access SRX466559.20.bed: No such file or directory mv: cannot stat ‘SRX466559.20.bed’: No such file or directory mv: cannot stat ‘SRX466559.20.bb’: No such file or directory