Job ID = 6368577 SRX = SRX5020803 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:20 prefetch.2.10.7: 1) Downloading 'SRR8201426'... 2020-06-16T00:14:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:20:48 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:20:48 prefetch.2.10.7: 1) 'SRR8201426' was downloaded successfully 2020-06-16T00:20:48 prefetch.2.10.7: 'SRR8201426' has 0 unresolved dependencies Read 36772981 spots for SRR8201426/SRR8201426.sra Written 36772981 spots for SRR8201426/SRR8201426.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: 00:12:19 36772981 reads; of these: 36772981 (100.00%) were unpaired; of these: 2200528 (5.98%) aligned 0 times 28846649 (78.45%) aligned exactly 1 time 5725804 (15.57%) aligned >1 times 94.02% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 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] 6352198 / 34572453 = 0.1837 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 09:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.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 09:43:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:03: 1000000 INFO @ Tue, 16 Jun 2020 09:44:10: 2000000 INFO @ Tue, 16 Jun 2020 09:44:17: 3000000 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 09:44:25: 4000000 INFO @ Tue, 16 Jun 2020 09:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.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 09:44:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:33: 5000000 INFO @ Tue, 16 Jun 2020 09:44:34: 1000000 INFO @ Tue, 16 Jun 2020 09:44:41: 6000000 INFO @ Tue, 16 Jun 2020 09:44:42: 2000000 INFO @ Tue, 16 Jun 2020 09:44:49: 7000000 INFO @ Tue, 16 Jun 2020 09:44:49: 3000000 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 09:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.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 09:44:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:57: 8000000 INFO @ Tue, 16 Jun 2020 09:44:58: 4000000 INFO @ Tue, 16 Jun 2020 09:45:04: 1000000 INFO @ Tue, 16 Jun 2020 09:45:06: 9000000 INFO @ Tue, 16 Jun 2020 09:45:06: 5000000 INFO @ Tue, 16 Jun 2020 09:45:12: 2000000 INFO @ Tue, 16 Jun 2020 09:45:13: 10000000 INFO @ Tue, 16 Jun 2020 09:45:14: 6000000 INFO @ Tue, 16 Jun 2020 09:45:20: 3000000 INFO @ Tue, 16 Jun 2020 09:45:22: 11000000 INFO @ Tue, 16 Jun 2020 09:45:22: 7000000 INFO @ Tue, 16 Jun 2020 09:45:28: 4000000 INFO @ Tue, 16 Jun 2020 09:45:29: 12000000 INFO @ Tue, 16 Jun 2020 09:45:31: 8000000 INFO @ Tue, 16 Jun 2020 09:45:36: 5000000 INFO @ Tue, 16 Jun 2020 09:45:37: 13000000 INFO @ Tue, 16 Jun 2020 09:45:39: 9000000 INFO @ Tue, 16 Jun 2020 09:45:44: 6000000 INFO @ Tue, 16 Jun 2020 09:45:44: 14000000 INFO @ Tue, 16 Jun 2020 09:45:47: 10000000 INFO @ Tue, 16 Jun 2020 09:45:51: 15000000 INFO @ Tue, 16 Jun 2020 09:45:52: 7000000 INFO @ Tue, 16 Jun 2020 09:45:55: 11000000 INFO @ Tue, 16 Jun 2020 09:45:59: 16000000 INFO @ Tue, 16 Jun 2020 09:46:00: 8000000 INFO @ Tue, 16 Jun 2020 09:46:03: 12000000 INFO @ Tue, 16 Jun 2020 09:46:06: 17000000 INFO @ Tue, 16 Jun 2020 09:46:08: 9000000 INFO @ Tue, 16 Jun 2020 09:46:12: 13000000 INFO @ Tue, 16 Jun 2020 09:46:13: 18000000 INFO @ Tue, 16 Jun 2020 09:46:16: 10000000 INFO @ Tue, 16 Jun 2020 09:46:20: 14000000 INFO @ Tue, 16 Jun 2020 09:46:21: 19000000 INFO @ Tue, 16 Jun 2020 09:46:24: 11000000 INFO @ Tue, 16 Jun 2020 09:46:28: 15000000 INFO @ Tue, 16 Jun 2020 09:46:28: 20000000 INFO @ Tue, 16 Jun 2020 09:46:32: 12000000 INFO @ Tue, 16 Jun 2020 09:46:35: 21000000 INFO @ Tue, 16 Jun 2020 09:46:36: 16000000 INFO @ Tue, 16 Jun 2020 09:46:40: 13000000 INFO @ Tue, 16 Jun 2020 09:46:43: 22000000 INFO @ Tue, 16 Jun 2020 09:46:44: 17000000 INFO @ Tue, 16 Jun 2020 09:46:48: 14000000 INFO @ Tue, 16 Jun 2020 09:46:50: 23000000 INFO @ Tue, 16 Jun 2020 09:46:52: 18000000 INFO @ Tue, 16 Jun 2020 09:46:56: 15000000 INFO @ Tue, 16 Jun 2020 09:46:57: 24000000 INFO @ Tue, 16 Jun 2020 09:47:00: 19000000 INFO @ Tue, 16 Jun 2020 09:47:04: 16000000 INFO @ Tue, 16 Jun 2020 09:47:05: 25000000 INFO @ Tue, 16 Jun 2020 09:47:09: 20000000 INFO @ Tue, 16 Jun 2020 09:47:12: 17000000 INFO @ Tue, 16 Jun 2020 09:47:12: 26000000 INFO @ Tue, 16 Jun 2020 09:47:17: 21000000 INFO @ Tue, 16 Jun 2020 09:47:20: 27000000 INFO @ Tue, 16 Jun 2020 09:47:20: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:47:25: 22000000 INFO @ Tue, 16 Jun 2020 09:47:27: 28000000 INFO @ Tue, 16 Jun 2020 09:47:28: 19000000 INFO @ Tue, 16 Jun 2020 09:47:29: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:47:29: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:47:29: #1 total tags in treatment: 28220255 INFO @ Tue, 16 Jun 2020 09:47:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:29: #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 09:47:29: #1 tags after filtering in treatment: 28220255 INFO @ Tue, 16 Jun 2020 09:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:31: #2 number of paired peaks: 103 WARNING @ Tue, 16 Jun 2020 09:47:31: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:31: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:47:31: #2 alternative fragment length(s) may be 0,31,47,49,65,533,585 bps INFO @ Tue, 16 Jun 2020 09:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.05_model.r WARNING @ Tue, 16 Jun 2020 09:47:31: #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 09:47:31: #2 You may need to consider one of the other alternative d(s): 0,31,47,49,65,533,585 WARNING @ Tue, 16 Jun 2020 09:47:31: #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 09:47:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:33: 23000000 INFO @ Tue, 16 Jun 2020 09:47:36: 20000000 INFO @ Tue, 16 Jun 2020 09:47:42: 24000000 INFO @ Tue, 16 Jun 2020 09:47:44: 21000000 INFO @ Tue, 16 Jun 2020 09:47:50: 25000000 INFO @ Tue, 16 Jun 2020 09:47:52: 22000000 INFO @ Tue, 16 Jun 2020 09:47:58: 26000000 INFO @ Tue, 16 Jun 2020 09:48:00: 23000000 INFO @ Tue, 16 Jun 2020 09:48:07: 27000000 INFO @ Tue, 16 Jun 2020 09:48:08: 24000000 INFO @ Tue, 16 Jun 2020 09:48:15: 28000000 INFO @ Tue, 16 Jun 2020 09:48:16: 25000000 INFO @ Tue, 16 Jun 2020 09:48:17: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:48:17: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:48:17: #1 total tags in treatment: 28220255 INFO @ Tue, 16 Jun 2020 09:48:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:17: #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 09:48:17: #1 tags after filtering in treatment: 28220255 INFO @ Tue, 16 Jun 2020 09:48:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:19: #2 number of paired peaks: 103 WARNING @ Tue, 16 Jun 2020 09:48:19: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:20: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:48:20: #2 alternative fragment length(s) may be 0,31,47,49,65,533,585 bps INFO @ Tue, 16 Jun 2020 09:48:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020803/SRX5020803.10_model.r WARNING @ Tue, 16 Jun 2020 09:48:20: #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 09:48:20: #2 You may need to consider one of the other alternative d(s): 0,31,47,49,65,533,585 WARNING @ Tue, 16 Jun 2020 09:48:20: #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 09:48:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at155/job_scripts/6368577: line 271: 20476 Terminated MACS $i /var/spool/uge/at155/job_scripts/6368577: line 271: 41913 Terminated MACS $i /var/spool/uge/at155/job_scripts/6368577: line 271: 42444 Terminated MACS $i ls: cannot access SRX5020803.05.bed: No such file or directory mv: cannot stat ‘SRX5020803.05.bed’: No such file or directory mv: cannot stat ‘SRX5020803.05.bb’: No such file or directory ls: cannot access SRX5020803.10.bed: No such file or directory mv: cannot stat ‘SRX5020803.10.bed’: No such file or directory mv: cannot stat ‘SRX5020803.10.bb’: No such file or directory ls: cannot access SRX5020803.20.bed: No such file or directory mv: cannot stat ‘SRX5020803.20.bed’: No such file or directory mv: cannot stat ‘SRX5020803.20.bb’: No such file or directory