Job ID = 6368735 SRX = SRX5402759 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:32:12 prefetch.2.10.7: 1) Downloading 'SRR8602993'... 2020-06-16T00:32:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:53 prefetch.2.10.7: 1) 'SRR8602993' was downloaded successfully Read 38836323 spots for SRR8602993/SRR8602993.sra Written 38836323 spots for SRR8602993/SRR8602993.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: 00:08:34 38836323 reads; of these: 38836323 (100.00%) were unpaired; of these: 3703939 (9.54%) aligned 0 times 28346284 (72.99%) aligned exactly 1 time 6786100 (17.47%) aligned >1 times 90.46% overall alignment rate Time searching: 00:08:34 Overall time: 00:08:34 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] 8783280 / 35132384 = 0.2500 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 09:54:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.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 09:54:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:35: 1000000 INFO @ Tue, 16 Jun 2020 09:54:40: 2000000 INFO @ Tue, 16 Jun 2020 09:54:46: 3000000 INFO @ Tue, 16 Jun 2020 09:54:52: 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 09:54:57: 5000000 INFO @ Tue, 16 Jun 2020 09:55:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.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 09:55:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:03: 6000000 INFO @ Tue, 16 Jun 2020 09:55:08: 1000000 INFO @ Tue, 16 Jun 2020 09:55:10: 7000000 INFO @ Tue, 16 Jun 2020 09:55:14: 2000000 INFO @ Tue, 16 Jun 2020 09:55:16: 8000000 INFO @ Tue, 16 Jun 2020 09:55:20: 3000000 INFO @ Tue, 16 Jun 2020 09:55:22: 9000000 INFO @ Tue, 16 Jun 2020 09:55:27: 4000000 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 09:55:29: 10000000 INFO @ Tue, 16 Jun 2020 09:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.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 09:55:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:33: 5000000 INFO @ Tue, 16 Jun 2020 09:55:35: 11000000 INFO @ Tue, 16 Jun 2020 09:55:36: 1000000 INFO @ Tue, 16 Jun 2020 09:55:40: 6000000 INFO @ Tue, 16 Jun 2020 09:55:41: 12000000 INFO @ Tue, 16 Jun 2020 09:55:42: 2000000 INFO @ Tue, 16 Jun 2020 09:55:46: 7000000 INFO @ Tue, 16 Jun 2020 09:55:48: 13000000 INFO @ Tue, 16 Jun 2020 09:55:49: 3000000 INFO @ Tue, 16 Jun 2020 09:55:53: 8000000 INFO @ Tue, 16 Jun 2020 09:55:54: 14000000 INFO @ Tue, 16 Jun 2020 09:55:55: 4000000 INFO @ Tue, 16 Jun 2020 09:55:59: 9000000 INFO @ Tue, 16 Jun 2020 09:56:00: 15000000 INFO @ Tue, 16 Jun 2020 09:56:02: 5000000 INFO @ Tue, 16 Jun 2020 09:56:06: 10000000 INFO @ Tue, 16 Jun 2020 09:56:06: 16000000 INFO @ Tue, 16 Jun 2020 09:56:08: 6000000 INFO @ Tue, 16 Jun 2020 09:56:13: 11000000 INFO @ Tue, 16 Jun 2020 09:56:13: 17000000 INFO @ Tue, 16 Jun 2020 09:56:15: 7000000 INFO @ Tue, 16 Jun 2020 09:56:19: 18000000 INFO @ Tue, 16 Jun 2020 09:56:19: 12000000 INFO @ Tue, 16 Jun 2020 09:56:22: 8000000 INFO @ Tue, 16 Jun 2020 09:56:25: 19000000 INFO @ Tue, 16 Jun 2020 09:56:26: 13000000 INFO @ Tue, 16 Jun 2020 09:56:28: 9000000 INFO @ Tue, 16 Jun 2020 09:56:32: 20000000 INFO @ Tue, 16 Jun 2020 09:56:33: 14000000 INFO @ Tue, 16 Jun 2020 09:56:35: 10000000 INFO @ Tue, 16 Jun 2020 09:56:38: 21000000 INFO @ Tue, 16 Jun 2020 09:56:39: 15000000 INFO @ Tue, 16 Jun 2020 09:56:41: 11000000 INFO @ Tue, 16 Jun 2020 09:56:45: 22000000 INFO @ Tue, 16 Jun 2020 09:56:46: 16000000 INFO @ Tue, 16 Jun 2020 09:56:48: 12000000 INFO @ Tue, 16 Jun 2020 09:56:51: 23000000 INFO @ Tue, 16 Jun 2020 09:56:52: 17000000 INFO @ Tue, 16 Jun 2020 09:56:55: 13000000 INFO @ Tue, 16 Jun 2020 09:56:57: 24000000 INFO @ Tue, 16 Jun 2020 09:56:59: 18000000 INFO @ Tue, 16 Jun 2020 09:57:01: 14000000 INFO @ Tue, 16 Jun 2020 09:57:04: 25000000 INFO @ Tue, 16 Jun 2020 09:57:05: 19000000 INFO @ Tue, 16 Jun 2020 09:57:08: 15000000 INFO @ Tue, 16 Jun 2020 09:57:10: 26000000 INFO @ Tue, 16 Jun 2020 09:57:12: 20000000 INFO @ Tue, 16 Jun 2020 09:57:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:57:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:57:12: #1 total tags in treatment: 26349104 INFO @ Tue, 16 Jun 2020 09:57:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:12: #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 09:57:13: #1 tags after filtering in treatment: 26349104 INFO @ Tue, 16 Jun 2020 09:57:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:14: 16000000 INFO @ Tue, 16 Jun 2020 09:57:15: #2 number of paired peaks: 159 WARNING @ Tue, 16 Jun 2020 09:57:15: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:15: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:57:15: #2 alternative fragment length(s) may be 0,13,37,408,440,532,556,559,588 bps INFO @ Tue, 16 Jun 2020 09:57:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.05_model.r WARNING @ Tue, 16 Jun 2020 09:57:15: #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 09:57:15: #2 You may need to consider one of the other alternative d(s): 0,13,37,408,440,532,556,559,588 WARNING @ Tue, 16 Jun 2020 09:57:15: #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 09:57:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:18: 21000000 INFO @ Tue, 16 Jun 2020 09:57:20: 17000000 INFO @ Tue, 16 Jun 2020 09:57:24: 22000000 INFO @ Tue, 16 Jun 2020 09:57:26: 18000000 INFO @ Tue, 16 Jun 2020 09:57:30: 23000000 INFO @ Tue, 16 Jun 2020 09:57:32: 19000000 INFO @ Tue, 16 Jun 2020 09:57:36: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:57:39: 20000000 INFO @ Tue, 16 Jun 2020 09:57:43: 25000000 INFO @ Tue, 16 Jun 2020 09:57:45: 21000000 INFO @ Tue, 16 Jun 2020 09:57:49: 26000000 INFO @ Tue, 16 Jun 2020 09:57:51: 22000000 INFO @ Tue, 16 Jun 2020 09:57:51: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:57:51: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:57:51: #1 total tags in treatment: 26349104 INFO @ Tue, 16 Jun 2020 09:57:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:51: #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 09:57:51: #1 tags after filtering in treatment: 26349104 INFO @ Tue, 16 Jun 2020 09:57:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:53: #2 number of paired peaks: 159 WARNING @ Tue, 16 Jun 2020 09:57:53: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:53: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:57:53: #2 alternative fragment length(s) may be 0,13,37,408,440,532,556,559,588 bps INFO @ Tue, 16 Jun 2020 09:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.10_model.r WARNING @ Tue, 16 Jun 2020 09:57:53: #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 09:57:53: #2 You may need to consider one of the other alternative d(s): 0,13,37,408,440,532,556,559,588 WARNING @ Tue, 16 Jun 2020 09:57:53: #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 09:57:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:57: 23000000 INFO @ Tue, 16 Jun 2020 09:58:03: 24000000 INFO @ Tue, 16 Jun 2020 09:58:08: 25000000 INFO @ Tue, 16 Jun 2020 09:58:14: 26000000 INFO @ Tue, 16 Jun 2020 09:58:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:58:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:58:16: #1 total tags in treatment: 26349104 INFO @ Tue, 16 Jun 2020 09:58:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:16: #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 09:58:17: #1 tags after filtering in treatment: 26349104 INFO @ Tue, 16 Jun 2020 09:58:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:18: #2 number of paired peaks: 159 WARNING @ Tue, 16 Jun 2020 09:58:18: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 16 Jun 2020 09:58:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:19: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:58:19: #2 alternative fragment length(s) may be 0,13,37,408,440,532,556,559,588 bps INFO @ Tue, 16 Jun 2020 09:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402759/SRX5402759.20_model.r WARNING @ Tue, 16 Jun 2020 09:58:19: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:58:19: #2 You may need to consider one of the other alternative d(s): 0,13,37,408,440,532,556,559,588 WARNING @ Tue, 16 Jun 2020 09:58:19: #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 09:58:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at162/job_scripts/6368735: line 271: 59920 Terminated MACS $i /var/spool/uge/at162/job_scripts/6368735: line 271: 60323 Terminated MACS $i /var/spool/uge/at162/job_scripts/6368735: line 271: 60726 Terminated MACS $i ls: cannot access SRX5402759.05.bed: No such file or directory mv: cannot stat ‘SRX5402759.05.bed’: No such file or directory mv: cannot stat ‘SRX5402759.05.bb’: No such file or directory ls: cannot access SRX5402759.10.bed: No such file or directory mv: cannot stat ‘SRX5402759.10.bed’: No such file or directory mv: cannot stat ‘SRX5402759.10.bb’: No such file or directory ls: cannot access SRX5402759.20.bed: No such file or directory mv: cannot stat ‘SRX5402759.20.bed’: No such file or directory mv: cannot stat ‘SRX5402759.20.bb’: No such file or directory