Job ID = 6366660 SRX = SRX216761 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:15 prefetch.2.10.7: 1) Downloading 'SRR648395'... 2020-06-15T22:56:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:41 prefetch.2.10.7: 1) 'SRR648395' was downloaded successfully Read 28318925 spots for SRR648395/SRR648395.sra Written 28318925 spots for SRR648395/SRR648395.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: 00:06:11 28318925 reads; of these: 28318925 (100.00%) were unpaired; of these: 1303413 (4.60%) aligned 0 times 22924645 (80.95%) aligned exactly 1 time 4090867 (14.45%) aligned >1 times 95.40% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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 12 files... [bam_rmdupse_core] 3439344 / 27015512 = 0.1273 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 08:12:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.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 08:12:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:02: 1000000 INFO @ Tue, 16 Jun 2020 08:13:07: 2000000 INFO @ Tue, 16 Jun 2020 08:13:13: 3000000 INFO @ Tue, 16 Jun 2020 08:13:18: 4000000 INFO @ Tue, 16 Jun 2020 08:13:23: 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 08:13:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.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 08:13:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:28: 6000000 INFO @ Tue, 16 Jun 2020 08:13:32: 1000000 INFO @ Tue, 16 Jun 2020 08:13:33: 7000000 INFO @ Tue, 16 Jun 2020 08:13:38: 2000000 INFO @ Tue, 16 Jun 2020 08:13:38: 8000000 INFO @ Tue, 16 Jun 2020 08:13:43: 3000000 INFO @ Tue, 16 Jun 2020 08:13:44: 9000000 INFO @ Tue, 16 Jun 2020 08:13:48: 4000000 INFO @ Tue, 16 Jun 2020 08:13:49: 10000000 INFO @ Tue, 16 Jun 2020 08:13:53: 5000000 INFO @ Tue, 16 Jun 2020 08:13:54: 11000000 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 08:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.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 08:13:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:58: 6000000 INFO @ Tue, 16 Jun 2020 08:13:59: 12000000 INFO @ Tue, 16 Jun 2020 08:14:02: 1000000 INFO @ Tue, 16 Jun 2020 08:14:04: 7000000 INFO @ Tue, 16 Jun 2020 08:14:04: 13000000 INFO @ Tue, 16 Jun 2020 08:14:08: 2000000 INFO @ Tue, 16 Jun 2020 08:14:09: 8000000 INFO @ Tue, 16 Jun 2020 08:14:10: 14000000 INFO @ Tue, 16 Jun 2020 08:14:13: 3000000 INFO @ Tue, 16 Jun 2020 08:14:15: 9000000 INFO @ Tue, 16 Jun 2020 08:14:15: 15000000 INFO @ Tue, 16 Jun 2020 08:14:18: 4000000 INFO @ Tue, 16 Jun 2020 08:14:20: 10000000 INFO @ Tue, 16 Jun 2020 08:14:20: 16000000 INFO @ Tue, 16 Jun 2020 08:14:23: 5000000 INFO @ Tue, 16 Jun 2020 08:14:25: 11000000 INFO @ Tue, 16 Jun 2020 08:14:25: 17000000 INFO @ Tue, 16 Jun 2020 08:14:28: 6000000 INFO @ Tue, 16 Jun 2020 08:14:30: 12000000 INFO @ Tue, 16 Jun 2020 08:14:31: 18000000 INFO @ Tue, 16 Jun 2020 08:14:34: 7000000 INFO @ Tue, 16 Jun 2020 08:14:36: 13000000 INFO @ Tue, 16 Jun 2020 08:14:36: 19000000 INFO @ Tue, 16 Jun 2020 08:14:39: 8000000 INFO @ Tue, 16 Jun 2020 08:14:41: 14000000 INFO @ Tue, 16 Jun 2020 08:14:41: 20000000 INFO @ Tue, 16 Jun 2020 08:14:44: 9000000 INFO @ Tue, 16 Jun 2020 08:14:46: 21000000 INFO @ Tue, 16 Jun 2020 08:14:46: 15000000 INFO @ Tue, 16 Jun 2020 08:14:49: 10000000 INFO @ Tue, 16 Jun 2020 08:14:52: 22000000 INFO @ Tue, 16 Jun 2020 08:14:52: 16000000 INFO @ Tue, 16 Jun 2020 08:14:55: 11000000 INFO @ Tue, 16 Jun 2020 08:14:57: 23000000 INFO @ Tue, 16 Jun 2020 08:14:57: 17000000 INFO @ Tue, 16 Jun 2020 08:15:00: 12000000 INFO @ Tue, 16 Jun 2020 08:15:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:15:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:15:00: #1 total tags in treatment: 23576168 INFO @ Tue, 16 Jun 2020 08:15:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:00: #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 08:15:01: #1 tags after filtering in treatment: 23576168 INFO @ Tue, 16 Jun 2020 08:15:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:02: #2 number of paired peaks: 185 WARNING @ Tue, 16 Jun 2020 08:15:02: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:02: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:15:02: #2 alternative fragment length(s) may be 0,19,43,581,598 bps INFO @ Tue, 16 Jun 2020 08:15:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.05_model.r WARNING @ Tue, 16 Jun 2020 08:15:02: #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 08:15:02: #2 You may need to consider one of the other alternative d(s): 0,19,43,581,598 WARNING @ Tue, 16 Jun 2020 08:15:02: #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 08:15:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:03: 18000000 INFO @ Tue, 16 Jun 2020 08:15:05: 13000000 INFO @ Tue, 16 Jun 2020 08:15:08: 19000000 INFO @ Tue, 16 Jun 2020 08:15:11: 14000000 INFO @ Tue, 16 Jun 2020 08:15:13: 20000000 INFO @ Tue, 16 Jun 2020 08:15:16: 15000000 INFO @ Tue, 16 Jun 2020 08:15:18: 21000000 INFO @ Tue, 16 Jun 2020 08:15:21: 16000000 INFO @ Tue, 16 Jun 2020 08:15:24: 22000000 INFO @ Tue, 16 Jun 2020 08:15:27: 17000000 INFO @ Tue, 16 Jun 2020 08:15:29: 23000000 INFO @ Tue, 16 Jun 2020 08:15:32: 18000000 INFO @ Tue, 16 Jun 2020 08:15:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:15:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:15:32: #1 total tags in treatment: 23576168 INFO @ Tue, 16 Jun 2020 08:15:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:32: #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 08:15:33: #1 tags after filtering in treatment: 23576168 INFO @ Tue, 16 Jun 2020 08:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:34: #2 number of paired peaks: 185 WARNING @ Tue, 16 Jun 2020 08:15:34: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:35: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:15:35: #2 alternative fragment length(s) may be 0,19,43,581,598 bps INFO @ Tue, 16 Jun 2020 08:15:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:35: #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 08:15:35: #2 You may need to consider one of the other alternative d(s): 0,19,43,581,598 WARNING @ Tue, 16 Jun 2020 08:15:35: #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 08:15:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:37: 19000000 INFO @ Tue, 16 Jun 2020 08:15:42: 20000000 INFO @ Tue, 16 Jun 2020 08:15:48: 21000000 INFO @ Tue, 16 Jun 2020 08:15:53: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:58: 23000000 INFO @ Tue, 16 Jun 2020 08:16:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:16:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:16:01: #1 total tags in treatment: 23576168 INFO @ Tue, 16 Jun 2020 08:16:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:01: #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 08:16:02: #1 tags after filtering in treatment: 23576168 INFO @ Tue, 16 Jun 2020 08:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:03: #2 number of paired peaks: 185 WARNING @ Tue, 16 Jun 2020 08:16:03: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:03: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:16:03: #2 alternative fragment length(s) may be 0,19,43,581,598 bps INFO @ Tue, 16 Jun 2020 08:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216761/SRX216761.20_model.r WARNING @ Tue, 16 Jun 2020 08:16:03: #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 08:16:03: #2 You may need to consider one of the other alternative d(s): 0,19,43,581,598 WARNING @ Tue, 16 Jun 2020 08:16:03: #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 08:16:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at157/job_scripts/6366660: line 271: 69588 Terminated MACS $i /var/spool/uge/at157/job_scripts/6366660: line 271: 70020 Terminated MACS $i /var/spool/uge/at157/job_scripts/6366660: line 271: 70298 Terminated MACS $i ls: cannot access SRX216761.05.bed: No such file or directory mv: cannot stat ‘SRX216761.05.bed’: No such file or directory mv: cannot stat ‘SRX216761.05.bb’: No such file or directory ls: cannot access SRX216761.10.bed: No such file or directory mv: cannot stat ‘SRX216761.10.bed’: No such file or directory mv: cannot stat ‘SRX216761.10.bb’: No such file or directory ls: cannot access SRX216761.20.bed: No such file or directory mv: cannot stat ‘SRX216761.20.bed’: No such file or directory mv: cannot stat ‘SRX216761.20.bb’: No such file or directory