Job ID = 6529111 SRX = SRX5402767 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:08:17 42012466 reads; of these: 42012466 (100.00%) were unpaired; of these: 9981206 (23.76%) aligned 0 times 25880638 (61.60%) aligned exactly 1 time 6150622 (14.64%) aligned >1 times 76.24% overall alignment rate Time searching: 00:08:17 Overall time: 00:08:17 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] 5244627 / 32031260 = 0.1637 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, 30 Jun 2020 01:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.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, 30 Jun 2020 01:40:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:32: 1000000 INFO @ Tue, 30 Jun 2020 01:40:38: 2000000 INFO @ Tue, 30 Jun 2020 01:40:45: 3000000 INFO @ Tue, 30 Jun 2020 01:40:51: 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, 30 Jun 2020 01:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.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, 30 Jun 2020 01:40:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:58: 5000000 INFO @ Tue, 30 Jun 2020 01:41:03: 1000000 INFO @ Tue, 30 Jun 2020 01:41:04: 6000000 INFO @ Tue, 30 Jun 2020 01:41:11: 7000000 INFO @ Tue, 30 Jun 2020 01:41:11: 2000000 INFO @ Tue, 30 Jun 2020 01:41:18: 8000000 INFO @ Tue, 30 Jun 2020 01:41:19: 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, 30 Jun 2020 01:41:25: 9000000 INFO @ Tue, 30 Jun 2020 01:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.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, 30 Jun 2020 01:41:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:41:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:41:27: 4000000 INFO @ Tue, 30 Jun 2020 01:41:32: 10000000 INFO @ Tue, 30 Jun 2020 01:41:32: 1000000 INFO @ Tue, 30 Jun 2020 01:41:35: 5000000 INFO @ Tue, 30 Jun 2020 01:41:39: 11000000 INFO @ Tue, 30 Jun 2020 01:41:39: 2000000 INFO @ Tue, 30 Jun 2020 01:41:43: 6000000 INFO @ Tue, 30 Jun 2020 01:41:46: 12000000 INFO @ Tue, 30 Jun 2020 01:41:46: 3000000 INFO @ Tue, 30 Jun 2020 01:41:51: 7000000 INFO @ Tue, 30 Jun 2020 01:41:53: 4000000 INFO @ Tue, 30 Jun 2020 01:41:53: 13000000 INFO @ Tue, 30 Jun 2020 01:41:58: 8000000 INFO @ Tue, 30 Jun 2020 01:42:00: 14000000 INFO @ Tue, 30 Jun 2020 01:42:00: 5000000 INFO @ Tue, 30 Jun 2020 01:42:06: 9000000 INFO @ Tue, 30 Jun 2020 01:42:07: 15000000 INFO @ Tue, 30 Jun 2020 01:42:09: 6000000 INFO @ Tue, 30 Jun 2020 01:42:14: 10000000 INFO @ Tue, 30 Jun 2020 01:42:15: 16000000 INFO @ Tue, 30 Jun 2020 01:42:17: 7000000 INFO @ Tue, 30 Jun 2020 01:42:22: 11000000 INFO @ Tue, 30 Jun 2020 01:42:22: 17000000 INFO @ Tue, 30 Jun 2020 01:42:26: 8000000 INFO @ Tue, 30 Jun 2020 01:42:29: 18000000 INFO @ Tue, 30 Jun 2020 01:42:30: 12000000 INFO @ Tue, 30 Jun 2020 01:42:34: 9000000 INFO @ Tue, 30 Jun 2020 01:42:36: 19000000 INFO @ Tue, 30 Jun 2020 01:42:38: 13000000 INFO @ Tue, 30 Jun 2020 01:42:42: 10000000 INFO @ Tue, 30 Jun 2020 01:42:43: 20000000 INFO @ Tue, 30 Jun 2020 01:42:46: 14000000 INFO @ Tue, 30 Jun 2020 01:42:49: 21000000 INFO @ Tue, 30 Jun 2020 01:42:50: 11000000 INFO @ Tue, 30 Jun 2020 01:42:54: 15000000 INFO @ Tue, 30 Jun 2020 01:42:56: 22000000 INFO @ Tue, 30 Jun 2020 01:42:59: 12000000 INFO @ Tue, 30 Jun 2020 01:43:02: 23000000 INFO @ Tue, 30 Jun 2020 01:43:03: 16000000 INFO @ Tue, 30 Jun 2020 01:43:07: 13000000 INFO @ Tue, 30 Jun 2020 01:43:09: 24000000 INFO @ Tue, 30 Jun 2020 01:43:11: 17000000 INFO @ Tue, 30 Jun 2020 01:43:15: 14000000 INFO @ Tue, 30 Jun 2020 01:43:16: 25000000 INFO @ Tue, 30 Jun 2020 01:43:19: 18000000 INFO @ Tue, 30 Jun 2020 01:43:22: 26000000 INFO @ Tue, 30 Jun 2020 01:43:23: 15000000 INFO @ Tue, 30 Jun 2020 01:43:27: 19000000 INFO @ Tue, 30 Jun 2020 01:43:27: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:43:27: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:43:27: #1 total tags in treatment: 26786633 INFO @ Tue, 30 Jun 2020 01:43:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:43:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:43:28: #1 tags after filtering in treatment: 26786633 INFO @ Tue, 30 Jun 2020 01:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:43:28: #1 finished! INFO @ Tue, 30 Jun 2020 01:43:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:43:30: #2 number of paired peaks: 113 WARNING @ Tue, 30 Jun 2020 01:43:30: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 30 Jun 2020 01:43:30: start model_add_line... INFO @ Tue, 30 Jun 2020 01:43:30: start X-correlation... INFO @ Tue, 30 Jun 2020 01:43:30: end of X-cor INFO @ Tue, 30 Jun 2020 01:43:30: #2 finished! INFO @ Tue, 30 Jun 2020 01:43:30: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 01:43:30: #2 alternative fragment length(s) may be 0,43,580 bps INFO @ Tue, 30 Jun 2020 01:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.05_model.r WARNING @ Tue, 30 Jun 2020 01:43:30: #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, 30 Jun 2020 01:43:30: #2 You may need to consider one of the other alternative d(s): 0,43,580 WARNING @ Tue, 30 Jun 2020 01:43:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:43:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:43:31: 16000000 INFO @ Tue, 30 Jun 2020 01:43:34: 20000000 INFO @ Tue, 30 Jun 2020 01:43:39: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:43:42: 21000000 INFO @ Tue, 30 Jun 2020 01:43:47: 18000000 INFO @ Tue, 30 Jun 2020 01:43:50: 22000000 INFO @ Tue, 30 Jun 2020 01:43:54: 19000000 INFO @ Tue, 30 Jun 2020 01:43:58: 23000000 INFO @ Tue, 30 Jun 2020 01:44:02: 20000000 INFO @ Tue, 30 Jun 2020 01:44:06: 24000000 INFO @ Tue, 30 Jun 2020 01:44:10: 21000000 INFO @ Tue, 30 Jun 2020 01:44:14: 25000000 INFO @ Tue, 30 Jun 2020 01:44:18: 22000000 INFO @ Tue, 30 Jun 2020 01:44:22: 26000000 INFO @ Tue, 30 Jun 2020 01:44:26: 23000000 INFO @ Tue, 30 Jun 2020 01:44:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:44:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:44:29: #1 total tags in treatment: 26786633 INFO @ Tue, 30 Jun 2020 01:44:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:44:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:44:29: #1 tags after filtering in treatment: 26786633 INFO @ Tue, 30 Jun 2020 01:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:44:29: #1 finished! INFO @ Tue, 30 Jun 2020 01:44:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:44:31: #2 number of paired peaks: 113 WARNING @ Tue, 30 Jun 2020 01:44:31: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 30 Jun 2020 01:44:31: start model_add_line... INFO @ Tue, 30 Jun 2020 01:44:31: start X-correlation... INFO @ Tue, 30 Jun 2020 01:44:31: end of X-cor INFO @ Tue, 30 Jun 2020 01:44:31: #2 finished! INFO @ Tue, 30 Jun 2020 01:44:31: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 01:44:31: #2 alternative fragment length(s) may be 0,43,580 bps INFO @ Tue, 30 Jun 2020 01:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402767/SRX5402767.10_model.r WARNING @ Tue, 30 Jun 2020 01:44:31: #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, 30 Jun 2020 01:44:31: #2 You may need to consider one of the other alternative d(s): 0,43,580 WARNING @ Tue, 30 Jun 2020 01:44:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:44:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:44:34: 24000000 INFO @ Tue, 30 Jun 2020 01:44:42: 25000000 INFO @ Tue, 30 Jun 2020 01:44:50: 26000000 BigWig に変換しました。 /var/spool/uge/it029/job_scripts/6529111: line 293: 5876 Terminated MACS $i /var/spool/uge/it029/job_scripts/6529111: line 293: 5990 Terminated MACS $i /var/spool/uge/it029/job_scripts/6529111: line 293: 6099 Terminated MACS $i ls: cannot access SRX5402767.05.bed: No such file or directory mv: cannot stat ‘SRX5402767.05.bed’: No such file or directory mv: cannot stat ‘SRX5402767.05.bb’: No such file or directory ls: cannot access SRX5402767.10.bed: No such file or directory mv: cannot stat ‘SRX5402767.10.bed’: No such file or directory mv: cannot stat ‘SRX5402767.10.bb’: No such file or directory ls: cannot access SRX5402767.20.bed: No such file or directory mv: cannot stat ‘SRX5402767.20.bed’: No such file or directory mv: cannot stat ‘SRX5402767.20.bb’: No such file or directory