Job ID = 2590226 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,139,730 reads read : 60,279,460 reads written : 30,139,730 reads 0-length : 30,139,730 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:08:42 30139730 reads; of these: 30139730 (100.00%) were unpaired; of these: 990407 (3.29%) aligned 0 times 24346259 (80.78%) aligned exactly 1 time 4803064 (15.94%) aligned >1 times 96.71% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 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] 6277377 / 29149323 = 0.2154 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 20:33:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.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 @ Mon, 12 Aug 2019 20:33:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:33:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:33:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.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 @ Mon, 12 Aug 2019 20:33:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:33:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.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 @ Mon, 12 Aug 2019 20:33:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:33:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:33:46: 1000000 INFO @ Mon, 12 Aug 2019 20:33:47: 1000000 INFO @ Mon, 12 Aug 2019 20:33:48: 1000000 INFO @ Mon, 12 Aug 2019 20:33:54: 2000000 INFO @ Mon, 12 Aug 2019 20:33:55: 2000000 INFO @ Mon, 12 Aug 2019 20:33:55: 2000000 INFO @ Mon, 12 Aug 2019 20:34:02: 3000000 INFO @ Mon, 12 Aug 2019 20:34:03: 3000000 INFO @ Mon, 12 Aug 2019 20:34:03: 3000000 INFO @ Mon, 12 Aug 2019 20:34:09: 4000000 INFO @ Mon, 12 Aug 2019 20:34:10: 4000000 INFO @ Mon, 12 Aug 2019 20:34:11: 4000000 INFO @ Mon, 12 Aug 2019 20:34:17: 5000000 INFO @ Mon, 12 Aug 2019 20:34:17: 5000000 INFO @ Mon, 12 Aug 2019 20:34:19: 5000000 INFO @ Mon, 12 Aug 2019 20:34:24: 6000000 INFO @ Mon, 12 Aug 2019 20:34:25: 6000000 INFO @ Mon, 12 Aug 2019 20:34:28: 6000000 INFO @ Mon, 12 Aug 2019 20:34:31: 7000000 INFO @ Mon, 12 Aug 2019 20:34:32: 7000000 INFO @ Mon, 12 Aug 2019 20:34:36: 7000000 INFO @ Mon, 12 Aug 2019 20:34:38: 8000000 INFO @ Mon, 12 Aug 2019 20:34:39: 8000000 INFO @ Mon, 12 Aug 2019 20:34:44: 8000000 INFO @ Mon, 12 Aug 2019 20:34:45: 9000000 INFO @ Mon, 12 Aug 2019 20:34:46: 9000000 INFO @ Mon, 12 Aug 2019 20:34:53: 10000000 INFO @ Mon, 12 Aug 2019 20:34:53: 9000000 INFO @ Mon, 12 Aug 2019 20:34:54: 10000000 INFO @ Mon, 12 Aug 2019 20:35:00: 11000000 INFO @ Mon, 12 Aug 2019 20:35:01: 11000000 INFO @ Mon, 12 Aug 2019 20:35:01: 10000000 INFO @ Mon, 12 Aug 2019 20:35:07: 12000000 INFO @ Mon, 12 Aug 2019 20:35:08: 12000000 INFO @ Mon, 12 Aug 2019 20:35:09: 11000000 INFO @ Mon, 12 Aug 2019 20:35:14: 13000000 INFO @ Mon, 12 Aug 2019 20:35:15: 13000000 INFO @ Mon, 12 Aug 2019 20:35:18: 12000000 INFO @ Mon, 12 Aug 2019 20:35:21: 14000000 INFO @ Mon, 12 Aug 2019 20:35:23: 14000000 INFO @ Mon, 12 Aug 2019 20:35:26: 13000000 INFO @ Mon, 12 Aug 2019 20:35:28: 15000000 INFO @ Mon, 12 Aug 2019 20:35:30: 15000000 INFO @ Mon, 12 Aug 2019 20:35:34: 14000000 INFO @ Mon, 12 Aug 2019 20:35:36: 16000000 INFO @ Mon, 12 Aug 2019 20:35:37: 16000000 INFO @ Mon, 12 Aug 2019 20:35:42: 15000000 INFO @ Mon, 12 Aug 2019 20:35:43: 17000000 INFO @ Mon, 12 Aug 2019 20:35:44: 17000000 INFO @ Mon, 12 Aug 2019 20:35:50: 18000000 INFO @ Mon, 12 Aug 2019 20:35:51: 16000000 INFO @ Mon, 12 Aug 2019 20:35:52: 18000000 INFO @ Mon, 12 Aug 2019 20:35:57: 19000000 INFO @ Mon, 12 Aug 2019 20:35:59: 19000000 INFO @ Mon, 12 Aug 2019 20:35:59: 17000000 INFO @ Mon, 12 Aug 2019 20:36:04: 20000000 INFO @ Mon, 12 Aug 2019 20:36:06: 20000000 INFO @ Mon, 12 Aug 2019 20:36:07: 18000000 INFO @ Mon, 12 Aug 2019 20:36:11: 21000000 INFO @ Mon, 12 Aug 2019 20:36:13: 21000000 INFO @ Mon, 12 Aug 2019 20:36:16: 19000000 INFO @ Mon, 12 Aug 2019 20:36:19: 22000000 INFO @ Mon, 12 Aug 2019 20:36:20: 22000000 INFO @ Mon, 12 Aug 2019 20:36:24: 20000000 INFO @ Mon, 12 Aug 2019 20:36:25: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:36:25: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:36:25: #1 total tags in treatment: 22871946 INFO @ Mon, 12 Aug 2019 20:36:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:36:25: #1 tags after filtering in treatment: 22871946 INFO @ Mon, 12 Aug 2019 20:36:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:25: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:27: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:36:27: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:36:27: #1 total tags in treatment: 22871946 INFO @ Mon, 12 Aug 2019 20:36:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:36:27: #2 number of paired peaks: 189 WARNING @ Mon, 12 Aug 2019 20:36:27: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Mon, 12 Aug 2019 20:36:27: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:27: #1 tags after filtering in treatment: 22871946 INFO @ Mon, 12 Aug 2019 20:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:27: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:28: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:28: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:28: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:28: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:36:28: #2 alternative fragment length(s) may be 0,46,558,585 bps INFO @ Mon, 12 Aug 2019 20:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.10_model.r WARNING @ Mon, 12 Aug 2019 20:36:28: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:36:28: #2 You may need to consider one of the other alternative d(s): 0,46,558,585 WARNING @ Mon, 12 Aug 2019 20:36:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:36:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:29: #2 number of paired peaks: 189 WARNING @ Mon, 12 Aug 2019 20:36:29: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Mon, 12 Aug 2019 20:36:29: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:30: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:30: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:30: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:30: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:36:30: #2 alternative fragment length(s) may be 0,46,558,585 bps INFO @ Mon, 12 Aug 2019 20:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.20_model.r WARNING @ Mon, 12 Aug 2019 20:36:30: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:36:30: #2 You may need to consider one of the other alternative d(s): 0,46,558,585 WARNING @ Mon, 12 Aug 2019 20:36:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:36:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:32: 21000000 INFO @ Mon, 12 Aug 2019 20:36:40: 22000000 INFO @ Mon, 12 Aug 2019 20:36:47: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:36:47: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:36:47: #1 total tags in treatment: 22871946 INFO @ Mon, 12 Aug 2019 20:36:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:36:48: #1 tags after filtering in treatment: 22871946 INFO @ Mon, 12 Aug 2019 20:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:48: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:50: #2 number of paired peaks: 189 WARNING @ Mon, 12 Aug 2019 20:36:50: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Mon, 12 Aug 2019 20:36:50: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:50: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:50: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:50: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:50: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:36:50: #2 alternative fragment length(s) may be 0,46,558,585 bps INFO @ Mon, 12 Aug 2019 20:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709767/SRX5709767.05_model.r WARNING @ Mon, 12 Aug 2019 20:36:50: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:36:50: #2 You may need to consider one of the other alternative d(s): 0,46,558,585 WARNING @ Mon, 12 Aug 2019 20:36:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:36:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 ls: cannot access SRX5709767.05.bed: No such file or directory mv: cannot stat ‘SRX5709767.05.bed’: No such file or directory /var/spool/uge/at091/job_scripts/2590226: line 335: 21982 Terminated MACS $i /var/spool/uge/at091/job_scripts/2590226: line 335: 21996 Terminated MACS $i /var/spool/uge/at091/job_scripts/2590226: line 335: 22010 Terminated MACS $i mv: cannot stat ‘SRX5709767.05.bb’: No such file or directory ls: cannot access SRX5709767.10.bed: No such file or directory mv: cannot stat ‘SRX5709767.10.bed’: No such file or directory mv: cannot stat ‘SRX5709767.10.bb’: No such file or directory ls: cannot access SRX5709767.20.bed: No such file or directory mv: cannot stat ‘SRX5709767.20.bed’: No such file or directory mv: cannot stat ‘SRX5709767.20.bb’: No such file or directory