Job ID = 2590080 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,570,721 reads read : 32,570,721 reads written : 32,570,721 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: 00:08:36 32570721 reads; of these: 32570721 (100.00%) were unpaired; of these: 779467 (2.39%) aligned 0 times 25992230 (79.80%) aligned exactly 1 time 5799024 (17.80%) aligned >1 times 97.61% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 5125936 / 31791254 = 0.1612 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 20:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.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 20:00:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.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 20:00:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.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 20:00:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:57: 1000000 INFO @ Mon, 12 Aug 2019 20:00:58: 1000000 INFO @ Mon, 12 Aug 2019 20:00:58: 1000000 INFO @ Mon, 12 Aug 2019 20:01:03: 2000000 INFO @ Mon, 12 Aug 2019 20:01:05: 2000000 INFO @ Mon, 12 Aug 2019 20:01:06: 2000000 INFO @ Mon, 12 Aug 2019 20:01:09: 3000000 INFO @ Mon, 12 Aug 2019 20:01:12: 3000000 INFO @ Mon, 12 Aug 2019 20:01:14: 3000000 INFO @ Mon, 12 Aug 2019 20:01:16: 4000000 INFO @ Mon, 12 Aug 2019 20:01:18: 4000000 INFO @ Mon, 12 Aug 2019 20:01:22: 4000000 INFO @ Mon, 12 Aug 2019 20:01:23: 5000000 INFO @ Mon, 12 Aug 2019 20:01:25: 5000000 INFO @ Mon, 12 Aug 2019 20:01:30: 6000000 INFO @ Mon, 12 Aug 2019 20:01:31: 5000000 INFO @ Mon, 12 Aug 2019 20:01:32: 6000000 INFO @ Mon, 12 Aug 2019 20:01:36: 7000000 INFO @ Mon, 12 Aug 2019 20:01:37: 6000000 INFO @ Mon, 12 Aug 2019 20:01:39: 7000000 INFO @ Mon, 12 Aug 2019 20:01:43: 8000000 INFO @ Mon, 12 Aug 2019 20:01:44: 7000000 INFO @ Mon, 12 Aug 2019 20:01:46: 8000000 INFO @ Mon, 12 Aug 2019 20:01:50: 9000000 INFO @ Mon, 12 Aug 2019 20:01:51: 8000000 INFO @ Mon, 12 Aug 2019 20:01:52: 9000000 INFO @ Mon, 12 Aug 2019 20:01:57: 10000000 INFO @ Mon, 12 Aug 2019 20:01:58: 9000000 INFO @ Mon, 12 Aug 2019 20:01:59: 10000000 INFO @ Mon, 12 Aug 2019 20:02:04: 11000000 INFO @ Mon, 12 Aug 2019 20:02:05: 10000000 INFO @ Mon, 12 Aug 2019 20:02:06: 11000000 INFO @ Mon, 12 Aug 2019 20:02:11: 12000000 INFO @ Mon, 12 Aug 2019 20:02:12: 11000000 INFO @ Mon, 12 Aug 2019 20:02:13: 12000000 INFO @ Mon, 12 Aug 2019 20:02:18: 13000000 INFO @ Mon, 12 Aug 2019 20:02:19: 12000000 INFO @ Mon, 12 Aug 2019 20:02:20: 13000000 INFO @ Mon, 12 Aug 2019 20:02:25: 14000000 INFO @ Mon, 12 Aug 2019 20:02:26: 13000000 INFO @ Mon, 12 Aug 2019 20:02:27: 14000000 INFO @ Mon, 12 Aug 2019 20:02:32: 15000000 INFO @ Mon, 12 Aug 2019 20:02:33: 14000000 INFO @ Mon, 12 Aug 2019 20:02:34: 15000000 INFO @ Mon, 12 Aug 2019 20:02:39: 16000000 INFO @ Mon, 12 Aug 2019 20:02:40: 15000000 INFO @ Mon, 12 Aug 2019 20:02:42: 16000000 INFO @ Mon, 12 Aug 2019 20:02:46: 17000000 INFO @ Mon, 12 Aug 2019 20:02:47: 16000000 INFO @ Mon, 12 Aug 2019 20:02:48: 17000000 INFO @ Mon, 12 Aug 2019 20:02:53: 17000000 INFO @ Mon, 12 Aug 2019 20:02:54: 18000000 INFO @ Mon, 12 Aug 2019 20:02:55: 18000000 INFO @ Mon, 12 Aug 2019 20:03:00: 18000000 INFO @ Mon, 12 Aug 2019 20:03:02: 19000000 INFO @ Mon, 12 Aug 2019 20:03:03: 19000000 INFO @ Mon, 12 Aug 2019 20:03:07: 19000000 INFO @ Mon, 12 Aug 2019 20:03:09: 20000000 INFO @ Mon, 12 Aug 2019 20:03:10: 20000000 INFO @ Mon, 12 Aug 2019 20:03:14: 20000000 INFO @ Mon, 12 Aug 2019 20:03:16: 21000000 INFO @ Mon, 12 Aug 2019 20:03:18: 21000000 INFO @ Mon, 12 Aug 2019 20:03:21: 21000000 INFO @ Mon, 12 Aug 2019 20:03:23: 22000000 INFO @ Mon, 12 Aug 2019 20:03:26: 22000000 INFO @ Mon, 12 Aug 2019 20:03:28: 22000000 INFO @ Mon, 12 Aug 2019 20:03:30: 23000000 INFO @ Mon, 12 Aug 2019 20:03:33: 23000000 INFO @ Mon, 12 Aug 2019 20:03:34: 23000000 INFO @ Mon, 12 Aug 2019 20:03:36: 24000000 INFO @ Mon, 12 Aug 2019 20:03:41: 24000000 INFO @ Mon, 12 Aug 2019 20:03:41: 24000000 INFO @ Mon, 12 Aug 2019 20:03:43: 25000000 INFO @ Mon, 12 Aug 2019 20:03:48: 25000000 INFO @ Mon, 12 Aug 2019 20:03:49: 25000000 INFO @ Mon, 12 Aug 2019 20:03:50: 26000000 INFO @ Mon, 12 Aug 2019 20:03:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:03:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:03:55: #1 total tags in treatment: 26665318 INFO @ Mon, 12 Aug 2019 20:03:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:03:55: #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 20:03:55: 26000000 INFO @ Mon, 12 Aug 2019 20:03:56: #1 tags after filtering in treatment: 26665318 INFO @ Mon, 12 Aug 2019 20:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:03:56: #1 finished! INFO @ Mon, 12 Aug 2019 20:03:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:03:57: 26000000 INFO @ Mon, 12 Aug 2019 20:03:58: #2 number of paired peaks: 142 WARNING @ Mon, 12 Aug 2019 20:03:58: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 12 Aug 2019 20:03:58: start model_add_line... INFO @ Mon, 12 Aug 2019 20:03:58: start X-correlation... INFO @ Mon, 12 Aug 2019 20:03:58: end of X-cor INFO @ Mon, 12 Aug 2019 20:03:58: #2 finished! INFO @ Mon, 12 Aug 2019 20:03:58: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:03:58: #2 alternative fragment length(s) may be 0,47,242,529,552 bps INFO @ Mon, 12 Aug 2019 20:03:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.20_model.r WARNING @ Mon, 12 Aug 2019 20:03:58: #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 20:03:58: #2 You may need to consider one of the other alternative d(s): 0,47,242,529,552 WARNING @ Mon, 12 Aug 2019 20:03:58: #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 20:03:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:03:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:04:00: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:04:00: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:04:00: #1 total tags in treatment: 26665318 INFO @ Mon, 12 Aug 2019 20:04:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:04:00: #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 20:04:01: #1 tags after filtering in treatment: 26665318 INFO @ Mon, 12 Aug 2019 20:04:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:04:01: #1 finished! INFO @ Mon, 12 Aug 2019 20:04:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:04:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:04:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:04:02: #1 total tags in treatment: 26665318 INFO @ Mon, 12 Aug 2019 20:04:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:04:02: #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 20:04:03: #1 tags after filtering in treatment: 26665318 INFO @ Mon, 12 Aug 2019 20:04:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:04:03: #1 finished! INFO @ Mon, 12 Aug 2019 20:04:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:04:03: #2 number of paired peaks: 142 WARNING @ Mon, 12 Aug 2019 20:04:03: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 12 Aug 2019 20:04:03: start model_add_line... INFO @ Mon, 12 Aug 2019 20:04:03: start X-correlation... INFO @ Mon, 12 Aug 2019 20:04:03: end of X-cor INFO @ Mon, 12 Aug 2019 20:04:03: #2 finished! INFO @ Mon, 12 Aug 2019 20:04:03: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:04:03: #2 alternative fragment length(s) may be 0,47,242,529,552 bps INFO @ Mon, 12 Aug 2019 20:04:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.05_model.r WARNING @ Mon, 12 Aug 2019 20:04:03: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:04:03: #2 You may need to consider one of the other alternative d(s): 0,47,242,529,552 WARNING @ Mon, 12 Aug 2019 20:04:03: #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 20:04:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:04:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:04:05: #2 number of paired peaks: 142 WARNING @ Mon, 12 Aug 2019 20:04:05: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 12 Aug 2019 20:04:05: start model_add_line... INFO @ Mon, 12 Aug 2019 20:04:05: start X-correlation... INFO @ Mon, 12 Aug 2019 20:04:05: end of X-cor INFO @ Mon, 12 Aug 2019 20:04:05: #2 finished! INFO @ Mon, 12 Aug 2019 20:04:05: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:04:05: #2 alternative fragment length(s) may be 0,47,242,529,552 bps INFO @ Mon, 12 Aug 2019 20:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494922/SRX494922.10_model.r WARNING @ Mon, 12 Aug 2019 20:04:05: #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 20:04:05: #2 You may need to consider one of the other alternative d(s): 0,47,242,529,552 WARNING @ Mon, 12 Aug 2019 20:04:05: #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 20:04:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:04:05: #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 SRX494922.05.bed: No such file or directory mv: cannot stat ‘SRX494922.05.bed’: No such file or directory /var/spool/uge/at078/job_scripts/2590080: line 335: 60434 Terminated MACS $i /var/spool/uge/at078/job_scripts/2590080: line 335: 60449 Terminated MACS $i /var/spool/uge/at078/job_scripts/2590080: line 335: 60465 Terminated MACS $i mv: cannot stat ‘SRX494922.05.bb’: No such file or directory ls: cannot access SRX494922.10.bed: No such file or directory mv: cannot stat ‘SRX494922.10.bed’: No such file or directory mv: cannot stat ‘SRX494922.10.bb’: No such file or directory ls: cannot access SRX494922.20.bed: No such file or directory mv: cannot stat ‘SRX494922.20.bed’: No such file or directory mv: cannot stat ‘SRX494922.20.bb’: No such file or directory