Job ID = 2590212 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,706,298 reads read : 29,706,298 reads written : 29,706,298 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: 00:05:02 29706298 reads; of these: 29706298 (100.00%) were unpaired; of these: 7084735 (23.85%) aligned 0 times 18663271 (62.83%) aligned exactly 1 time 3958292 (13.32%) aligned >1 times 76.15% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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 8 files... [bam_rmdupse_core] 2635954 / 22621563 = 0.1165 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 20:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.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 20:24:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.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 20:24:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.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 20:24:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:25:04: 1000000 INFO @ Mon, 12 Aug 2019 20:25:04: 1000000 INFO @ Mon, 12 Aug 2019 20:25:06: 1000000 INFO @ Mon, 12 Aug 2019 20:25:11: 2000000 INFO @ Mon, 12 Aug 2019 20:25:12: 2000000 INFO @ Mon, 12 Aug 2019 20:25:14: 2000000 INFO @ Mon, 12 Aug 2019 20:25:18: 3000000 INFO @ Mon, 12 Aug 2019 20:25:21: 3000000 INFO @ Mon, 12 Aug 2019 20:25:22: 3000000 INFO @ Mon, 12 Aug 2019 20:25:26: 4000000 INFO @ Mon, 12 Aug 2019 20:25:29: 4000000 INFO @ Mon, 12 Aug 2019 20:25:31: 4000000 INFO @ Mon, 12 Aug 2019 20:25:33: 5000000 INFO @ Mon, 12 Aug 2019 20:25:37: 5000000 INFO @ Mon, 12 Aug 2019 20:25:39: 5000000 INFO @ Mon, 12 Aug 2019 20:25:40: 6000000 INFO @ Mon, 12 Aug 2019 20:25:45: 6000000 INFO @ Mon, 12 Aug 2019 20:25:47: 6000000 INFO @ Mon, 12 Aug 2019 20:25:47: 7000000 INFO @ Mon, 12 Aug 2019 20:25:54: 7000000 INFO @ Mon, 12 Aug 2019 20:25:54: 8000000 INFO @ Mon, 12 Aug 2019 20:25:55: 7000000 INFO @ Mon, 12 Aug 2019 20:26:01: 9000000 INFO @ Mon, 12 Aug 2019 20:26:02: 8000000 INFO @ Mon, 12 Aug 2019 20:26:03: 8000000 INFO @ Mon, 12 Aug 2019 20:26:09: 10000000 INFO @ Mon, 12 Aug 2019 20:26:10: 9000000 INFO @ Mon, 12 Aug 2019 20:26:11: 9000000 INFO @ Mon, 12 Aug 2019 20:26:16: 11000000 INFO @ Mon, 12 Aug 2019 20:26:19: 10000000 INFO @ Mon, 12 Aug 2019 20:26:20: 10000000 INFO @ Mon, 12 Aug 2019 20:26:23: 12000000 INFO @ Mon, 12 Aug 2019 20:26:27: 11000000 INFO @ Mon, 12 Aug 2019 20:26:28: 11000000 INFO @ Mon, 12 Aug 2019 20:26:30: 13000000 INFO @ Mon, 12 Aug 2019 20:26:35: 12000000 INFO @ Mon, 12 Aug 2019 20:26:36: 12000000 INFO @ Mon, 12 Aug 2019 20:26:37: 14000000 INFO @ Mon, 12 Aug 2019 20:26:43: 13000000 INFO @ Mon, 12 Aug 2019 20:26:44: 13000000 INFO @ Mon, 12 Aug 2019 20:26:44: 15000000 INFO @ Mon, 12 Aug 2019 20:26:52: 14000000 INFO @ Mon, 12 Aug 2019 20:26:52: 16000000 INFO @ Mon, 12 Aug 2019 20:26:52: 14000000 INFO @ Mon, 12 Aug 2019 20:26:59: 17000000 INFO @ Mon, 12 Aug 2019 20:26:59: 15000000 INFO @ Mon, 12 Aug 2019 20:27:00: 15000000 INFO @ Mon, 12 Aug 2019 20:27:06: 18000000 INFO @ Mon, 12 Aug 2019 20:27:07: 16000000 INFO @ Mon, 12 Aug 2019 20:27:08: 16000000 INFO @ Mon, 12 Aug 2019 20:27:13: 19000000 INFO @ Mon, 12 Aug 2019 20:27:15: 17000000 INFO @ Mon, 12 Aug 2019 20:27:16: 17000000 INFO @ Mon, 12 Aug 2019 20:27:20: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:27:20: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:27:20: #1 total tags in treatment: 19985609 INFO @ Mon, 12 Aug 2019 20:27:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:27:20: #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 20:27:21: #1 tags after filtering in treatment: 19985609 INFO @ Mon, 12 Aug 2019 20:27:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:27:21: #1 finished! INFO @ Mon, 12 Aug 2019 20:27:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:27:22: #2 number of paired peaks: 175 WARNING @ Mon, 12 Aug 2019 20:27:22: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Mon, 12 Aug 2019 20:27:22: start model_add_line... INFO @ Mon, 12 Aug 2019 20:27:23: start X-correlation... INFO @ Mon, 12 Aug 2019 20:27:23: end of X-cor INFO @ Mon, 12 Aug 2019 20:27:23: #2 finished! INFO @ Mon, 12 Aug 2019 20:27:23: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:27:23: #2 alternative fragment length(s) may be 0,29,179,181,416,463,565 bps INFO @ Mon, 12 Aug 2019 20:27:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.10_model.r WARNING @ Mon, 12 Aug 2019 20:27:23: #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 20:27:23: #2 You may need to consider one of the other alternative d(s): 0,29,179,181,416,463,565 WARNING @ Mon, 12 Aug 2019 20:27:23: #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 20:27:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:27:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:27:23: 18000000 INFO @ Mon, 12 Aug 2019 20:27:25: 18000000 INFO @ Mon, 12 Aug 2019 20:27:31: 19000000 INFO @ Mon, 12 Aug 2019 20:27:33: 19000000 INFO @ Mon, 12 Aug 2019 20:27:39: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:27:39: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:27:39: #1 total tags in treatment: 19985609 INFO @ Mon, 12 Aug 2019 20:27:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:27:39: #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 20:27:40: #1 tags after filtering in treatment: 19985609 INFO @ Mon, 12 Aug 2019 20:27:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:27:40: #1 finished! INFO @ Mon, 12 Aug 2019 20:27:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:27:41: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:27:41: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:27:41: #1 total tags in treatment: 19985609 INFO @ Mon, 12 Aug 2019 20:27:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:27:41: #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 20:27:41: #1 tags after filtering in treatment: 19985609 INFO @ Mon, 12 Aug 2019 20:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:27:41: #1 finished! INFO @ Mon, 12 Aug 2019 20:27:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:27:42: #2 number of paired peaks: 175 WARNING @ Mon, 12 Aug 2019 20:27:42: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Mon, 12 Aug 2019 20:27:42: start model_add_line... INFO @ Mon, 12 Aug 2019 20:27:42: start X-correlation... INFO @ Mon, 12 Aug 2019 20:27:42: end of X-cor INFO @ Mon, 12 Aug 2019 20:27:42: #2 finished! INFO @ Mon, 12 Aug 2019 20:27:42: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:27:42: #2 alternative fragment length(s) may be 0,29,179,181,416,463,565 bps INFO @ Mon, 12 Aug 2019 20:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.20_model.r WARNING @ Mon, 12 Aug 2019 20:27:42: #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 20:27:42: #2 You may need to consider one of the other alternative d(s): 0,29,179,181,416,463,565 WARNING @ Mon, 12 Aug 2019 20:27:42: #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 20:27:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:27:43: #2 number of paired peaks: 175 WARNING @ Mon, 12 Aug 2019 20:27:43: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Mon, 12 Aug 2019 20:27:43: start model_add_line... INFO @ Mon, 12 Aug 2019 20:27:43: start X-correlation... INFO @ Mon, 12 Aug 2019 20:27:43: end of X-cor INFO @ Mon, 12 Aug 2019 20:27:43: #2 finished! INFO @ Mon, 12 Aug 2019 20:27:43: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:27:43: #2 alternative fragment length(s) may be 0,29,179,181,416,463,565 bps INFO @ Mon, 12 Aug 2019 20:27:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529218/SRX529218.05_model.r WARNING @ Mon, 12 Aug 2019 20:27:43: #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 20:27:43: #2 You may need to consider one of the other alternative d(s): 0,29,179,181,416,463,565 WARNING @ Mon, 12 Aug 2019 20:27:43: #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 20:27:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:27:43: #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 SRX529218.05.bed: No such file or directory mv: cannot stat ‘SRX529218.05.bed’: No such file or directory /var/spool/uge/at106/job_scripts/2590212: line 335: 34232 Terminated MACS $i /var/spool/uge/at106/job_scripts/2590212: line 335: 34248 Terminated MACS $i /var/spool/uge/at106/job_scripts/2590212: line 335: 34266 Terminated MACS $i mv: cannot stat ‘SRX529218.05.bb’: No such file or directory ls: cannot access SRX529218.10.bed: No such file or directory mv: cannot stat ‘SRX529218.10.bed’: No such file or directory mv: cannot stat ‘SRX529218.10.bb’: No such file or directory ls: cannot access SRX529218.20.bed: No such file or directory mv: cannot stat ‘SRX529218.20.bed’: No such file or directory mv: cannot stat ‘SRX529218.20.bb’: No such file or directory