Job ID = 2589375 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,066,908 reads read : 29,066,908 reads written : 29,066,908 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: 00:08:46 29066908 reads; of these: 29066908 (100.00%) were unpaired; of these: 402789 (1.39%) aligned 0 times 23672907 (81.44%) aligned exactly 1 time 4991212 (17.17%) aligned >1 times 98.61% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 4065285 / 28664119 = 0.1418 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 18:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.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 18:05:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:05:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.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 18:05:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:05:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:05:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.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 18:05:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:05:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:05:32: 1000000 INFO @ Mon, 12 Aug 2019 18:05:33: 1000000 INFO @ Mon, 12 Aug 2019 18:05:33: 1000000 INFO @ Mon, 12 Aug 2019 18:05:40: 2000000 INFO @ Mon, 12 Aug 2019 18:05:41: 2000000 INFO @ Mon, 12 Aug 2019 18:05:42: 2000000 INFO @ Mon, 12 Aug 2019 18:05:48: 3000000 INFO @ Mon, 12 Aug 2019 18:05:48: 3000000 INFO @ Mon, 12 Aug 2019 18:05:51: 3000000 INFO @ Mon, 12 Aug 2019 18:05:55: 4000000 INFO @ Mon, 12 Aug 2019 18:05:57: 4000000 INFO @ Mon, 12 Aug 2019 18:06:01: 4000000 INFO @ Mon, 12 Aug 2019 18:06:03: 5000000 INFO @ Mon, 12 Aug 2019 18:06:05: 5000000 INFO @ Mon, 12 Aug 2019 18:06:10: 6000000 INFO @ Mon, 12 Aug 2019 18:06:10: 5000000 INFO @ Mon, 12 Aug 2019 18:06:14: 6000000 INFO @ Mon, 12 Aug 2019 18:06:18: 7000000 INFO @ Mon, 12 Aug 2019 18:06:20: 6000000 INFO @ Mon, 12 Aug 2019 18:06:22: 7000000 INFO @ Mon, 12 Aug 2019 18:06:25: 8000000 INFO @ Mon, 12 Aug 2019 18:06:30: 7000000 INFO @ Mon, 12 Aug 2019 18:06:30: 8000000 INFO @ Mon, 12 Aug 2019 18:06:33: 9000000 INFO @ Mon, 12 Aug 2019 18:06:38: 9000000 INFO @ Mon, 12 Aug 2019 18:06:40: 8000000 INFO @ Mon, 12 Aug 2019 18:06:40: 10000000 INFO @ Mon, 12 Aug 2019 18:06:47: 10000000 INFO @ Mon, 12 Aug 2019 18:06:47: 11000000 INFO @ Mon, 12 Aug 2019 18:06:49: 9000000 INFO @ Mon, 12 Aug 2019 18:06:54: 12000000 INFO @ Mon, 12 Aug 2019 18:06:55: 11000000 INFO @ Mon, 12 Aug 2019 18:06:59: 10000000 INFO @ Mon, 12 Aug 2019 18:07:02: 13000000 INFO @ Mon, 12 Aug 2019 18:07:03: 12000000 INFO @ Mon, 12 Aug 2019 18:07:08: 11000000 INFO @ Mon, 12 Aug 2019 18:07:09: 14000000 INFO @ Mon, 12 Aug 2019 18:07:11: 13000000 INFO @ Mon, 12 Aug 2019 18:07:16: 15000000 INFO @ Mon, 12 Aug 2019 18:07:18: 12000000 INFO @ Mon, 12 Aug 2019 18:07:19: 14000000 INFO @ Mon, 12 Aug 2019 18:07:24: 16000000 INFO @ Mon, 12 Aug 2019 18:07:27: 13000000 INFO @ Mon, 12 Aug 2019 18:07:27: 15000000 INFO @ Mon, 12 Aug 2019 18:07:31: 17000000 INFO @ Mon, 12 Aug 2019 18:07:35: 16000000 INFO @ Mon, 12 Aug 2019 18:07:36: 14000000 INFO @ Mon, 12 Aug 2019 18:07:38: 18000000 INFO @ Mon, 12 Aug 2019 18:07:43: 17000000 INFO @ Mon, 12 Aug 2019 18:07:45: 19000000 INFO @ Mon, 12 Aug 2019 18:07:46: 15000000 INFO @ Mon, 12 Aug 2019 18:07:51: 18000000 INFO @ Mon, 12 Aug 2019 18:07:53: 20000000 INFO @ Mon, 12 Aug 2019 18:07:55: 16000000 INFO @ Mon, 12 Aug 2019 18:07:59: 19000000 INFO @ Mon, 12 Aug 2019 18:08:00: 21000000 INFO @ Mon, 12 Aug 2019 18:08:05: 17000000 INFO @ Mon, 12 Aug 2019 18:08:07: 22000000 INFO @ Mon, 12 Aug 2019 18:08:08: 20000000 INFO @ Mon, 12 Aug 2019 18:08:14: 18000000 INFO @ Mon, 12 Aug 2019 18:08:14: 23000000 INFO @ Mon, 12 Aug 2019 18:08:16: 21000000 INFO @ Mon, 12 Aug 2019 18:08:22: 24000000 INFO @ Mon, 12 Aug 2019 18:08:23: 19000000 INFO @ Mon, 12 Aug 2019 18:08:24: 22000000 INFO @ Mon, 12 Aug 2019 18:08:26: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:08:26: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:08:26: #1 total tags in treatment: 24598834 INFO @ Mon, 12 Aug 2019 18:08:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:08:26: #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 18:08:27: #1 tags after filtering in treatment: 24598834 INFO @ Mon, 12 Aug 2019 18:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:08:27: #1 finished! INFO @ Mon, 12 Aug 2019 18:08:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:08:29: #2 number of paired peaks: 201 WARNING @ Mon, 12 Aug 2019 18:08:29: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Mon, 12 Aug 2019 18:08:29: start model_add_line... INFO @ Mon, 12 Aug 2019 18:08:29: start X-correlation... INFO @ Mon, 12 Aug 2019 18:08:29: end of X-cor INFO @ Mon, 12 Aug 2019 18:08:29: #2 finished! INFO @ Mon, 12 Aug 2019 18:08:29: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 18:08:29: #2 alternative fragment length(s) may be 0,18,38,585 bps INFO @ Mon, 12 Aug 2019 18:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.20_model.r WARNING @ Mon, 12 Aug 2019 18:08:29: #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 18:08:29: #2 You may need to consider one of the other alternative d(s): 0,18,38,585 WARNING @ Mon, 12 Aug 2019 18:08:29: #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 18:08:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:08:32: 23000000 INFO @ Mon, 12 Aug 2019 18:08:33: 20000000 INFO @ Mon, 12 Aug 2019 18:08:40: 24000000 INFO @ Mon, 12 Aug 2019 18:08:42: 21000000 INFO @ Mon, 12 Aug 2019 18:08:45: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:08:45: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:08:45: #1 total tags in treatment: 24598834 INFO @ Mon, 12 Aug 2019 18:08:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:08:45: #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 18:08:45: #1 tags after filtering in treatment: 24598834 INFO @ Mon, 12 Aug 2019 18:08:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:08:45: #1 finished! INFO @ Mon, 12 Aug 2019 18:08:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:08:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:08:47: #2 number of paired peaks: 201 WARNING @ Mon, 12 Aug 2019 18:08:47: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Mon, 12 Aug 2019 18:08:47: start model_add_line... INFO @ Mon, 12 Aug 2019 18:08:47: start X-correlation... INFO @ Mon, 12 Aug 2019 18:08:47: end of X-cor INFO @ Mon, 12 Aug 2019 18:08:47: #2 finished! INFO @ Mon, 12 Aug 2019 18:08:47: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 18:08:47: #2 alternative fragment length(s) may be 0,18,38,585 bps INFO @ Mon, 12 Aug 2019 18:08:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.05_model.r WARNING @ Mon, 12 Aug 2019 18:08:47: #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 18:08:47: #2 You may need to consider one of the other alternative d(s): 0,18,38,585 WARNING @ Mon, 12 Aug 2019 18:08:47: #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 18:08:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:08:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:08:51: 22000000 INFO @ Mon, 12 Aug 2019 18:09:00: 23000000 INFO @ Mon, 12 Aug 2019 18:09:09: 24000000 INFO @ Mon, 12 Aug 2019 18:09:15: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:09:15: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:09:15: #1 total tags in treatment: 24598834 INFO @ Mon, 12 Aug 2019 18:09:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:09:15: #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 18:09:15: #1 tags after filtering in treatment: 24598834 INFO @ Mon, 12 Aug 2019 18:09:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:09:15: #1 finished! INFO @ Mon, 12 Aug 2019 18:09:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:09:17: #2 number of paired peaks: 201 WARNING @ Mon, 12 Aug 2019 18:09:17: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Mon, 12 Aug 2019 18:09:17: start model_add_line... INFO @ Mon, 12 Aug 2019 18:09:18: start X-correlation... INFO @ Mon, 12 Aug 2019 18:09:18: end of X-cor INFO @ Mon, 12 Aug 2019 18:09:18: #2 finished! INFO @ Mon, 12 Aug 2019 18:09:18: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 18:09:18: #2 alternative fragment length(s) may be 0,18,38,585 bps INFO @ Mon, 12 Aug 2019 18:09:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078726/SRX1078726.10_model.r WARNING @ Mon, 12 Aug 2019 18:09:18: #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 18:09:18: #2 You may need to consider one of the other alternative d(s): 0,18,38,585 WARNING @ Mon, 12 Aug 2019 18:09:18: #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 18:09:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:09:18: #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 SRX1078726.05.bed: No such file or directory mv: cannot stat ‘SRX1078726.05.bed’: No such file or directory /var/spool/uge/at096/job_scripts/2589375: line 335: 1230 Terminated MACS $i /var/spool/uge/at096/job_scripts/2589375: line 335: 1245 Terminated MACS $i /var/spool/uge/at096/job_scripts/2589375: line 335: 1258 Terminated MACS $i mv: cannot stat ‘SRX1078726.05.bb’: No such file or directory ls: cannot access SRX1078726.10.bed: No such file or directory mv: cannot stat ‘SRX1078726.10.bed’: No such file or directory mv: cannot stat ‘SRX1078726.10.bb’: No such file or directory ls: cannot access SRX1078726.20.bed: No such file or directory mv: cannot stat ‘SRX1078726.20.bed’: No such file or directory mv: cannot stat ‘SRX1078726.20.bb’: No such file or directory