Job ID = 1292021 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,720,049 reads read : 61,440,098 reads written : 30,720,049 reads 0-length : 30,720,049 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:09:59 30720049 reads; of these: 30720049 (100.00%) were unpaired; of these: 703121 (2.29%) aligned 0 times 25054720 (81.56%) aligned exactly 1 time 4962208 (16.15%) aligned >1 times 97.71% overall alignment rate Time searching: 00:09:59 Overall time: 00:09:59 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] 3577427 / 30016928 = 0.1192 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 @ Sun, 02 Jun 2019 17:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.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 @ Sun, 02 Jun 2019 17:34:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:34:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.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 @ Sun, 02 Jun 2019 17:34:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:34:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.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 @ Sun, 02 Jun 2019 17:34:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:34:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:34:24: 1000000 INFO @ Sun, 02 Jun 2019 17:34:25: 1000000 INFO @ Sun, 02 Jun 2019 17:34:26: 1000000 INFO @ Sun, 02 Jun 2019 17:34:33: 2000000 INFO @ Sun, 02 Jun 2019 17:34:35: 2000000 INFO @ Sun, 02 Jun 2019 17:34:36: 2000000 INFO @ Sun, 02 Jun 2019 17:34:42: 3000000 INFO @ Sun, 02 Jun 2019 17:34:44: 3000000 INFO @ Sun, 02 Jun 2019 17:34:46: 3000000 INFO @ Sun, 02 Jun 2019 17:34:50: 4000000 INFO @ Sun, 02 Jun 2019 17:34:53: 4000000 INFO @ Sun, 02 Jun 2019 17:34:57: 4000000 INFO @ Sun, 02 Jun 2019 17:34:59: 5000000 INFO @ Sun, 02 Jun 2019 17:35:02: 5000000 INFO @ Sun, 02 Jun 2019 17:35:07: 5000000 INFO @ Sun, 02 Jun 2019 17:35:07: 6000000 INFO @ Sun, 02 Jun 2019 17:35:11: 6000000 INFO @ Sun, 02 Jun 2019 17:35:16: 7000000 INFO @ Sun, 02 Jun 2019 17:35:17: 6000000 INFO @ Sun, 02 Jun 2019 17:35:20: 7000000 INFO @ Sun, 02 Jun 2019 17:35:24: 8000000 INFO @ Sun, 02 Jun 2019 17:35:27: 7000000 INFO @ Sun, 02 Jun 2019 17:35:30: 8000000 INFO @ Sun, 02 Jun 2019 17:35:33: 9000000 INFO @ Sun, 02 Jun 2019 17:35:37: 8000000 INFO @ Sun, 02 Jun 2019 17:35:39: 9000000 INFO @ Sun, 02 Jun 2019 17:35:41: 10000000 INFO @ Sun, 02 Jun 2019 17:35:46: 9000000 INFO @ Sun, 02 Jun 2019 17:35:48: 10000000 INFO @ Sun, 02 Jun 2019 17:35:50: 11000000 INFO @ Sun, 02 Jun 2019 17:35:56: 10000000 INFO @ Sun, 02 Jun 2019 17:35:57: 11000000 INFO @ Sun, 02 Jun 2019 17:35:59: 12000000 INFO @ Sun, 02 Jun 2019 17:36:06: 12000000 INFO @ Sun, 02 Jun 2019 17:36:07: 11000000 INFO @ Sun, 02 Jun 2019 17:36:07: 13000000 INFO @ Sun, 02 Jun 2019 17:36:15: 13000000 INFO @ Sun, 02 Jun 2019 17:36:16: 14000000 INFO @ Sun, 02 Jun 2019 17:36:17: 12000000 INFO @ Sun, 02 Jun 2019 17:36:24: 15000000 INFO @ Sun, 02 Jun 2019 17:36:24: 14000000 INFO @ Sun, 02 Jun 2019 17:36:27: 13000000 INFO @ Sun, 02 Jun 2019 17:36:32: 16000000 INFO @ Sun, 02 Jun 2019 17:36:34: 15000000 INFO @ Sun, 02 Jun 2019 17:36:38: 14000000 INFO @ Sun, 02 Jun 2019 17:36:41: 17000000 INFO @ Sun, 02 Jun 2019 17:36:43: 16000000 INFO @ Sun, 02 Jun 2019 17:36:48: 15000000 INFO @ Sun, 02 Jun 2019 17:36:49: 18000000 INFO @ Sun, 02 Jun 2019 17:36:52: 17000000 INFO @ Sun, 02 Jun 2019 17:36:57: 16000000 INFO @ Sun, 02 Jun 2019 17:36:58: 19000000 INFO @ Sun, 02 Jun 2019 17:37:02: 18000000 INFO @ Sun, 02 Jun 2019 17:37:06: 20000000 INFO @ Sun, 02 Jun 2019 17:37:08: 17000000 INFO @ Sun, 02 Jun 2019 17:37:11: 19000000 INFO @ Sun, 02 Jun 2019 17:37:15: 21000000 INFO @ Sun, 02 Jun 2019 17:37:17: 18000000 INFO @ Sun, 02 Jun 2019 17:37:20: 20000000 INFO @ Sun, 02 Jun 2019 17:37:23: 22000000 INFO @ Sun, 02 Jun 2019 17:37:27: 19000000 INFO @ Sun, 02 Jun 2019 17:37:29: 21000000 INFO @ Sun, 02 Jun 2019 17:37:32: 23000000 INFO @ Sun, 02 Jun 2019 17:37:37: 20000000 INFO @ Sun, 02 Jun 2019 17:37:38: 22000000 INFO @ Sun, 02 Jun 2019 17:37:40: 24000000 INFO @ Sun, 02 Jun 2019 17:37:47: 21000000 INFO @ Sun, 02 Jun 2019 17:37:47: 23000000 INFO @ Sun, 02 Jun 2019 17:37:48: 25000000 INFO @ Sun, 02 Jun 2019 17:37:55: 26000000 INFO @ Sun, 02 Jun 2019 17:37:56: 24000000 INFO @ Sun, 02 Jun 2019 17:37:58: 22000000 INFO @ Sun, 02 Jun 2019 17:37:59: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:37:59: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:37:59: #1 total tags in treatment: 26439501 INFO @ Sun, 02 Jun 2019 17:37:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:37:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:38:00: #1 tags after filtering in treatment: 26439501 INFO @ Sun, 02 Jun 2019 17:38:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:38:00: #1 finished! INFO @ Sun, 02 Jun 2019 17:38:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:38:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:38:02: #2 number of paired peaks: 114 WARNING @ Sun, 02 Jun 2019 17:38:02: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sun, 02 Jun 2019 17:38:02: start model_add_line... INFO @ Sun, 02 Jun 2019 17:38:03: start X-correlation... INFO @ Sun, 02 Jun 2019 17:38:03: end of X-cor INFO @ Sun, 02 Jun 2019 17:38:03: #2 finished! INFO @ Sun, 02 Jun 2019 17:38:03: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 17:38:03: #2 alternative fragment length(s) may be 0,48,435,488,585 bps INFO @ Sun, 02 Jun 2019 17:38:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.10_model.r WARNING @ Sun, 02 Jun 2019 17:38:03: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:38:03: #2 You may need to consider one of the other alternative d(s): 0,48,435,488,585 WARNING @ Sun, 02 Jun 2019 17:38:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:38:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:38:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:38:05: 25000000 INFO @ Sun, 02 Jun 2019 17:38:08: 23000000 INFO @ Sun, 02 Jun 2019 17:38:13: 26000000 INFO @ Sun, 02 Jun 2019 17:38:17: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:38:17: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:38:17: #1 total tags in treatment: 26439501 INFO @ Sun, 02 Jun 2019 17:38:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:38:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:38:18: #1 tags after filtering in treatment: 26439501 INFO @ Sun, 02 Jun 2019 17:38:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:38:18: #1 finished! INFO @ Sun, 02 Jun 2019 17:38:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:38:18: 24000000 INFO @ Sun, 02 Jun 2019 17:38:21: #2 number of paired peaks: 114 WARNING @ Sun, 02 Jun 2019 17:38:21: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sun, 02 Jun 2019 17:38:21: start model_add_line... INFO @ Sun, 02 Jun 2019 17:38:21: start X-correlation... INFO @ Sun, 02 Jun 2019 17:38:21: end of X-cor INFO @ Sun, 02 Jun 2019 17:38:21: #2 finished! INFO @ Sun, 02 Jun 2019 17:38:21: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 17:38:21: #2 alternative fragment length(s) may be 0,48,435,488,585 bps INFO @ Sun, 02 Jun 2019 17:38:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.20_model.r WARNING @ Sun, 02 Jun 2019 17:38:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:38:21: #2 You may need to consider one of the other alternative d(s): 0,48,435,488,585 WARNING @ Sun, 02 Jun 2019 17:38:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:38:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:38:28: 25000000 INFO @ Sun, 02 Jun 2019 17:38:38: 26000000 INFO @ Sun, 02 Jun 2019 17:38:42: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:38:42: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:38:42: #1 total tags in treatment: 26439501 INFO @ Sun, 02 Jun 2019 17:38:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:38:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:38:43: #1 tags after filtering in treatment: 26439501 INFO @ Sun, 02 Jun 2019 17:38:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:38:43: #1 finished! INFO @ Sun, 02 Jun 2019 17:38:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:38:45: #2 number of paired peaks: 114 WARNING @ Sun, 02 Jun 2019 17:38:45: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sun, 02 Jun 2019 17:38:45: start model_add_line... INFO @ Sun, 02 Jun 2019 17:38:46: start X-correlation... INFO @ Sun, 02 Jun 2019 17:38:46: end of X-cor INFO @ Sun, 02 Jun 2019 17:38:46: #2 finished! INFO @ Sun, 02 Jun 2019 17:38:46: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 17:38:46: #2 alternative fragment length(s) may be 0,48,435,488,585 bps INFO @ Sun, 02 Jun 2019 17:38:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104611/SRX3104611.05_model.r WARNING @ Sun, 02 Jun 2019 17:38:46: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:38:46: #2 You may need to consider one of the other alternative d(s): 0,48,435,488,585 WARNING @ Sun, 02 Jun 2019 17:38:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:38:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:38:46: #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 SRX3104611.05.bed: No such file or directory mv: cannot stat ‘SRX3104611.05.bed’: No such file or directory /var/spool/uge/at100/job_scripts/1292021: line 321: 39093 Terminated MACS $i /var/spool/uge/at100/job_scripts/1292021: line 321: 39094 Terminated MACS $i /var/spool/uge/at100/job_scripts/1292021: line 321: 39095 Terminated MACS $i mv: cannot stat ‘SRX3104611.05.bb’: No such file or directory ls: cannot access SRX3104611.10.bed: No such file or directory mv: cannot stat ‘SRX3104611.10.bed’: No such file or directory mv: cannot stat ‘SRX3104611.10.bb’: No such file or directory ls: cannot access SRX3104611.20.bed: No such file or directory mv: cannot stat ‘SRX3104611.20.bed’: No such file or directory mv: cannot stat ‘SRX3104611.20.bb’: No such file or directory