Job ID = 1292526 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,788,149 reads read : 30,788,149 reads written : 30,788,149 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: 00:06:23 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171811 (0.56%) aligned 0 times 25273676 (82.09%) aligned exactly 1 time 5342662 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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] 4711279 / 30616338 = 0.1539 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 19:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.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 19:40:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:40:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.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 19:40:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:40:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.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 19:40:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:40:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:40:57: 1000000 INFO @ Sun, 02 Jun 2019 19:40:59: 1000000 INFO @ Sun, 02 Jun 2019 19:40:59: 1000000 INFO @ Sun, 02 Jun 2019 19:41:04: 2000000 INFO @ Sun, 02 Jun 2019 19:41:09: 2000000 INFO @ Sun, 02 Jun 2019 19:41:09: 2000000 INFO @ Sun, 02 Jun 2019 19:41:11: 3000000 INFO @ Sun, 02 Jun 2019 19:41:17: 4000000 INFO @ Sun, 02 Jun 2019 19:41:18: 3000000 INFO @ Sun, 02 Jun 2019 19:41:19: 3000000 INFO @ Sun, 02 Jun 2019 19:41:24: 5000000 INFO @ Sun, 02 Jun 2019 19:41:28: 4000000 INFO @ Sun, 02 Jun 2019 19:41:28: 4000000 INFO @ Sun, 02 Jun 2019 19:41:31: 6000000 INFO @ Sun, 02 Jun 2019 19:41:37: 5000000 INFO @ Sun, 02 Jun 2019 19:41:38: 5000000 INFO @ Sun, 02 Jun 2019 19:41:38: 7000000 INFO @ Sun, 02 Jun 2019 19:41:45: 8000000 INFO @ Sun, 02 Jun 2019 19:41:46: 6000000 INFO @ Sun, 02 Jun 2019 19:41:47: 6000000 INFO @ Sun, 02 Jun 2019 19:41:52: 9000000 INFO @ Sun, 02 Jun 2019 19:41:56: 7000000 INFO @ Sun, 02 Jun 2019 19:41:57: 7000000 INFO @ Sun, 02 Jun 2019 19:42:00: 10000000 INFO @ Sun, 02 Jun 2019 19:42:05: 8000000 INFO @ Sun, 02 Jun 2019 19:42:06: 8000000 INFO @ Sun, 02 Jun 2019 19:42:06: 11000000 INFO @ Sun, 02 Jun 2019 19:42:13: 12000000 INFO @ Sun, 02 Jun 2019 19:42:14: 9000000 INFO @ Sun, 02 Jun 2019 19:42:15: 9000000 INFO @ Sun, 02 Jun 2019 19:42:20: 13000000 INFO @ Sun, 02 Jun 2019 19:42:24: 10000000 INFO @ Sun, 02 Jun 2019 19:42:25: 10000000 INFO @ Sun, 02 Jun 2019 19:42:26: 14000000 INFO @ Sun, 02 Jun 2019 19:42:33: 15000000 INFO @ Sun, 02 Jun 2019 19:42:34: 11000000 INFO @ Sun, 02 Jun 2019 19:42:34: 11000000 INFO @ Sun, 02 Jun 2019 19:42:39: 16000000 INFO @ Sun, 02 Jun 2019 19:42:43: 12000000 INFO @ Sun, 02 Jun 2019 19:42:44: 12000000 INFO @ Sun, 02 Jun 2019 19:42:46: 17000000 INFO @ Sun, 02 Jun 2019 19:42:52: 18000000 INFO @ Sun, 02 Jun 2019 19:42:52: 13000000 INFO @ Sun, 02 Jun 2019 19:42:53: 13000000 INFO @ Sun, 02 Jun 2019 19:42:59: 19000000 INFO @ Sun, 02 Jun 2019 19:43:01: 14000000 INFO @ Sun, 02 Jun 2019 19:43:03: 14000000 INFO @ Sun, 02 Jun 2019 19:43:05: 20000000 INFO @ Sun, 02 Jun 2019 19:43:10: 15000000 INFO @ Sun, 02 Jun 2019 19:43:12: 21000000 INFO @ Sun, 02 Jun 2019 19:43:12: 15000000 INFO @ Sun, 02 Jun 2019 19:43:19: 22000000 INFO @ Sun, 02 Jun 2019 19:43:20: 16000000 INFO @ Sun, 02 Jun 2019 19:43:21: 16000000 INFO @ Sun, 02 Jun 2019 19:43:25: 23000000 INFO @ Sun, 02 Jun 2019 19:43:29: 17000000 INFO @ Sun, 02 Jun 2019 19:43:31: 17000000 INFO @ Sun, 02 Jun 2019 19:43:32: 24000000 INFO @ Sun, 02 Jun 2019 19:43:38: 18000000 INFO @ Sun, 02 Jun 2019 19:43:38: 25000000 INFO @ Sun, 02 Jun 2019 19:43:40: 18000000 INFO @ Sun, 02 Jun 2019 19:43:45: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:43:45: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:43:45: #1 total tags in treatment: 25905059 INFO @ Sun, 02 Jun 2019 19:43:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:43:45: #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 19:43:45: #1 tags after filtering in treatment: 25905059 INFO @ Sun, 02 Jun 2019 19:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:43:45: #1 finished! INFO @ Sun, 02 Jun 2019 19:43:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:43:47: 19000000 INFO @ Sun, 02 Jun 2019 19:43:47: #2 number of paired peaks: 136 WARNING @ Sun, 02 Jun 2019 19:43:47: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sun, 02 Jun 2019 19:43:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:43:47: start X-correlation... INFO @ Sun, 02 Jun 2019 19:43:48: end of X-cor INFO @ Sun, 02 Jun 2019 19:43:48: #2 finished! INFO @ Sun, 02 Jun 2019 19:43:48: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:43:48: #2 alternative fragment length(s) may be 0,31,309,475,545 bps INFO @ Sun, 02 Jun 2019 19:43:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.20_model.r WARNING @ Sun, 02 Jun 2019 19:43:48: #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 19:43:48: #2 You may need to consider one of the other alternative d(s): 0,31,309,475,545 WARNING @ Sun, 02 Jun 2019 19:43:48: #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 19:43:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:43:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:43:48: 19000000 INFO @ Sun, 02 Jun 2019 19:43:55: 20000000 INFO @ Sun, 02 Jun 2019 19:43:57: 20000000 INFO @ Sun, 02 Jun 2019 19:44:04: 21000000 INFO @ Sun, 02 Jun 2019 19:44:06: 21000000 INFO @ Sun, 02 Jun 2019 19:44:13: 22000000 INFO @ Sun, 02 Jun 2019 19:44:15: 22000000 INFO @ Sun, 02 Jun 2019 19:44:23: 23000000 INFO @ Sun, 02 Jun 2019 19:44:24: 23000000 INFO @ Sun, 02 Jun 2019 19:44:31: 24000000 INFO @ Sun, 02 Jun 2019 19:44:33: 24000000 INFO @ Sun, 02 Jun 2019 19:44:40: 25000000 INFO @ Sun, 02 Jun 2019 19:44:42: 25000000 INFO @ Sun, 02 Jun 2019 19:44:48: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:44:48: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:44:48: #1 total tags in treatment: 25905059 INFO @ Sun, 02 Jun 2019 19:44:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:44:48: #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 19:44:49: #1 tags after filtering in treatment: 25905059 INFO @ Sun, 02 Jun 2019 19:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:44:49: #1 finished! INFO @ Sun, 02 Jun 2019 19:44:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:44:51: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:44:51: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:44:51: #1 total tags in treatment: 25905059 INFO @ Sun, 02 Jun 2019 19:44:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:44:51: #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 19:44:51: #1 tags after filtering in treatment: 25905059 INFO @ Sun, 02 Jun 2019 19:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:44:51: #1 finished! INFO @ Sun, 02 Jun 2019 19:44:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:44:51: #2 number of paired peaks: 136 WARNING @ Sun, 02 Jun 2019 19:44:51: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sun, 02 Jun 2019 19:44:51: start model_add_line... INFO @ Sun, 02 Jun 2019 19:44:51: start X-correlation... INFO @ Sun, 02 Jun 2019 19:44:51: end of X-cor INFO @ Sun, 02 Jun 2019 19:44:51: #2 finished! INFO @ Sun, 02 Jun 2019 19:44:51: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:44:51: #2 alternative fragment length(s) may be 0,31,309,475,545 bps INFO @ Sun, 02 Jun 2019 19:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.10_model.r WARNING @ Sun, 02 Jun 2019 19:44:51: #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 19:44:51: #2 You may need to consider one of the other alternative d(s): 0,31,309,475,545 WARNING @ Sun, 02 Jun 2019 19:44:51: #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 19:44:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:44:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:44:53: #2 number of paired peaks: 136 WARNING @ Sun, 02 Jun 2019 19:44:53: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sun, 02 Jun 2019 19:44:53: start model_add_line... INFO @ Sun, 02 Jun 2019 19:44:53: start X-correlation... INFO @ Sun, 02 Jun 2019 19:44:53: end of X-cor INFO @ Sun, 02 Jun 2019 19:44:53: #2 finished! INFO @ Sun, 02 Jun 2019 19:44:53: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:44:53: #2 alternative fragment length(s) may be 0,31,309,475,545 bps INFO @ Sun, 02 Jun 2019 19:44:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466540/SRX466540.05_model.r WARNING @ Sun, 02 Jun 2019 19:44:53: #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 19:44:53: #2 You may need to consider one of the other alternative d(s): 0,31,309,475,545 WARNING @ Sun, 02 Jun 2019 19:44:53: #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 19:44:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:44:53: #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 SRX466540.05.bed: No such file or directory mv: cannot stat ‘SRX466540.05.bed’: No such file or directory /var/spool/uge/at128/job_scripts/1292526: line 321: 31426 Terminated MACS $i /var/spool/uge/at128/job_scripts/1292526: line 321: 31427 Terminated MACS $i /var/spool/uge/at128/job_scripts/1292526: line 321: 31428 Terminated MACS $i mv: cannot stat ‘SRX466540.05.bb’: No such file or directory ls: cannot access SRX466540.10.bed: No such file or directory mv: cannot stat ‘SRX466540.10.bed’: No such file or directory mv: cannot stat ‘SRX466540.10.bb’: No such file or directory ls: cannot access SRX466540.20.bed: No such file or directory mv: cannot stat ‘SRX466540.20.bed’: No such file or directory mv: cannot stat ‘SRX466540.20.bb’: No such file or directory