Job ID = 1293214 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,322,596 reads read : 32,322,596 reads written : 32,322,596 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: 00:07:23 32322596 reads; of these: 32322596 (100.00%) were unpaired; of these: 3127654 (9.68%) aligned 0 times 23562716 (72.90%) aligned exactly 1 time 5632226 (17.43%) aligned >1 times 90.32% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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 12 files... [bam_rmdupse_core] 4158696 / 29194942 = 0.1424 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 22:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.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 22:43:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:43:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.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 22:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.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 22:43:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:43:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:43:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:43:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:43:40: 1000000 INFO @ Sun, 02 Jun 2019 22:43:40: 1000000 INFO @ Sun, 02 Jun 2019 22:43:40: 1000000 INFO @ Sun, 02 Jun 2019 22:43:48: 2000000 INFO @ Sun, 02 Jun 2019 22:43:48: 2000000 INFO @ Sun, 02 Jun 2019 22:43:49: 2000000 INFO @ Sun, 02 Jun 2019 22:43:55: 3000000 INFO @ Sun, 02 Jun 2019 22:43:55: 3000000 INFO @ Sun, 02 Jun 2019 22:43:57: 3000000 INFO @ Sun, 02 Jun 2019 22:44:03: 4000000 INFO @ Sun, 02 Jun 2019 22:44:03: 4000000 INFO @ Sun, 02 Jun 2019 22:44:05: 4000000 INFO @ Sun, 02 Jun 2019 22:44:12: 5000000 INFO @ Sun, 02 Jun 2019 22:44:12: 5000000 INFO @ Sun, 02 Jun 2019 22:44:14: 5000000 INFO @ Sun, 02 Jun 2019 22:44:20: 6000000 INFO @ Sun, 02 Jun 2019 22:44:20: 6000000 INFO @ Sun, 02 Jun 2019 22:44:23: 6000000 INFO @ Sun, 02 Jun 2019 22:44:28: 7000000 INFO @ Sun, 02 Jun 2019 22:44:28: 7000000 INFO @ Sun, 02 Jun 2019 22:44:31: 7000000 INFO @ Sun, 02 Jun 2019 22:44:36: 8000000 INFO @ Sun, 02 Jun 2019 22:44:36: 8000000 INFO @ Sun, 02 Jun 2019 22:44:40: 8000000 INFO @ Sun, 02 Jun 2019 22:44:44: 9000000 INFO @ Sun, 02 Jun 2019 22:44:45: 9000000 INFO @ Sun, 02 Jun 2019 22:44:49: 9000000 INFO @ Sun, 02 Jun 2019 22:44:53: 10000000 INFO @ Sun, 02 Jun 2019 22:44:53: 10000000 INFO @ Sun, 02 Jun 2019 22:44:58: 10000000 INFO @ Sun, 02 Jun 2019 22:45:01: 11000000 INFO @ Sun, 02 Jun 2019 22:45:01: 11000000 INFO @ Sun, 02 Jun 2019 22:45:07: 11000000 INFO @ Sun, 02 Jun 2019 22:45:08: 12000000 INFO @ Sun, 02 Jun 2019 22:45:08: 12000000 INFO @ Sun, 02 Jun 2019 22:45:14: 13000000 INFO @ Sun, 02 Jun 2019 22:45:15: 13000000 INFO @ Sun, 02 Jun 2019 22:45:16: 12000000 INFO @ Sun, 02 Jun 2019 22:45:21: 14000000 INFO @ Sun, 02 Jun 2019 22:45:22: 14000000 INFO @ Sun, 02 Jun 2019 22:45:25: 13000000 INFO @ Sun, 02 Jun 2019 22:45:28: 15000000 INFO @ Sun, 02 Jun 2019 22:45:29: 15000000 INFO @ Sun, 02 Jun 2019 22:45:33: 14000000 INFO @ Sun, 02 Jun 2019 22:45:35: 16000000 INFO @ Sun, 02 Jun 2019 22:45:36: 16000000 INFO @ Sun, 02 Jun 2019 22:45:41: 15000000 INFO @ Sun, 02 Jun 2019 22:45:41: 17000000 INFO @ Sun, 02 Jun 2019 22:45:43: 17000000 INFO @ Sun, 02 Jun 2019 22:45:48: 18000000 INFO @ Sun, 02 Jun 2019 22:45:50: 16000000 INFO @ Sun, 02 Jun 2019 22:45:50: 18000000 INFO @ Sun, 02 Jun 2019 22:45:55: 19000000 INFO @ Sun, 02 Jun 2019 22:45:57: 19000000 INFO @ Sun, 02 Jun 2019 22:45:59: 17000000 INFO @ Sun, 02 Jun 2019 22:46:01: 20000000 INFO @ Sun, 02 Jun 2019 22:46:04: 20000000 INFO @ Sun, 02 Jun 2019 22:46:07: 18000000 INFO @ Sun, 02 Jun 2019 22:46:08: 21000000 INFO @ Sun, 02 Jun 2019 22:46:11: 21000000 INFO @ Sun, 02 Jun 2019 22:46:15: 22000000 INFO @ Sun, 02 Jun 2019 22:46:16: 19000000 INFO @ Sun, 02 Jun 2019 22:46:18: 22000000 INFO @ Sun, 02 Jun 2019 22:46:21: 23000000 INFO @ Sun, 02 Jun 2019 22:46:24: 20000000 INFO @ Sun, 02 Jun 2019 22:46:25: 23000000 INFO @ Sun, 02 Jun 2019 22:46:28: 24000000 INFO @ Sun, 02 Jun 2019 22:46:32: 24000000 INFO @ Sun, 02 Jun 2019 22:46:32: 21000000 INFO @ Sun, 02 Jun 2019 22:46:35: 25000000 INFO @ Sun, 02 Jun 2019 22:46:35: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:46:35: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:46:35: #1 total tags in treatment: 25036246 INFO @ Sun, 02 Jun 2019 22:46:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:46:35: #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 22:46:36: #1 tags after filtering in treatment: 25036246 INFO @ Sun, 02 Jun 2019 22:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:46:36: #1 finished! INFO @ Sun, 02 Jun 2019 22:46:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:46:38: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 22:46:38: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 22:46:38: start model_add_line... INFO @ Sun, 02 Jun 2019 22:46:38: start X-correlation... INFO @ Sun, 02 Jun 2019 22:46:38: end of X-cor INFO @ Sun, 02 Jun 2019 22:46:38: #2 finished! INFO @ Sun, 02 Jun 2019 22:46:38: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:46:38: #2 alternative fragment length(s) may be 0,23,523,547 bps INFO @ Sun, 02 Jun 2019 22:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.05_model.r WARNING @ Sun, 02 Jun 2019 22:46:38: #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 22:46:38: #2 You may need to consider one of the other alternative d(s): 0,23,523,547 WARNING @ Sun, 02 Jun 2019 22:46:38: #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 22:46:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:46:39: 25000000 INFO @ Sun, 02 Jun 2019 22:46:39: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:46:39: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:46:39: #1 total tags in treatment: 25036246 INFO @ Sun, 02 Jun 2019 22:46:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:46:39: #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 22:46:40: #1 tags after filtering in treatment: 25036246 INFO @ Sun, 02 Jun 2019 22:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:46:40: #1 finished! INFO @ Sun, 02 Jun 2019 22:46:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:46:41: 22000000 INFO @ Sun, 02 Jun 2019 22:46:42: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 22:46:42: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 22:46:42: start model_add_line... INFO @ Sun, 02 Jun 2019 22:46:42: start X-correlation... INFO @ Sun, 02 Jun 2019 22:46:42: end of X-cor INFO @ Sun, 02 Jun 2019 22:46:42: #2 finished! INFO @ Sun, 02 Jun 2019 22:46:42: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:46:42: #2 alternative fragment length(s) may be 0,23,523,547 bps INFO @ Sun, 02 Jun 2019 22:46:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.10_model.r WARNING @ Sun, 02 Jun 2019 22:46:42: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:46:42: #2 You may need to consider one of the other alternative d(s): 0,23,523,547 WARNING @ Sun, 02 Jun 2019 22:46:42: #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 22:46:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:46:49: 23000000 INFO @ Sun, 02 Jun 2019 22:46:57: 24000000 INFO @ Sun, 02 Jun 2019 22:47:05: 25000000 INFO @ Sun, 02 Jun 2019 22:47:06: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:47:06: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:47:06: #1 total tags in treatment: 25036246 INFO @ Sun, 02 Jun 2019 22:47:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:47:06: #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 22:47:06: #1 tags after filtering in treatment: 25036246 INFO @ Sun, 02 Jun 2019 22:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:47:06: #1 finished! INFO @ Sun, 02 Jun 2019 22:47:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:47:08: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 22:47:08: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 22:47:08: start model_add_line... INFO @ Sun, 02 Jun 2019 22:47:09: start X-correlation... INFO @ Sun, 02 Jun 2019 22:47:09: end of X-cor INFO @ Sun, 02 Jun 2019 22:47:09: #2 finished! INFO @ Sun, 02 Jun 2019 22:47:09: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:47:09: #2 alternative fragment length(s) may be 0,23,523,547 bps INFO @ Sun, 02 Jun 2019 22:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402764/SRX5402764.20_model.r WARNING @ Sun, 02 Jun 2019 22:47:09: #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 22:47:09: #2 You may need to consider one of the other alternative d(s): 0,23,523,547 WARNING @ Sun, 02 Jun 2019 22:47:09: #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 22:47:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:47:09: #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 SRX5402764.05.bed: No such file or directory mv: cannot stat ‘SRX5402764.05.bed’: No such file or directory /var/spool/uge/at110/job_scripts/1293214: line 321: 7269 Terminated MACS $i /var/spool/uge/at110/job_scripts/1293214: line 321: 7270 Terminated MACS $i /var/spool/uge/at110/job_scripts/1293214: line 321: 7271 Terminated MACS $i mv: cannot stat ‘SRX5402764.05.bb’: No such file or directory ls: cannot access SRX5402764.10.bed: No such file or directory mv: cannot stat ‘SRX5402764.10.bed’: No such file or directory mv: cannot stat ‘SRX5402764.10.bb’: No such file or directory ls: cannot access SRX5402764.20.bed: No such file or directory mv: cannot stat ‘SRX5402764.20.bed’: No such file or directory mv: cannot stat ‘SRX5402764.20.bb’: No such file or directory