Job ID = 1293037 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,772,981 reads read : 73,545,962 reads written : 36,772,981 reads 0-length : 36,772,981 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: 00:13:04 36772981 reads; of these: 36772981 (100.00%) were unpaired; of these: 2200963 (5.99%) aligned 0 times 28846313 (78.44%) aligned exactly 1 time 5725705 (15.57%) aligned >1 times 94.01% overall alignment rate Time searching: 00:13:04 Overall time: 00:13:04 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] 6352148 / 34572018 = 0.1837 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 22:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.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 22:12:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.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 22:12:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.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 22:12:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:03: 1000000 INFO @ Sun, 02 Jun 2019 22:13:04: 1000000 INFO @ Sun, 02 Jun 2019 22:13:04: 1000000 INFO @ Sun, 02 Jun 2019 22:13:11: 2000000 INFO @ Sun, 02 Jun 2019 22:13:14: 2000000 INFO @ Sun, 02 Jun 2019 22:13:14: 2000000 INFO @ Sun, 02 Jun 2019 22:13:19: 3000000 INFO @ Sun, 02 Jun 2019 22:13:23: 3000000 INFO @ Sun, 02 Jun 2019 22:13:23: 3000000 INFO @ Sun, 02 Jun 2019 22:13:27: 4000000 INFO @ Sun, 02 Jun 2019 22:13:32: 4000000 INFO @ Sun, 02 Jun 2019 22:13:32: 4000000 INFO @ Sun, 02 Jun 2019 22:13:35: 5000000 INFO @ Sun, 02 Jun 2019 22:13:41: 5000000 INFO @ Sun, 02 Jun 2019 22:13:41: 5000000 INFO @ Sun, 02 Jun 2019 22:13:43: 6000000 INFO @ Sun, 02 Jun 2019 22:13:50: 6000000 INFO @ Sun, 02 Jun 2019 22:13:50: 6000000 INFO @ Sun, 02 Jun 2019 22:13:52: 7000000 INFO @ Sun, 02 Jun 2019 22:13:59: 7000000 INFO @ Sun, 02 Jun 2019 22:13:59: 7000000 INFO @ Sun, 02 Jun 2019 22:13:59: 8000000 INFO @ Sun, 02 Jun 2019 22:14:07: 9000000 INFO @ Sun, 02 Jun 2019 22:14:08: 8000000 INFO @ Sun, 02 Jun 2019 22:14:09: 8000000 INFO @ Sun, 02 Jun 2019 22:14:15: 10000000 INFO @ Sun, 02 Jun 2019 22:14:18: 9000000 INFO @ Sun, 02 Jun 2019 22:14:18: 9000000 INFO @ Sun, 02 Jun 2019 22:14:23: 11000000 INFO @ Sun, 02 Jun 2019 22:14:27: 10000000 INFO @ Sun, 02 Jun 2019 22:14:28: 10000000 INFO @ Sun, 02 Jun 2019 22:14:31: 12000000 INFO @ Sun, 02 Jun 2019 22:14:37: 11000000 INFO @ Sun, 02 Jun 2019 22:14:37: 11000000 INFO @ Sun, 02 Jun 2019 22:14:39: 13000000 INFO @ Sun, 02 Jun 2019 22:14:47: 12000000 INFO @ Sun, 02 Jun 2019 22:14:48: 12000000 INFO @ Sun, 02 Jun 2019 22:14:48: 14000000 INFO @ Sun, 02 Jun 2019 22:14:56: 15000000 INFO @ Sun, 02 Jun 2019 22:14:57: 13000000 INFO @ Sun, 02 Jun 2019 22:14:58: 13000000 INFO @ Sun, 02 Jun 2019 22:15:05: 16000000 INFO @ Sun, 02 Jun 2019 22:15:07: 14000000 INFO @ Sun, 02 Jun 2019 22:15:08: 14000000 INFO @ Sun, 02 Jun 2019 22:15:13: 17000000 INFO @ Sun, 02 Jun 2019 22:15:18: 15000000 INFO @ Sun, 02 Jun 2019 22:15:18: 15000000 INFO @ Sun, 02 Jun 2019 22:15:21: 18000000 INFO @ Sun, 02 Jun 2019 22:15:27: 16000000 INFO @ Sun, 02 Jun 2019 22:15:27: 16000000 INFO @ Sun, 02 Jun 2019 22:15:29: 19000000 INFO @ Sun, 02 Jun 2019 22:15:37: 17000000 INFO @ Sun, 02 Jun 2019 22:15:37: 17000000 INFO @ Sun, 02 Jun 2019 22:15:37: 20000000 INFO @ Sun, 02 Jun 2019 22:15:46: 21000000 INFO @ Sun, 02 Jun 2019 22:15:47: 18000000 INFO @ Sun, 02 Jun 2019 22:15:47: 18000000 INFO @ Sun, 02 Jun 2019 22:15:54: 22000000 INFO @ Sun, 02 Jun 2019 22:15:56: 19000000 INFO @ Sun, 02 Jun 2019 22:15:56: 19000000 INFO @ Sun, 02 Jun 2019 22:16:03: 23000000 INFO @ Sun, 02 Jun 2019 22:16:06: 20000000 INFO @ Sun, 02 Jun 2019 22:16:06: 20000000 INFO @ Sun, 02 Jun 2019 22:16:12: 24000000 INFO @ Sun, 02 Jun 2019 22:16:16: 21000000 INFO @ Sun, 02 Jun 2019 22:16:16: 21000000 INFO @ Sun, 02 Jun 2019 22:16:21: 25000000 INFO @ Sun, 02 Jun 2019 22:16:26: 22000000 INFO @ Sun, 02 Jun 2019 22:16:26: 22000000 INFO @ Sun, 02 Jun 2019 22:16:29: 26000000 INFO @ Sun, 02 Jun 2019 22:16:36: 23000000 INFO @ Sun, 02 Jun 2019 22:16:36: 23000000 INFO @ Sun, 02 Jun 2019 22:16:38: 27000000 INFO @ Sun, 02 Jun 2019 22:16:46: 24000000 INFO @ Sun, 02 Jun 2019 22:16:46: 24000000 INFO @ Sun, 02 Jun 2019 22:16:46: 28000000 INFO @ Sun, 02 Jun 2019 22:16:48: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 22:16:48: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 22:16:48: #1 total tags in treatment: 28219870 INFO @ Sun, 02 Jun 2019 22:16:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:16:48: #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 22:16:49: #1 tags after filtering in treatment: 28219870 INFO @ Sun, 02 Jun 2019 22:16:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:16:49: #1 finished! INFO @ Sun, 02 Jun 2019 22:16:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:16:51: #2 number of paired peaks: 105 WARNING @ Sun, 02 Jun 2019 22:16:51: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sun, 02 Jun 2019 22:16:51: start model_add_line... INFO @ Sun, 02 Jun 2019 22:16:51: start X-correlation... INFO @ Sun, 02 Jun 2019 22:16:51: end of X-cor INFO @ Sun, 02 Jun 2019 22:16:51: #2 finished! INFO @ Sun, 02 Jun 2019 22:16:51: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:16:51: #2 alternative fragment length(s) may be 0,30,46,65,534,575,582,585,588 bps INFO @ Sun, 02 Jun 2019 22:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.10_model.r WARNING @ Sun, 02 Jun 2019 22:16:51: #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 22:16:51: #2 You may need to consider one of the other alternative d(s): 0,30,46,65,534,575,582,585,588 WARNING @ Sun, 02 Jun 2019 22:16:51: #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 22:16:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:16:55: 25000000 INFO @ Sun, 02 Jun 2019 22:16:55: 25000000 INFO @ Sun, 02 Jun 2019 22:17:05: 26000000 INFO @ Sun, 02 Jun 2019 22:17:05: 26000000 INFO @ Sun, 02 Jun 2019 22:17:15: 27000000 INFO @ Sun, 02 Jun 2019 22:17:15: 27000000 INFO @ Sun, 02 Jun 2019 22:17:24: 28000000 INFO @ Sun, 02 Jun 2019 22:17:24: 28000000 INFO @ Sun, 02 Jun 2019 22:17:27: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 22:17:27: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 22:17:27: #1 total tags in treatment: 28219870 INFO @ Sun, 02 Jun 2019 22:17:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:17:27: #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 22:17:27: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 22:17:27: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 22:17:27: #1 total tags in treatment: 28219870 INFO @ Sun, 02 Jun 2019 22:17:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:17:27: #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 22:17:27: #1 tags after filtering in treatment: 28219870 INFO @ Sun, 02 Jun 2019 22:17:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:17:27: #1 finished! INFO @ Sun, 02 Jun 2019 22:17:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:17:27: #1 tags after filtering in treatment: 28219870 INFO @ Sun, 02 Jun 2019 22:17:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:17:27: #1 finished! INFO @ Sun, 02 Jun 2019 22:17:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:17:29: #2 number of paired peaks: 105 WARNING @ Sun, 02 Jun 2019 22:17:29: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sun, 02 Jun 2019 22:17:29: start model_add_line... INFO @ Sun, 02 Jun 2019 22:17:30: #2 number of paired peaks: 105 WARNING @ Sun, 02 Jun 2019 22:17:30: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sun, 02 Jun 2019 22:17:30: start model_add_line... INFO @ Sun, 02 Jun 2019 22:17:30: start X-correlation... INFO @ Sun, 02 Jun 2019 22:17:30: end of X-cor INFO @ Sun, 02 Jun 2019 22:17:30: #2 finished! INFO @ Sun, 02 Jun 2019 22:17:30: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:17:30: #2 alternative fragment length(s) may be 0,30,46,65,534,575,582,585,588 bps INFO @ Sun, 02 Jun 2019 22:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.20_model.r WARNING @ Sun, 02 Jun 2019 22:17:30: #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 22:17:30: #2 You may need to consider one of the other alternative d(s): 0,30,46,65,534,575,582,585,588 WARNING @ Sun, 02 Jun 2019 22:17:30: #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 22:17:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:17:30: start X-correlation... INFO @ Sun, 02 Jun 2019 22:17:30: end of X-cor INFO @ Sun, 02 Jun 2019 22:17:30: #2 finished! INFO @ Sun, 02 Jun 2019 22:17:30: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:17:30: #2 alternative fragment length(s) may be 0,30,46,65,534,575,582,585,588 bps INFO @ Sun, 02 Jun 2019 22:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020803/SRX5020803.05_model.r WARNING @ Sun, 02 Jun 2019 22:17:30: #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 22:17:30: #2 You may need to consider one of the other alternative d(s): 0,30,46,65,534,575,582,585,588 WARNING @ Sun, 02 Jun 2019 22:17:30: #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 22:17:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:17:30: #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 SRX5020803.05.bed: No such file or directory mv: cannot stat ‘SRX5020803.05.bed’: No such file or directory /var/spool/uge/at112/job_scripts/1293037: line 321: 61433 Terminated MACS $i /var/spool/uge/at112/job_scripts/1293037: line 321: 61434 Terminated MACS $i /var/spool/uge/at112/job_scripts/1293037: line 321: 61435 Terminated MACS $i mv: cannot stat ‘SRX5020803.05.bb’: No such file or directory ls: cannot access SRX5020803.10.bed: No such file or directory mv: cannot stat ‘SRX5020803.10.bed’: No such file or directory mv: cannot stat ‘SRX5020803.10.bb’: No such file or directory ls: cannot access SRX5020803.20.bed: No such file or directory mv: cannot stat ‘SRX5020803.20.bed’: No such file or directory mv: cannot stat ‘SRX5020803.20.bb’: No such file or directory