Job ID = 2590220 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,787,323 reads read : 63,574,646 reads written : 31,787,323 reads 0-length : 31,787,323 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: 00:08:23 31787323 reads; of these: 31787323 (100.00%) were unpaired; of these: 1591600 (5.01%) aligned 0 times 25125655 (79.04%) aligned exactly 1 time 5070068 (15.95%) aligned >1 times 94.99% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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 16 files... [bam_rmdupse_core] 6524345 / 30195723 = 0.2161 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 20:31:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.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 20:31:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:31:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:31:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.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 20:31:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:31:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.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 20:31:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:31:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:31:34: 1000000 INFO @ Mon, 12 Aug 2019 20:31:36: 1000000 INFO @ Mon, 12 Aug 2019 20:31:37: 1000000 INFO @ Mon, 12 Aug 2019 20:31:42: 2000000 INFO @ Mon, 12 Aug 2019 20:31:45: 2000000 INFO @ Mon, 12 Aug 2019 20:31:48: 2000000 INFO @ Mon, 12 Aug 2019 20:31:51: 3000000 INFO @ Mon, 12 Aug 2019 20:31:54: 3000000 INFO @ Mon, 12 Aug 2019 20:31:58: 3000000 INFO @ Mon, 12 Aug 2019 20:32:00: 4000000 INFO @ Mon, 12 Aug 2019 20:32:03: 4000000 INFO @ Mon, 12 Aug 2019 20:32:09: 4000000 INFO @ Mon, 12 Aug 2019 20:32:09: 5000000 INFO @ Mon, 12 Aug 2019 20:32:12: 5000000 INFO @ Mon, 12 Aug 2019 20:32:18: 6000000 INFO @ Mon, 12 Aug 2019 20:32:20: 5000000 INFO @ Mon, 12 Aug 2019 20:32:21: 6000000 INFO @ Mon, 12 Aug 2019 20:32:30: 7000000 INFO @ Mon, 12 Aug 2019 20:32:32: 7000000 INFO @ Mon, 12 Aug 2019 20:32:34: 6000000 INFO @ Mon, 12 Aug 2019 20:32:39: 8000000 INFO @ Mon, 12 Aug 2019 20:32:43: 8000000 INFO @ Mon, 12 Aug 2019 20:32:47: 7000000 INFO @ Mon, 12 Aug 2019 20:32:48: 9000000 INFO @ Mon, 12 Aug 2019 20:32:57: 10000000 INFO @ Mon, 12 Aug 2019 20:32:57: 9000000 INFO @ Mon, 12 Aug 2019 20:33:00: 8000000 INFO @ Mon, 12 Aug 2019 20:33:05: 11000000 INFO @ Mon, 12 Aug 2019 20:33:10: 10000000 INFO @ Mon, 12 Aug 2019 20:33:13: 9000000 INFO @ Mon, 12 Aug 2019 20:33:14: 12000000 INFO @ Mon, 12 Aug 2019 20:33:22: 11000000 INFO @ Mon, 12 Aug 2019 20:33:23: 13000000 INFO @ Mon, 12 Aug 2019 20:33:26: 10000000 INFO @ Mon, 12 Aug 2019 20:33:31: 14000000 INFO @ Mon, 12 Aug 2019 20:33:35: 12000000 INFO @ Mon, 12 Aug 2019 20:33:39: 11000000 INFO @ Mon, 12 Aug 2019 20:33:40: 15000000 INFO @ Mon, 12 Aug 2019 20:33:48: 13000000 INFO @ Mon, 12 Aug 2019 20:33:49: 16000000 INFO @ Mon, 12 Aug 2019 20:33:51: 12000000 INFO @ Mon, 12 Aug 2019 20:33:57: 17000000 INFO @ Mon, 12 Aug 2019 20:34:01: 14000000 INFO @ Mon, 12 Aug 2019 20:34:04: 13000000 INFO @ Mon, 12 Aug 2019 20:34:06: 18000000 INFO @ Mon, 12 Aug 2019 20:34:13: 15000000 INFO @ Mon, 12 Aug 2019 20:34:15: 19000000 INFO @ Mon, 12 Aug 2019 20:34:17: 14000000 INFO @ Mon, 12 Aug 2019 20:34:24: 20000000 INFO @ Mon, 12 Aug 2019 20:34:26: 16000000 INFO @ Mon, 12 Aug 2019 20:34:30: 15000000 INFO @ Mon, 12 Aug 2019 20:34:33: 21000000 INFO @ Mon, 12 Aug 2019 20:34:39: 17000000 INFO @ Mon, 12 Aug 2019 20:34:41: 22000000 INFO @ Mon, 12 Aug 2019 20:34:42: 16000000 INFO @ Mon, 12 Aug 2019 20:34:50: 23000000 INFO @ Mon, 12 Aug 2019 20:34:52: 18000000 INFO @ Mon, 12 Aug 2019 20:34:55: 17000000 INFO @ Mon, 12 Aug 2019 20:34:55: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:34:55: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:34:55: #1 total tags in treatment: 23671378 INFO @ Mon, 12 Aug 2019 20:34:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:34:55: #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 20:34:56: #1 tags after filtering in treatment: 23671378 INFO @ Mon, 12 Aug 2019 20:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:34:56: #1 finished! INFO @ Mon, 12 Aug 2019 20:34:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:34:58: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 20:34:58: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 20:34:58: start model_add_line... INFO @ Mon, 12 Aug 2019 20:34:58: start X-correlation... INFO @ Mon, 12 Aug 2019 20:34:58: end of X-cor INFO @ Mon, 12 Aug 2019 20:34:58: #2 finished! INFO @ Mon, 12 Aug 2019 20:34:58: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:34:58: #2 alternative fragment length(s) may be 0,12,45,526,553,596 bps INFO @ Mon, 12 Aug 2019 20:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.20_model.r WARNING @ Mon, 12 Aug 2019 20:34:58: #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 20:34:58: #2 You may need to consider one of the other alternative d(s): 0,12,45,526,553,596 WARNING @ Mon, 12 Aug 2019 20:34:58: #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 20:34:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:35:05: 19000000 INFO @ Mon, 12 Aug 2019 20:35:08: 18000000 INFO @ Mon, 12 Aug 2019 20:35:18: 20000000 INFO @ Mon, 12 Aug 2019 20:35:21: 19000000 INFO @ Mon, 12 Aug 2019 20:35:31: 21000000 INFO @ Mon, 12 Aug 2019 20:35:34: 20000000 INFO @ Mon, 12 Aug 2019 20:35:43: 22000000 INFO @ Mon, 12 Aug 2019 20:35:47: 21000000 INFO @ Mon, 12 Aug 2019 20:35:55: 23000000 INFO @ Mon, 12 Aug 2019 20:35:59: 22000000 INFO @ Mon, 12 Aug 2019 20:36:03: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:36:03: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:36:03: #1 total tags in treatment: 23671378 INFO @ Mon, 12 Aug 2019 20:36:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:03: #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 20:36:04: #1 tags after filtering in treatment: 23671378 INFO @ Mon, 12 Aug 2019 20:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:04: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:06: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 20:36:06: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 20:36:06: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:06: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:06: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:06: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:06: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:36:06: #2 alternative fragment length(s) may be 0,12,45,526,553,596 bps INFO @ Mon, 12 Aug 2019 20:36:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.05_model.r WARNING @ Mon, 12 Aug 2019 20:36:06: #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 20:36:06: #2 You may need to consider one of the other alternative d(s): 0,12,45,526,553,596 WARNING @ Mon, 12 Aug 2019 20:36:06: #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 20:36:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:10: 23000000 INFO @ Mon, 12 Aug 2019 20:36:16: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:36:16: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:36:16: #1 total tags in treatment: 23671378 INFO @ Mon, 12 Aug 2019 20:36:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:16: #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 20:36:17: #1 tags after filtering in treatment: 23671378 INFO @ Mon, 12 Aug 2019 20:36:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:17: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:19: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 20:36:19: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 20:36:19: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:19: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:19: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:19: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:19: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:36:19: #2 alternative fragment length(s) may be 0,12,45,526,553,596 bps INFO @ Mon, 12 Aug 2019 20:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709761/SRX5709761.10_model.r WARNING @ Mon, 12 Aug 2019 20:36:19: #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 20:36:19: #2 You may need to consider one of the other alternative d(s): 0,12,45,526,553,596 WARNING @ Mon, 12 Aug 2019 20:36:19: #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 20:36:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:19: #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 SRX5709761.05.bed: No such file or directory mv: cannot stat ‘SRX5709761.05.bed’: No such file or directory /var/spool/uge/at120/job_scripts/2590220: line 335: 39348 Terminated MACS $i /var/spool/uge/at120/job_scripts/2590220: line 335: 39362 Terminated MACS $i /var/spool/uge/at120/job_scripts/2590220: line 335: 39376 Terminated MACS $i mv: cannot stat ‘SRX5709761.05.bb’: No such file or directory ls: cannot access SRX5709761.10.bed: No such file or directory mv: cannot stat ‘SRX5709761.10.bed’: No such file or directory mv: cannot stat ‘SRX5709761.10.bb’: No such file or directory ls: cannot access SRX5709761.20.bed: No such file or directory mv: cannot stat ‘SRX5709761.20.bed’: No such file or directory mv: cannot stat ‘SRX5709761.20.bb’: No such file or directory