Job ID = 9157365 sra ファイルのダウンロード中... Completed: 857164K bytes transferred in 9 seconds (770842K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 23564314 spots for /home/okishinya/chipatlas/results/ce10/SRX1099842/SRR2105914.sra Written 23564314 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:07:26 23564314 reads; of these: 23564314 (100.00%) were unpaired; of these: 333326 (1.41%) aligned 0 times 19415540 (82.39%) aligned exactly 1 time 3815448 (16.19%) aligned >1 times 98.59% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 2467303 / 23230988 = 0.1062 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 @ Tue, 27 Jun 2017 11:42:18: # Command line: callpeak -t SRX1099842.bam -f BAM -g ce -n SRX1099842.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1099842.10 # format = BAM # ChIP-seq file = ['SRX1099842.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 @ Tue, 27 Jun 2017 11:42:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:42:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:42:18: # Command line: callpeak -t SRX1099842.bam -f BAM -g ce -n SRX1099842.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1099842.05 # format = BAM # ChIP-seq file = ['SRX1099842.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 @ Tue, 27 Jun 2017 11:42:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:42:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:42:18: # Command line: callpeak -t SRX1099842.bam -f BAM -g ce -n SRX1099842.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1099842.20 # format = BAM # ChIP-seq file = ['SRX1099842.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 @ Tue, 27 Jun 2017 11:42:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:42:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:42:25: 1000000 INFO @ Tue, 27 Jun 2017 11:42:27: 1000000 INFO @ Tue, 27 Jun 2017 11:42:27: 1000000 INFO @ Tue, 27 Jun 2017 11:42:33: 2000000 INFO @ Tue, 27 Jun 2017 11:42:36: 2000000 INFO @ Tue, 27 Jun 2017 11:42:36: 2000000 INFO @ Tue, 27 Jun 2017 11:42:40: 3000000 INFO @ Tue, 27 Jun 2017 11:42:45: 3000000 INFO @ Tue, 27 Jun 2017 11:42:45: 3000000 INFO @ Tue, 27 Jun 2017 11:42:48: 4000000 INFO @ Tue, 27 Jun 2017 11:42:55: 4000000 INFO @ Tue, 27 Jun 2017 11:42:55: 4000000 INFO @ Tue, 27 Jun 2017 11:42:55: 5000000 INFO @ Tue, 27 Jun 2017 11:43:03: 6000000 INFO @ Tue, 27 Jun 2017 11:43:04: 5000000 INFO @ Tue, 27 Jun 2017 11:43:04: 5000000 INFO @ Tue, 27 Jun 2017 11:43:10: 7000000 INFO @ Tue, 27 Jun 2017 11:43:13: 6000000 INFO @ Tue, 27 Jun 2017 11:43:13: 6000000 INFO @ Tue, 27 Jun 2017 11:43:18: 8000000 INFO @ Tue, 27 Jun 2017 11:43:22: 7000000 INFO @ Tue, 27 Jun 2017 11:43:23: 7000000 INFO @ Tue, 27 Jun 2017 11:43:25: 9000000 INFO @ Tue, 27 Jun 2017 11:43:32: 8000000 INFO @ Tue, 27 Jun 2017 11:43:32: 8000000 INFO @ Tue, 27 Jun 2017 11:43:33: 10000000 INFO @ Tue, 27 Jun 2017 11:43:40: 11000000 INFO @ Tue, 27 Jun 2017 11:43:41: 9000000 INFO @ Tue, 27 Jun 2017 11:43:41: 9000000 INFO @ Tue, 27 Jun 2017 11:43:47: 12000000 INFO @ Tue, 27 Jun 2017 11:43:50: 10000000 INFO @ Tue, 27 Jun 2017 11:43:51: 10000000 INFO @ Tue, 27 Jun 2017 11:43:55: 13000000 INFO @ Tue, 27 Jun 2017 11:44:00: 11000000 INFO @ Tue, 27 Jun 2017 11:44:00: 11000000 INFO @ Tue, 27 Jun 2017 11:44:02: 14000000 INFO @ Tue, 27 Jun 2017 11:44:09: 12000000 INFO @ Tue, 27 Jun 2017 11:44:09: 12000000 INFO @ Tue, 27 Jun 2017 11:44:10: 15000000 INFO @ Tue, 27 Jun 2017 11:44:17: 16000000 INFO @ Tue, 27 Jun 2017 11:44:18: 13000000 INFO @ Tue, 27 Jun 2017 11:44:18: 13000000 INFO @ Tue, 27 Jun 2017 11:44:24: 17000000 INFO @ Tue, 27 Jun 2017 11:44:27: 14000000 INFO @ Tue, 27 Jun 2017 11:44:28: 14000000 INFO @ Tue, 27 Jun 2017 11:44:32: 18000000 INFO @ Tue, 27 Jun 2017 11:44:37: 15000000 INFO @ Tue, 27 Jun 2017 11:44:37: 15000000 INFO @ Tue, 27 Jun 2017 11:44:39: 19000000 INFO @ Tue, 27 Jun 2017 11:44:46: 16000000 INFO @ Tue, 27 Jun 2017 11:44:46: 16000000 INFO @ Tue, 27 Jun 2017 11:44:47: 20000000 INFO @ Tue, 27 Jun 2017 11:44:52: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:44:52: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:44:52: #1 total tags in treatment: 20763685 INFO @ Tue, 27 Jun 2017 11:44:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:44:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:44:53: #1 tags after filtering in treatment: 20763685 INFO @ Tue, 27 Jun 2017 11:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:44:53: #1 finished! INFO @ Tue, 27 Jun 2017 11:44:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:44:54: #2 number of paired peaks: 189 WARNING @ Tue, 27 Jun 2017 11:44:54: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 27 Jun 2017 11:44:54: start model_add_line... INFO @ Tue, 27 Jun 2017 11:44:54: start X-correlation... INFO @ Tue, 27 Jun 2017 11:44:54: end of X-cor INFO @ Tue, 27 Jun 2017 11:44:54: #2 finished! INFO @ Tue, 27 Jun 2017 11:44:54: #2 predicted fragment length is 0 bps INFO @ Tue, 27 Jun 2017 11:44:54: #2 alternative fragment length(s) may be 0,47,525,569 bps INFO @ Tue, 27 Jun 2017 11:44:54: #2.2 Generate R script for model : SRX1099842.10_model.r WARNING @ Tue, 27 Jun 2017 11:44:54: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:44:54: #2 You may need to consider one of the other alternative d(s): 0,47,525,569 WARNING @ Tue, 27 Jun 2017 11:44:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:44:54: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:44:55: 17000000 INFO @ Tue, 27 Jun 2017 11:44:55: 17000000 INFO @ Tue, 27 Jun 2017 11:45:05: 18000000 INFO @ Tue, 27 Jun 2017 11:45:05: 18000000 INFO @ Tue, 27 Jun 2017 11:45:14: 19000000 INFO @ Tue, 27 Jun 2017 11:45:14: 19000000 INFO @ Tue, 27 Jun 2017 11:45:23: 20000000 INFO @ Tue, 27 Jun 2017 11:45:23: 20000000 INFO @ Tue, 27 Jun 2017 11:45:30: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:45:30: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:45:30: #1 total tags in treatment: 20763685 INFO @ Tue, 27 Jun 2017 11:45:30: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:45:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:45:30: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:45:30: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:45:30: #1 total tags in treatment: 20763685 INFO @ Tue, 27 Jun 2017 11:45:30: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:45:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:45:31: #1 tags after filtering in treatment: 20763685 INFO @ Tue, 27 Jun 2017 11:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:45:31: #1 finished! INFO @ Tue, 27 Jun 2017 11:45:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:45:31: #1 tags after filtering in treatment: 20763685 INFO @ Tue, 27 Jun 2017 11:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:45:31: #1 finished! INFO @ Tue, 27 Jun 2017 11:45:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:45:32: #2 number of paired peaks: 189 WARNING @ Tue, 27 Jun 2017 11:45:32: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 27 Jun 2017 11:45:32: start model_add_line... INFO @ Tue, 27 Jun 2017 11:45:32: #2 number of paired peaks: 189 WARNING @ Tue, 27 Jun 2017 11:45:32: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 27 Jun 2017 11:45:32: start model_add_line... INFO @ Tue, 27 Jun 2017 11:45:32: start X-correlation... INFO @ Tue, 27 Jun 2017 11:45:32: end of X-cor INFO @ Tue, 27 Jun 2017 11:45:32: #2 finished! INFO @ Tue, 27 Jun 2017 11:45:32: #2 predicted fragment length is 0 bps INFO @ Tue, 27 Jun 2017 11:45:32: #2 alternative fragment length(s) may be 0,47,525,569 bps INFO @ Tue, 27 Jun 2017 11:45:32: #2.2 Generate R script for model : SRX1099842.05_model.r WARNING @ Tue, 27 Jun 2017 11:45:32: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:45:32: #2 You may need to consider one of the other alternative d(s): 0,47,525,569 WARNING @ Tue, 27 Jun 2017 11:45:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:45:32: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:45:32: start X-correlation... INFO @ Tue, 27 Jun 2017 11:45:32: end of X-cor INFO @ Tue, 27 Jun 2017 11:45:32: #2 finished! INFO @ Tue, 27 Jun 2017 11:45:32: #2 predicted fragment length is 0 bps INFO @ Tue, 27 Jun 2017 11:45:32: #2 alternative fragment length(s) may be 0,47,525,569 bps INFO @ Tue, 27 Jun 2017 11:45:32: #2.2 Generate R script for model : SRX1099842.20_model.r WARNING @ Tue, 27 Jun 2017 11:45:32: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:45:32: #2 You may need to consider one of the other alternative d(s): 0,47,525,569 WARNING @ Tue, 27 Jun 2017 11:45:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:45:32: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:45:32: #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 SRX1099842.05.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1099842.05.bed': そのようなファイルやディレクトリはありません /var/spool/uge/nt021i/job_scripts/9157365: line 231: 28221 終了しました MACS $i /var/spool/uge/nt021i/job_scripts/9157365: line 231: 28222 終了しました MACS $i /var/spool/uge/nt021i/job_scripts/9157365: line 231: 28224 終了しました MACS $i mv: cannot stat `SRX1099842.05.bb': そのようなファイルやディレクトリはありません ls: cannot access SRX1099842.10.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1099842.10.bed': そのようなファイルやディレクトリはありません mv: cannot stat `SRX1099842.10.bb': そのようなファイルやディレクトリはありません ls: cannot access SRX1099842.20.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1099842.20.bed': そのようなファイルやディレクトリはありません mv: cannot stat `SRX1099842.20.bb': そのようなファイルやディレクトリはありません