Job ID = 10608980 sra ファイルのダウンロード中... Completed: 877584K bytes transferred in 63 seconds (113231K bits/sec), in 1 file. 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 27674237 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2745374/SRR5457305.sra Written 27674237 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:08:41 27674237 reads; of these: 27674237 (100.00%) were unpaired; of these: 6553504 (23.68%) aligned 0 times 9454097 (34.16%) aligned exactly 1 time 11666636 (42.16%) aligned >1 times 76.32% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 17271007 / 21120733 = 0.8177 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 @ Thu, 03 May 2018 23:07:33: # Command line: callpeak -t SRX2745374.bam -f BAM -g 12100000 -n SRX2745374.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745374.10 # format = BAM # ChIP-seq file = ['SRX2745374.bam'] # control file = None # effective genome size = 1.21e+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 @ Thu, 03 May 2018 23:07:33: #1 read tag files... INFO @ Thu, 03 May 2018 23:07:33: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:07:33: # Command line: callpeak -t SRX2745374.bam -f BAM -g 12100000 -n SRX2745374.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745374.05 # format = BAM # ChIP-seq file = ['SRX2745374.bam'] # control file = None # effective genome size = 1.21e+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 @ Thu, 03 May 2018 23:07:33: #1 read tag files... INFO @ Thu, 03 May 2018 23:07:33: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:07:33: # Command line: callpeak -t SRX2745374.bam -f BAM -g 12100000 -n SRX2745374.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745374.20 # format = BAM # ChIP-seq file = ['SRX2745374.bam'] # control file = None # effective genome size = 1.21e+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 @ Thu, 03 May 2018 23:07:33: #1 read tag files... INFO @ Thu, 03 May 2018 23:07:33: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:07:40: 1000000 INFO @ Thu, 03 May 2018 23:07:41: 1000000 INFO @ Thu, 03 May 2018 23:07:41: 1000000 INFO @ Thu, 03 May 2018 23:07:48: 2000000 INFO @ Thu, 03 May 2018 23:07:48: 2000000 INFO @ Thu, 03 May 2018 23:07:48: 2000000 INFO @ Thu, 03 May 2018 23:07:56: 3000000 INFO @ Thu, 03 May 2018 23:07:56: 3000000 INFO @ Thu, 03 May 2018 23:07:56: 3000000 INFO @ Thu, 03 May 2018 23:08:02: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:08:02: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:08:02: #1 total tags in treatment: 3849726 INFO @ Thu, 03 May 2018 23:08:02: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:08:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:08:02: #1 tags after filtering in treatment: 3849726 INFO @ Thu, 03 May 2018 23:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:08:02: #1 finished! INFO @ Thu, 03 May 2018 23:08:02: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:08:02: #2 number of paired peaks: 177 WARNING @ Thu, 03 May 2018 23:08:02: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Thu, 03 May 2018 23:08:02: start model_add_line... INFO @ Thu, 03 May 2018 23:08:02: start X-correlation... INFO @ Thu, 03 May 2018 23:08:02: end of X-cor INFO @ Thu, 03 May 2018 23:08:02: #2 finished! INFO @ Thu, 03 May 2018 23:08:02: #2 predicted fragment length is 0 bps INFO @ Thu, 03 May 2018 23:08:02: #2 alternative fragment length(s) may be 0,18,50,79,144,187,200,210,216,223,231,236,263,305,327,352,374,419,435,461,485,507,514,565,579 bps INFO @ Thu, 03 May 2018 23:08:02: #2.2 Generate R script for model : SRX2745374.20_model.r WARNING @ Thu, 03 May 2018 23:08:02: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:08:02: #2 You may need to consider one of the other alternative d(s): 0,18,50,79,144,187,200,210,216,223,231,236,263,305,327,352,374,419,435,461,485,507,514,565,579 WARNING @ Thu, 03 May 2018 23:08:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:08:02: #3 Call peaks... INFO @ Thu, 03 May 2018 23:08:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:08:03: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:08:03: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:08:03: #1 total tags in treatment: 3849726 INFO @ Thu, 03 May 2018 23:08:03: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:08:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:08:03: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:08:03: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:08:03: #1 total tags in treatment: 3849726 INFO @ Thu, 03 May 2018 23:08:03: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:08:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:08:03: #1 tags after filtering in treatment: 3849726 INFO @ Thu, 03 May 2018 23:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:08:03: #1 finished! INFO @ Thu, 03 May 2018 23:08:03: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:08:03: #1 tags after filtering in treatment: 3849726 INFO @ Thu, 03 May 2018 23:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:08:03: #1 finished! INFO @ Thu, 03 May 2018 23:08:03: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:08:03: #2 number of paired peaks: 177 WARNING @ Thu, 03 May 2018 23:08:03: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Thu, 03 May 2018 23:08:03: start model_add_line... INFO @ Thu, 03 May 2018 23:08:03: #2 number of paired peaks: 177 WARNING @ Thu, 03 May 2018 23:08:03: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Thu, 03 May 2018 23:08:03: start model_add_line... INFO @ Thu, 03 May 2018 23:08:03: start X-correlation... INFO @ Thu, 03 May 2018 23:08:03: end of X-cor INFO @ Thu, 03 May 2018 23:08:03: #2 finished! INFO @ Thu, 03 May 2018 23:08:03: #2 predicted fragment length is 0 bps INFO @ Thu, 03 May 2018 23:08:03: #2 alternative fragment length(s) may be 0,18,50,79,144,187,200,210,216,223,231,236,263,305,327,352,374,419,435,461,485,507,514,565,579 bps INFO @ Thu, 03 May 2018 23:08:03: #2.2 Generate R script for model : SRX2745374.10_model.r INFO @ Thu, 03 May 2018 23:08:03: start X-correlation... WARNING @ Thu, 03 May 2018 23:08:03: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:08:03: #2 You may need to consider one of the other alternative d(s): 0,18,50,79,144,187,200,210,216,223,231,236,263,305,327,352,374,419,435,461,485,507,514,565,579 WARNING @ Thu, 03 May 2018 23:08:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:08:03: #3 Call peaks... INFO @ Thu, 03 May 2018 23:08:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:08:03: end of X-cor INFO @ Thu, 03 May 2018 23:08:03: #2 finished! INFO @ Thu, 03 May 2018 23:08:03: #2 predicted fragment length is 0 bps INFO @ Thu, 03 May 2018 23:08:03: #2 alternative fragment length(s) may be 0,18,50,79,144,187,200,210,216,223,231,236,263,305,327,352,374,419,435,461,485,507,514,565,579 bps INFO @ Thu, 03 May 2018 23:08:03: #2.2 Generate R script for model : SRX2745374.05_model.r WARNING @ Thu, 03 May 2018 23:08:03: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:08:03: #2 You may need to consider one of the other alternative d(s): 0,18,50,79,144,187,200,210,216,223,231,236,263,305,327,352,374,419,435,461,485,507,514,565,579 WARNING @ Thu, 03 May 2018 23:08:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:08:03: #3 Call peaks... INFO @ Thu, 03 May 2018 23:08:03: #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 SRX2745374.05.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 `SRX2745374.05.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/nt031i/job_scripts/10608980: line 254: 2199 終了しました MACS $i /var/spool/uge/nt031i/job_scripts/10608980: line 254: 2200 終了しました MACS $i /var/spool/uge/nt031i/job_scripts/10608980: line 254: 2201 終了しました MACS $i mv: cannot stat `SRX2745374.05.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 SRX2745374.10.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 `SRX2745374.10.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 `SRX2745374.10.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 SRX2745374.20.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 `SRX2745374.20.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 `SRX2745374.20.bb': そのようなファイルやディレクトリはありません