Job ID = 10608978 sra ファイルのダウンロード中... Completed: 541325K bytes transferred in 46 seconds (95909K 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 16636544 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2745372/SRR5457303.sra Written 16636544 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: 00:04:44 16636544 reads; of these: 16636544 (100.00%) were unpaired; of these: 3225153 (19.39%) aligned 0 times 9423660 (56.64%) aligned exactly 1 time 3987731 (23.97%) aligned >1 times 80.61% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 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 8 files... [bam_rmdupse_core] 10364776 / 13411391 = 0.7728 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 23:01:17: # Command line: callpeak -t SRX2745372.bam -f BAM -g 12100000 -n SRX2745372.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745372.10 # format = BAM # ChIP-seq file = ['SRX2745372.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 23:01:17: #1 read tag files... INFO @ Thu, 03 May 2018 23:01:17: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:01:17: # Command line: callpeak -t SRX2745372.bam -f BAM -g 12100000 -n SRX2745372.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745372.05 # format = BAM # ChIP-seq file = ['SRX2745372.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 23:01:17: #1 read tag files... INFO @ Thu, 03 May 2018 23:01:17: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:01:17: # Command line: callpeak -t SRX2745372.bam -f BAM -g 12100000 -n SRX2745372.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745372.20 # format = BAM # ChIP-seq file = ['SRX2745372.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 23:01:17: #1 read tag files... INFO @ Thu, 03 May 2018 23:01:17: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:01:27: 1000000 INFO @ Thu, 03 May 2018 23:01:27: 1000000 INFO @ Thu, 03 May 2018 23:01:27: 1000000 INFO @ Thu, 03 May 2018 23:01:37: 2000000 INFO @ Thu, 03 May 2018 23:01:37: 2000000 INFO @ Thu, 03 May 2018 23:01:37: 2000000 INFO @ Thu, 03 May 2018 23:01:47: 3000000 INFO @ Thu, 03 May 2018 23:01:47: 3000000 INFO @ Thu, 03 May 2018 23:01:47: 3000000 INFO @ Thu, 03 May 2018 23:01:47: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:01:47: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:01:47: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:01:47: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:01:47: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:01:47: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:01:47: #1 total tags in treatment: 3046615 INFO @ Thu, 03 May 2018 23:01:47: #1 total tags in treatment: 3046615 INFO @ Thu, 03 May 2018 23:01:47: #1 total tags in treatment: 3046615 INFO @ Thu, 03 May 2018 23:01:47: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:01:47: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:01:47: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:01:47: #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 23:01:47: #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 23:01:47: #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 23:01:47: #1 tags after filtering in treatment: 3046615 INFO @ Thu, 03 May 2018 23:01:47: #1 tags after filtering in treatment: 3046615 INFO @ Thu, 03 May 2018 23:01:47: #1 tags after filtering in treatment: 3046615 INFO @ Thu, 03 May 2018 23:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:01:47: #1 finished! INFO @ Thu, 03 May 2018 23:01:47: #1 finished! INFO @ Thu, 03 May 2018 23:01:47: #1 finished! INFO @ Thu, 03 May 2018 23:01:47: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:01:47: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:01:47: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:01:47: #2 number of paired peaks: 197 INFO @ Thu, 03 May 2018 23:01:47: #2 number of paired peaks: 197 WARNING @ Thu, 03 May 2018 23:01:47: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! WARNING @ Thu, 03 May 2018 23:01:47: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Thu, 03 May 2018 23:01:47: start model_add_line... INFO @ Thu, 03 May 2018 23:01:47: start model_add_line... INFO @ Thu, 03 May 2018 23:01:47: #2 number of paired peaks: 197 WARNING @ Thu, 03 May 2018 23:01:47: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Thu, 03 May 2018 23:01:47: start model_add_line... INFO @ Thu, 03 May 2018 23:01:47: start X-correlation... INFO @ Thu, 03 May 2018 23:01:47: start X-correlation... INFO @ Thu, 03 May 2018 23:01:47: start X-correlation... INFO @ Thu, 03 May 2018 23:01:47: end of X-cor INFO @ Thu, 03 May 2018 23:01:47: end of X-cor INFO @ Thu, 03 May 2018 23:01:47: #2 finished! INFO @ Thu, 03 May 2018 23:01:47: #2 finished! INFO @ Thu, 03 May 2018 23:01:47: #2 predicted fragment length is 0 bps INFO @ Thu, 03 May 2018 23:01:47: #2 predicted fragment length is 0 bps INFO @ Thu, 03 May 2018 23:01:47: #2 alternative fragment length(s) may be 0,20,52,96,124,158,219,236,250,281,307,363,413,471,504,547,582 bps INFO @ Thu, 03 May 2018 23:01:47: #2 alternative fragment length(s) may be 0,20,52,96,124,158,219,236,250,281,307,363,413,471,504,547,582 bps INFO @ Thu, 03 May 2018 23:01:47: #2.2 Generate R script for model : SRX2745372.20_model.r INFO @ Thu, 03 May 2018 23:01:47: #2.2 Generate R script for model : SRX2745372.05_model.r INFO @ Thu, 03 May 2018 23:01:47: end of X-cor INFO @ Thu, 03 May 2018 23:01:47: #2 finished! INFO @ Thu, 03 May 2018 23:01:47: #2 predicted fragment length is 0 bps INFO @ Thu, 03 May 2018 23:01:47: #2 alternative fragment length(s) may be 0,20,52,96,124,158,219,236,250,281,307,363,413,471,504,547,582 bps INFO @ Thu, 03 May 2018 23:01:47: #2.2 Generate R script for model : SRX2745372.10_model.r WARNING @ Thu, 03 May 2018 23:01:47: #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 23:01:47: #2 You may need to consider one of the other alternative d(s): 0,20,52,96,124,158,219,236,250,281,307,363,413,471,504,547,582 WARNING @ Thu, 03 May 2018 23:01:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Thu, 03 May 2018 23:01:47: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Thu, 03 May 2018 23:01:47: #3 Call peaks... WARNING @ Thu, 03 May 2018 23:01:47: #2 You may need to consider one of the other alternative d(s): 0,20,52,96,124,158,219,236,250,281,307,363,413,471,504,547,582 WARNING @ Thu, 03 May 2018 23:01:47: #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 23:01:47: #3 Call peaks... INFO @ Thu, 03 May 2018 23:01:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:01:47: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 03 May 2018 23:01:47: #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 23:01:47: #2 You may need to consider one of the other alternative d(s): 0,20,52,96,124,158,219,236,250,281,307,363,413,471,504,547,582 WARNING @ Thu, 03 May 2018 23:01:47: #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 23:01:47: #3 Call peaks... INFO @ Thu, 03 May 2018 23:01:47: #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 SRX2745372.05.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 `SRX2745372.05.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/nt043i/job_scripts/10608978: line 254: 53283 終了しました MACS $i /var/spool/uge/nt043i/job_scripts/10608978: line 254: 53284 終了しました MACS $i /var/spool/uge/nt043i/job_scripts/10608978: line 254: 53286 終了しました MACS $i mv: cannot stat `SRX2745372.05.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 SRX2745372.10.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 `SRX2745372.10.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 `SRX2745372.10.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 SRX2745372.20.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 `SRX2745372.20.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 `SRX2745372.20.bb': そのようなファイルやディレクトリはありません