Job ID = 9162294 sra ファイルのダウンロード中... Completed: 671367K bytes transferred in 11 seconds (499315K 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: PAIRED fastq に変換中... Written 5499086 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872725/SRR3713198.sra Written 5499086 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: 00:07:42 5499086 reads; of these: 5499086 (100.00%) were paired; of these: 1245006 (22.64%) aligned concordantly 0 times 3443004 (62.61%) aligned concordantly exactly 1 time 811076 (14.75%) aligned concordantly >1 times ---- 1245006 pairs aligned concordantly 0 times; of these: 441087 (35.43%) aligned discordantly 1 time ---- 803919 pairs aligned 0 times concordantly or discordantly; of these: 1607838 mates make up the pairs; of these: 1258776 (78.29%) aligned 0 times 110021 (6.84%) aligned exactly 1 time 239041 (14.87%) aligned >1 times 88.55% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 85675 / 4646360 = 0.0184 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 @ Wed, 28 Jun 2017 07:26:35: # Command line: callpeak -t SRX1872725.bam -f BAM -g 12100000 -n SRX1872725.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872725.05 # format = BAM # ChIP-seq file = ['SRX1872725.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 @ Wed, 28 Jun 2017 07:26:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:26:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:26:35: # Command line: callpeak -t SRX1872725.bam -f BAM -g 12100000 -n SRX1872725.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872725.10 # format = BAM # ChIP-seq file = ['SRX1872725.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 @ Wed, 28 Jun 2017 07:26:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:26:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:26:35: # Command line: callpeak -t SRX1872725.bam -f BAM -g 12100000 -n SRX1872725.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872725.20 # format = BAM # ChIP-seq file = ['SRX1872725.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 @ Wed, 28 Jun 2017 07:26:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:26:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:26:43: 1000000 INFO @ Wed, 28 Jun 2017 07:26:45: 1000000 INFO @ Wed, 28 Jun 2017 07:26:45: 1000000 INFO @ Wed, 28 Jun 2017 07:26:51: 2000000 INFO @ Wed, 28 Jun 2017 07:26:55: 2000000 INFO @ Wed, 28 Jun 2017 07:26:55: 2000000 INFO @ Wed, 28 Jun 2017 07:26:58: 3000000 INFO @ Wed, 28 Jun 2017 07:27:03: 3000000 INFO @ Wed, 28 Jun 2017 07:27:03: 3000000 INFO @ Wed, 28 Jun 2017 07:27:05: 4000000 INFO @ Wed, 28 Jun 2017 07:27:11: 4000000 INFO @ Wed, 28 Jun 2017 07:27:11: 4000000 INFO @ Wed, 28 Jun 2017 07:27:13: 5000000 INFO @ Wed, 28 Jun 2017 07:27:19: 5000000 INFO @ Wed, 28 Jun 2017 07:27:19: 5000000 INFO @ Wed, 28 Jun 2017 07:27:20: 6000000 INFO @ Wed, 28 Jun 2017 07:27:27: 6000000 INFO @ Wed, 28 Jun 2017 07:27:27: 6000000 INFO @ Wed, 28 Jun 2017 07:27:27: 7000000 INFO @ Wed, 28 Jun 2017 07:27:34: 7000000 INFO @ Wed, 28 Jun 2017 07:27:34: 7000000 INFO @ Wed, 28 Jun 2017 07:27:35: 8000000 INFO @ Wed, 28 Jun 2017 07:27:42: 8000000 INFO @ Wed, 28 Jun 2017 07:27:42: 8000000 INFO @ Wed, 28 Jun 2017 07:27:42: 9000000 INFO @ Wed, 28 Jun 2017 07:27:46: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:27:46: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:27:46: #1 total tags in treatment: 4173931 INFO @ Wed, 28 Jun 2017 07:27:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:27:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:27:47: #1 tags after filtering in treatment: 3268970 INFO @ Wed, 28 Jun 2017 07:27:47: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 07:27:47: #1 finished! INFO @ Wed, 28 Jun 2017 07:27:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:27:47: #2 number of paired peaks: 164 WARNING @ Wed, 28 Jun 2017 07:27:47: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 28 Jun 2017 07:27:47: start model_add_line... INFO @ Wed, 28 Jun 2017 07:27:47: start X-correlation... INFO @ Wed, 28 Jun 2017 07:27:47: end of X-cor INFO @ Wed, 28 Jun 2017 07:27:47: #2 finished! INFO @ Wed, 28 Jun 2017 07:27:47: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:27:47: #2 alternative fragment length(s) may be 0,14,33,65,81,104,135,148,155,173,179,200,225,274,299,313,334,370,397,414,452,471,501,518,539,574,585 bps INFO @ Wed, 28 Jun 2017 07:27:47: #2.2 Generate R script for model : SRX1872725.05_model.r WARNING @ Wed, 28 Jun 2017 07:27:47: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:27:47: #2 You may need to consider one of the other alternative d(s): 0,14,33,65,81,104,135,148,155,173,179,200,225,274,299,313,334,370,397,414,452,471,501,518,539,574,585 WARNING @ Wed, 28 Jun 2017 07:27:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:27:47: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:27:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:27:50: 9000000 INFO @ Wed, 28 Jun 2017 07:27:50: 9000000 INFO @ Wed, 28 Jun 2017 07:27:54: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:27:54: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:27:54: #1 total tags in treatment: 4173931 INFO @ Wed, 28 Jun 2017 07:27:54: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:27:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:27:54: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:27:54: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:27:54: #1 total tags in treatment: 4173931 INFO @ Wed, 28 Jun 2017 07:27:54: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:27:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:27:54: #1 tags after filtering in treatment: 3268970 INFO @ Wed, 28 Jun 2017 07:27:54: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 07:27:54: #1 finished! INFO @ Wed, 28 Jun 2017 07:27:54: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:27:54: #1 tags after filtering in treatment: 3268970 INFO @ Wed, 28 Jun 2017 07:27:54: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 07:27:54: #1 finished! INFO @ Wed, 28 Jun 2017 07:27:54: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:27:54: #2 number of paired peaks: 164 WARNING @ Wed, 28 Jun 2017 07:27:54: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 28 Jun 2017 07:27:54: start model_add_line... INFO @ Wed, 28 Jun 2017 07:27:54: #2 number of paired peaks: 164 WARNING @ Wed, 28 Jun 2017 07:27:54: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Wed, 28 Jun 2017 07:27:54: start model_add_line... INFO @ Wed, 28 Jun 2017 07:27:54: start X-correlation... INFO @ Wed, 28 Jun 2017 07:27:54: start X-correlation... INFO @ Wed, 28 Jun 2017 07:27:54: end of X-cor INFO @ Wed, 28 Jun 2017 07:27:54: #2 finished! INFO @ Wed, 28 Jun 2017 07:27:54: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:27:54: #2 alternative fragment length(s) may be 0,14,33,65,81,104,135,148,155,173,179,200,225,274,299,313,334,370,397,414,452,471,501,518,539,574,585 bps INFO @ Wed, 28 Jun 2017 07:27:54: #2.2 Generate R script for model : SRX1872725.20_model.r INFO @ Wed, 28 Jun 2017 07:27:54: end of X-cor INFO @ Wed, 28 Jun 2017 07:27:54: #2 finished! INFO @ Wed, 28 Jun 2017 07:27:54: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:27:54: #2 alternative fragment length(s) may be 0,14,33,65,81,104,135,148,155,173,179,200,225,274,299,313,334,370,397,414,452,471,501,518,539,574,585 bps INFO @ Wed, 28 Jun 2017 07:27:54: #2.2 Generate R script for model : SRX1872725.10_model.r WARNING @ Wed, 28 Jun 2017 07:27:54: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:27:54: #2 You may need to consider one of the other alternative d(s): 0,14,33,65,81,104,135,148,155,173,179,200,225,274,299,313,334,370,397,414,452,471,501,518,539,574,585 WARNING @ Wed, 28 Jun 2017 07:27:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:27:54: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:27:54: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 28 Jun 2017 07:27:54: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:27:54: #2 You may need to consider one of the other alternative d(s): 0,14,33,65,81,104,135,148,155,173,179,200,225,274,299,313,334,370,397,414,452,471,501,518,539,574,585 WARNING @ Wed, 28 Jun 2017 07:27:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:27:54: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:27:54: #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 SRX1872725.05.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 `SRX1872725.05.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/nt013i/job_scripts/9162294: line 231: 23192 終了しました MACS $i /var/spool/uge/nt013i/job_scripts/9162294: line 231: 23193 終了しました MACS $i /var/spool/uge/nt013i/job_scripts/9162294: line 231: 23194 終了しました MACS $i mv: cannot stat `SRX1872725.05.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 SRX1872725.10.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 `SRX1872725.10.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 `SRX1872725.10.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 SRX1872725.20.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 `SRX1872725.20.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 `SRX1872725.20.bb': そのようなファイルやディレクトリはありません