Job ID = 9162304 sra ファイルのダウンロード中... Completed: 592659K bytes transferred in 11 seconds (408485K 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 4857877 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872745/SRR3713218.sra Written 4857877 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: 00:06:50 4857877 reads; of these: 4857877 (100.00%) were paired; of these: 1197040 (24.64%) aligned concordantly 0 times 2448801 (50.41%) aligned concordantly exactly 1 time 1212036 (24.95%) aligned concordantly >1 times ---- 1197040 pairs aligned concordantly 0 times; of these: 320222 (26.75%) aligned discordantly 1 time ---- 876818 pairs aligned 0 times concordantly or discordantly; of these: 1753636 mates make up the pairs; of these: 1276352 (72.78%) aligned 0 times 98091 (5.59%) aligned exactly 1 time 379193 (21.62%) aligned >1 times 86.86% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 251650 / 3941699 = 0.0638 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 07:25:37: # Command line: callpeak -t SRX1872745.bam -f BAM -g 12100000 -n SRX1872745.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872745.05 # format = BAM # ChIP-seq file = ['SRX1872745.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 07:25:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:25:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:25:37: # Command line: callpeak -t SRX1872745.bam -f BAM -g 12100000 -n SRX1872745.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872745.20 # format = BAM # ChIP-seq file = ['SRX1872745.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 07:25:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:25:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:25:37: # Command line: callpeak -t SRX1872745.bam -f BAM -g 12100000 -n SRX1872745.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872745.10 # format = BAM # ChIP-seq file = ['SRX1872745.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 07:25:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:25:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:25:46: 1000000 INFO @ Wed, 28 Jun 2017 07:25:47: 1000000 INFO @ Wed, 28 Jun 2017 07:25:47: 1000000 INFO @ Wed, 28 Jun 2017 07:25:54: 2000000 INFO @ Wed, 28 Jun 2017 07:25:56: 2000000 INFO @ Wed, 28 Jun 2017 07:25:56: 2000000 INFO @ Wed, 28 Jun 2017 07:26:03: 3000000 INFO @ Wed, 28 Jun 2017 07:26:06: 3000000 INFO @ Wed, 28 Jun 2017 07:26:06: 3000000 INFO @ Wed, 28 Jun 2017 07:26:11: 4000000 INFO @ Wed, 28 Jun 2017 07:26:16: 4000000 INFO @ Wed, 28 Jun 2017 07:26:16: 4000000 INFO @ Wed, 28 Jun 2017 07:26:19: 5000000 INFO @ Wed, 28 Jun 2017 07:26:25: 5000000 INFO @ Wed, 28 Jun 2017 07:26:25: 5000000 INFO @ Wed, 28 Jun 2017 07:26:28: 6000000 INFO @ Wed, 28 Jun 2017 07:26:34: 6000000 INFO @ Wed, 28 Jun 2017 07:26:34: 6000000 INFO @ Wed, 28 Jun 2017 07:26:36: 7000000 INFO @ Wed, 28 Jun 2017 07:26:46: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:26:46: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:26:46: #1 total tags in treatment: 3419929 INFO @ Wed, 28 Jun 2017 07:26:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:26:46: #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 07:26:46: #1 tags after filtering in treatment: 2196314 INFO @ Wed, 28 Jun 2017 07:26:46: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 28 Jun 2017 07:26:46: #1 finished! INFO @ Wed, 28 Jun 2017 07:26:46: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:26:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:26:46: #2 number of paired peaks: 175 WARNING @ Wed, 28 Jun 2017 07:26:46: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Wed, 28 Jun 2017 07:26:46: start model_add_line... INFO @ Wed, 28 Jun 2017 07:26:46: start X-correlation... INFO @ Wed, 28 Jun 2017 07:26:46: end of X-cor INFO @ Wed, 28 Jun 2017 07:26:46: #2 finished! INFO @ Wed, 28 Jun 2017 07:26:46: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:26:46: #2 alternative fragment length(s) may be 0,23,48,101,127,151,194,235,328,365,407,435,478,508,523,559,575,591 bps INFO @ Wed, 28 Jun 2017 07:26:46: #2.2 Generate R script for model : SRX1872745.05_model.r WARNING @ Wed, 28 Jun 2017 07:26:46: #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 07:26:46: #2 You may need to consider one of the other alternative d(s): 0,23,48,101,127,151,194,235,328,365,407,435,478,508,523,559,575,591 WARNING @ Wed, 28 Jun 2017 07:26:46: #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 07:26:46: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:26:47: 7000000 INFO @ Wed, 28 Jun 2017 07:26:47: 7000000 INFO @ Wed, 28 Jun 2017 07:26:58: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:26:58: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:26:58: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:26:58: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:26:58: #1 total tags in treatment: 3419929 INFO @ Wed, 28 Jun 2017 07:26:58: #1 total tags in treatment: 3419929 INFO @ Wed, 28 Jun 2017 07:26:58: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:26:58: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:26:58: #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 07:26:58: #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 07:26:58: #1 tags after filtering in treatment: 2196314 INFO @ Wed, 28 Jun 2017 07:26:58: #1 tags after filtering in treatment: 2196314 INFO @ Wed, 28 Jun 2017 07:26:58: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 28 Jun 2017 07:26:58: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 28 Jun 2017 07:26:58: #1 finished! INFO @ Wed, 28 Jun 2017 07:26:58: #1 finished! INFO @ Wed, 28 Jun 2017 07:26:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:26:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:26:59: #2 number of paired peaks: 175 INFO @ Wed, 28 Jun 2017 07:26:59: #2 number of paired peaks: 175 WARNING @ Wed, 28 Jun 2017 07:26:59: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! WARNING @ Wed, 28 Jun 2017 07:26:59: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Wed, 28 Jun 2017 07:26:59: start model_add_line... INFO @ Wed, 28 Jun 2017 07:26:59: start model_add_line... INFO @ Wed, 28 Jun 2017 07:26:59: start X-correlation... INFO @ Wed, 28 Jun 2017 07:26:59: start X-correlation... INFO @ Wed, 28 Jun 2017 07:26:59: end of X-cor INFO @ Wed, 28 Jun 2017 07:26:59: end of X-cor INFO @ Wed, 28 Jun 2017 07:26:59: #2 finished! INFO @ Wed, 28 Jun 2017 07:26:59: #2 finished! INFO @ Wed, 28 Jun 2017 07:26:59: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:26:59: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:26:59: #2 alternative fragment length(s) may be 0,23,48,101,127,151,194,235,328,365,407,435,478,508,523,559,575,591 bps INFO @ Wed, 28 Jun 2017 07:26:59: #2 alternative fragment length(s) may be 0,23,48,101,127,151,194,235,328,365,407,435,478,508,523,559,575,591 bps INFO @ Wed, 28 Jun 2017 07:26:59: #2.2 Generate R script for model : SRX1872745.20_model.r INFO @ Wed, 28 Jun 2017 07:26:59: #2.2 Generate R script for model : SRX1872745.10_model.r WARNING @ Wed, 28 Jun 2017 07:26:59: #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 07:26:59: #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 07:26:59: #2 You may need to consider one of the other alternative d(s): 0,23,48,101,127,151,194,235,328,365,407,435,478,508,523,559,575,591 WARNING @ Wed, 28 Jun 2017 07:26:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Wed, 28 Jun 2017 07:26:59: #2 You may need to consider one of the other alternative d(s): 0,23,48,101,127,151,194,235,328,365,407,435,478,508,523,559,575,591 INFO @ Wed, 28 Jun 2017 07:26:59: #3 Call peaks... WARNING @ Wed, 28 Jun 2017 07:26:59: #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 07:26:59: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:26:59: #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 SRX1872745.05.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 `SRX1872745.05.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/9162304: line 231: 22214 終了しました MACS $i /var/spool/uge/nt013i/job_scripts/9162304: line 231: 22215 終了しました MACS $i /var/spool/uge/nt013i/job_scripts/9162304: line 231: 22217 終了しました MACS $i mv: cannot stat `SRX1872745.05.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 SRX1872745.10.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 `SRX1872745.10.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 `SRX1872745.10.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 SRX1872745.20.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 `SRX1872745.20.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 `SRX1872745.20.bb': そのようなファイルやディレクトリはありません