Job ID = 9162296 sra ファイルのダウンロード中... Completed: 494467K bytes transferred in 11 seconds (364704K 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 4056372 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872729/SRR3713202.sra Written 4056372 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: 00:05:05 4056372 reads; of these: 4056372 (100.00%) were paired; of these: 1109304 (27.35%) aligned concordantly 0 times 2497255 (61.56%) aligned concordantly exactly 1 time 449813 (11.09%) aligned concordantly >1 times ---- 1109304 pairs aligned concordantly 0 times; of these: 225905 (20.36%) aligned discordantly 1 time ---- 883399 pairs aligned 0 times concordantly or discordantly; of these: 1766798 mates make up the pairs; of these: 1619818 (91.68%) aligned 0 times 49865 (2.82%) aligned exactly 1 time 97115 (5.50%) aligned >1 times 80.03% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 66418 / 3155977 = 0.0210 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 07:22:33: # Command line: callpeak -t SRX1872729.bam -f BAM -g 12100000 -n SRX1872729.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872729.20 # format = BAM # ChIP-seq file = ['SRX1872729.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 07:22:33: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:22:33: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:22:33: # Command line: callpeak -t SRX1872729.bam -f BAM -g 12100000 -n SRX1872729.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872729.10 # format = BAM # ChIP-seq file = ['SRX1872729.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 07:22:33: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:22:33: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:22:33: # Command line: callpeak -t SRX1872729.bam -f BAM -g 12100000 -n SRX1872729.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872729.05 # format = BAM # ChIP-seq file = ['SRX1872729.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 07:22:33: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:22:33: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:22:40: 1000000 INFO @ Wed, 28 Jun 2017 07:22:40: 1000000 INFO @ Wed, 28 Jun 2017 07:22:40: 1000000 INFO @ Wed, 28 Jun 2017 07:22:46: 2000000 INFO @ Wed, 28 Jun 2017 07:22:48: 2000000 INFO @ Wed, 28 Jun 2017 07:22:48: 2000000 INFO @ Wed, 28 Jun 2017 07:22:53: 3000000 INFO @ Wed, 28 Jun 2017 07:22:54: 3000000 INFO @ Wed, 28 Jun 2017 07:22:56: 3000000 INFO @ Wed, 28 Jun 2017 07:23:00: 4000000 INFO @ Wed, 28 Jun 2017 07:23:01: 4000000 INFO @ Wed, 28 Jun 2017 07:23:04: 4000000 INFO @ Wed, 28 Jun 2017 07:23:07: 5000000 INFO @ Wed, 28 Jun 2017 07:23:08: 5000000 INFO @ Wed, 28 Jun 2017 07:23:12: 5000000 INFO @ Wed, 28 Jun 2017 07:23:14: 6000000 INFO @ Wed, 28 Jun 2017 07:23:15: 6000000 INFO @ Wed, 28 Jun 2017 07:23:17: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:23:17: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:23:17: #1 total tags in treatment: 2886113 INFO @ Wed, 28 Jun 2017 07:23:17: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:23:17: #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 07:23:17: #1 tags after filtering in treatment: 1811900 INFO @ Wed, 28 Jun 2017 07:23:17: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 28 Jun 2017 07:23:17: #1 finished! INFO @ Wed, 28 Jun 2017 07:23:17: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:23:17: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:23:17: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:23:17: #1 total tags in treatment: 2886113 INFO @ Wed, 28 Jun 2017 07:23:17: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:23:17: #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 07:23:17: #1 tags after filtering in treatment: 1811900 INFO @ Wed, 28 Jun 2017 07:23:17: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 28 Jun 2017 07:23:17: #1 finished! INFO @ Wed, 28 Jun 2017 07:23:17: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:23:17: #2 number of paired peaks: 875 WARNING @ Wed, 28 Jun 2017 07:23:17: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Wed, 28 Jun 2017 07:23:17: start model_add_line... INFO @ Wed, 28 Jun 2017 07:23:17: start X-correlation... INFO @ Wed, 28 Jun 2017 07:23:17: end of X-cor INFO @ Wed, 28 Jun 2017 07:23:17: #2 finished! INFO @ Wed, 28 Jun 2017 07:23:17: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:23:17: #2 alternative fragment length(s) may be 0,14,19,34,56,84,97,111,156,177,211,246,489,585 bps INFO @ Wed, 28 Jun 2017 07:23:17: #2.2 Generate R script for model : SRX1872729.10_model.r WARNING @ Wed, 28 Jun 2017 07:23:17: #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 07:23:17: #2 You may need to consider one of the other alternative d(s): 0,14,19,34,56,84,97,111,156,177,211,246,489,585 WARNING @ Wed, 28 Jun 2017 07:23:17: #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 07:23:17: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:23:18: #2 number of paired peaks: 875 WARNING @ Wed, 28 Jun 2017 07:23:18: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Wed, 28 Jun 2017 07:23:18: start model_add_line... INFO @ Wed, 28 Jun 2017 07:23:18: start X-correlation... INFO @ Wed, 28 Jun 2017 07:23:18: end of X-cor INFO @ Wed, 28 Jun 2017 07:23:18: #2 finished! INFO @ Wed, 28 Jun 2017 07:23:18: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:23:18: #2 alternative fragment length(s) may be 0,14,19,34,56,84,97,111,156,177,211,246,489,585 bps INFO @ Wed, 28 Jun 2017 07:23:18: #2.2 Generate R script for model : SRX1872729.05_model.r WARNING @ Wed, 28 Jun 2017 07:23:18: #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 07:23:18: #2 You may need to consider one of the other alternative d(s): 0,14,19,34,56,84,97,111,156,177,211,246,489,585 WARNING @ Wed, 28 Jun 2017 07:23:18: #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 07:23:18: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:23:19: 6000000 INFO @ Wed, 28 Jun 2017 07:23:22: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:23:22: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:23:22: #1 total tags in treatment: 2886113 INFO @ Wed, 28 Jun 2017 07:23:22: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:23:22: #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 07:23:22: #1 tags after filtering in treatment: 1811900 INFO @ Wed, 28 Jun 2017 07:23:22: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 28 Jun 2017 07:23:22: #1 finished! INFO @ Wed, 28 Jun 2017 07:23:22: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:23:22: #2 number of paired peaks: 875 WARNING @ Wed, 28 Jun 2017 07:23:22: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Wed, 28 Jun 2017 07:23:22: start model_add_line... INFO @ Wed, 28 Jun 2017 07:23:22: start X-correlation... INFO @ Wed, 28 Jun 2017 07:23:22: end of X-cor INFO @ Wed, 28 Jun 2017 07:23:22: #2 finished! INFO @ Wed, 28 Jun 2017 07:23:22: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:23:22: #2 alternative fragment length(s) may be 0,14,19,34,56,84,97,111,156,177,211,246,489,585 bps INFO @ Wed, 28 Jun 2017 07:23:22: #2.2 Generate R script for model : SRX1872729.20_model.r WARNING @ Wed, 28 Jun 2017 07:23:22: #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 07:23:22: #2 You may need to consider one of the other alternative d(s): 0,14,19,34,56,84,97,111,156,177,211,246,489,585 WARNING @ Wed, 28 Jun 2017 07:23:22: #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 07:23:22: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:23:22: #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 SRX1872729.05.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 `SRX1872729.05.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/nt039i/job_scripts/9162296: line 231: 2473 終了しました MACS $i /var/spool/uge/nt039i/job_scripts/9162296: line 231: 2474 終了しました MACS $i /var/spool/uge/nt039i/job_scripts/9162296: line 231: 2475 終了しました MACS $i mv: cannot stat `SRX1872729.05.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 SRX1872729.10.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 `SRX1872729.10.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 `SRX1872729.10.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 SRX1872729.20.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 `SRX1872729.20.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 `SRX1872729.20.bb': そのようなファイルやディレクトリはありません