Job ID = 9162297 sra ファイルのダウンロード中... Completed: 703419K bytes transferred in 14 seconds (406737K 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 5798749 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872730/SRR3713203.sra Written 5798749 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: 00:07:37 5798749 reads; of these: 5798749 (100.00%) were paired; of these: 1790846 (30.88%) aligned concordantly 0 times 3393949 (58.53%) aligned concordantly exactly 1 time 613954 (10.59%) aligned concordantly >1 times ---- 1790846 pairs aligned concordantly 0 times; of these: 349730 (19.53%) aligned discordantly 1 time ---- 1441116 pairs aligned 0 times concordantly or discordantly; of these: 2882232 mates make up the pairs; of these: 2636901 (91.49%) aligned 0 times 84537 (2.93%) aligned exactly 1 time 160794 (5.58%) aligned >1 times 77.26% overall alignment rate Time searching: 00:07:37 Overall time: 00:07:37 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] 243777 / 4330926 = 0.0563 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 07:26:19: # Command line: callpeak -t SRX1872730.bam -f BAM -g 12100000 -n SRX1872730.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872730.10 # format = BAM # ChIP-seq file = ['SRX1872730.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 07:26:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:26:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:26:19: # Command line: callpeak -t SRX1872730.bam -f BAM -g 12100000 -n SRX1872730.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872730.05 # format = BAM # ChIP-seq file = ['SRX1872730.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 07:26:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:26:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:26:19: # Command line: callpeak -t SRX1872730.bam -f BAM -g 12100000 -n SRX1872730.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872730.20 # format = BAM # ChIP-seq file = ['SRX1872730.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 07:26:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:26:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:26:29: 1000000 INFO @ Wed, 28 Jun 2017 07:26:30: 1000000 INFO @ Wed, 28 Jun 2017 07:26:30: 1000000 INFO @ Wed, 28 Jun 2017 07:26:38: 2000000 INFO @ Wed, 28 Jun 2017 07:26:42: 2000000 INFO @ Wed, 28 Jun 2017 07:26:42: 2000000 INFO @ Wed, 28 Jun 2017 07:26:48: 3000000 INFO @ Wed, 28 Jun 2017 07:26:52: 3000000 INFO @ Wed, 28 Jun 2017 07:26:52: 3000000 INFO @ Wed, 28 Jun 2017 07:26:59: 4000000 INFO @ Wed, 28 Jun 2017 07:27:02: 4000000 INFO @ Wed, 28 Jun 2017 07:27:02: 4000000 INFO @ Wed, 28 Jun 2017 07:27:10: 5000000 INFO @ Wed, 28 Jun 2017 07:27:12: 5000000 INFO @ Wed, 28 Jun 2017 07:27:13: 5000000 INFO @ Wed, 28 Jun 2017 07:27:19: 6000000 INFO @ Wed, 28 Jun 2017 07:27:21: 6000000 INFO @ Wed, 28 Jun 2017 07:27:24: 6000000 INFO @ Wed, 28 Jun 2017 07:27:28: 7000000 INFO @ Wed, 28 Jun 2017 07:27:29: 7000000 INFO @ Wed, 28 Jun 2017 07:27:34: 7000000 INFO @ Wed, 28 Jun 2017 07:27:37: 8000000 INFO @ Wed, 28 Jun 2017 07:27:38: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 07:27:41: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:27:41: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:27:41: #1 total tags in treatment: 3785118 INFO @ Wed, 28 Jun 2017 07:27:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:27:41: #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 07:27:41: #1 tags after filtering in treatment: 1785965 INFO @ Wed, 28 Jun 2017 07:27:41: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 28 Jun 2017 07:27:41: #1 finished! INFO @ Wed, 28 Jun 2017 07:27:41: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:27:41: #2 number of paired peaks: 1017 INFO @ Wed, 28 Jun 2017 07:27:41: start model_add_line... INFO @ Wed, 28 Jun 2017 07:27:41: start X-correlation... INFO @ Wed, 28 Jun 2017 07:27:41: end of X-cor INFO @ Wed, 28 Jun 2017 07:27:41: #2 finished! INFO @ Wed, 28 Jun 2017 07:27:41: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:27:41: #2 alternative fragment length(s) may be 0,21,44,55,97,128,167,548 bps INFO @ Wed, 28 Jun 2017 07:27:41: #2.2 Generate R script for model : SRX1872730.10_model.r WARNING @ Wed, 28 Jun 2017 07:27:41: #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 07:27:41: #2 You may need to consider one of the other alternative d(s): 0,21,44,55,97,128,167,548 WARNING @ Wed, 28 Jun 2017 07:27:41: #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 07:27:41: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:27:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:27:42: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:27:42: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:27:42: #1 total tags in treatment: 3785118 INFO @ Wed, 28 Jun 2017 07:27:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:27:42: #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 07:27:42: #1 tags after filtering in treatment: 1785965 INFO @ Wed, 28 Jun 2017 07:27:42: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 28 Jun 2017 07:27:42: #1 finished! INFO @ Wed, 28 Jun 2017 07:27:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:27:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:27:42: #2 number of paired peaks: 1017 INFO @ Wed, 28 Jun 2017 07:27:42: start model_add_line... INFO @ Wed, 28 Jun 2017 07:27:42: start X-correlation... INFO @ Wed, 28 Jun 2017 07:27:42: end of X-cor INFO @ Wed, 28 Jun 2017 07:27:42: #2 finished! INFO @ Wed, 28 Jun 2017 07:27:42: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:27:42: #2 alternative fragment length(s) may be 0,21,44,55,97,128,167,548 bps INFO @ Wed, 28 Jun 2017 07:27:42: #2.2 Generate R script for model : SRX1872730.20_model.r WARNING @ Wed, 28 Jun 2017 07:27:42: #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 07:27:42: #2 You may need to consider one of the other alternative d(s): 0,21,44,55,97,128,167,548 WARNING @ Wed, 28 Jun 2017 07:27:42: #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 07:27:42: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:27:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 ls: cannot access SRX1872730.05.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 `SRX1872730.05.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/nt003i/job_scripts/9162297: line 231: 7369 終了しました MACS $i /var/spool/uge/nt003i/job_scripts/9162297: line 231: 7370 終了しました MACS $i /var/spool/uge/nt003i/job_scripts/9162297: line 231: 7372 終了しました MACS $i mv: cannot stat `SRX1872730.05.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 SRX1872730.10.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 `SRX1872730.10.bed': そのようなファイルやディレクトリはありません INFO @ Wed, 28 Jun 2017 07:27:44: 8000000 mv: cannot stat `SRX1872730.10.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 SRX1872730.20.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 `SRX1872730.20.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 `SRX1872730.20.bb': そのようなファイルやディレクトリはありません