Job ID = 9161942 sra ファイルのダウンロード中... Completed: 249352K bytes transferred in 5 seconds (407062K 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 3758571 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1419793/SRR2927542.sra Written 3758571 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: 00:04:15 3758571 reads; of these: 3758571 (100.00%) were paired; of these: 201740 (5.37%) aligned concordantly 0 times 3152047 (83.86%) aligned concordantly exactly 1 time 404784 (10.77%) aligned concordantly >1 times ---- 201740 pairs aligned concordantly 0 times; of these: 59905 (29.69%) aligned discordantly 1 time ---- 141835 pairs aligned 0 times concordantly or discordantly; of these: 283670 mates make up the pairs; of these: 239921 (84.58%) aligned 0 times 21838 (7.70%) aligned exactly 1 time 21911 (7.72%) aligned >1 times 96.81% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 97365 / 3609452 = 0.0270 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 05:08:15: # Command line: callpeak -t SRX1419793.bam -f BAM -g 12100000 -n SRX1419793.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1419793.05 # format = BAM # ChIP-seq file = ['SRX1419793.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 05:08:15: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:08:15: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:08:15: # Command line: callpeak -t SRX1419793.bam -f BAM -g 12100000 -n SRX1419793.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1419793.20 # format = BAM # ChIP-seq file = ['SRX1419793.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 05:08:15: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:08:15: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:08:15: # Command line: callpeak -t SRX1419793.bam -f BAM -g 12100000 -n SRX1419793.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1419793.10 # format = BAM # ChIP-seq file = ['SRX1419793.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 05:08:15: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:08:15: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:08:25: 1000000 INFO @ Wed, 28 Jun 2017 05:08:26: 1000000 INFO @ Wed, 28 Jun 2017 05:08:26: 1000000 INFO @ Wed, 28 Jun 2017 05:08:35: 2000000 INFO @ Wed, 28 Jun 2017 05:08:37: 2000000 INFO @ Wed, 28 Jun 2017 05:08:37: 2000000 INFO @ Wed, 28 Jun 2017 05:08:46: 3000000 INFO @ Wed, 28 Jun 2017 05:08:48: 3000000 INFO @ Wed, 28 Jun 2017 05:08:48: 3000000 INFO @ Wed, 28 Jun 2017 05:08:56: 4000000 INFO @ Wed, 28 Jun 2017 05:09:00: 4000000 INFO @ Wed, 28 Jun 2017 05:09:00: 4000000 INFO @ Wed, 28 Jun 2017 05:09:06: 5000000 INFO @ Wed, 28 Jun 2017 05:09:11: 5000000 INFO @ Wed, 28 Jun 2017 05:09:11: 5000000 INFO @ Wed, 28 Jun 2017 05:09:16: 6000000 INFO @ Wed, 28 Jun 2017 05:09:22: 6000000 INFO @ Wed, 28 Jun 2017 05:09:22: 6000000 INFO @ Wed, 28 Jun 2017 05:09:27: 7000000 INFO @ Wed, 28 Jun 2017 05:09:27: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:09:27: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:09:27: #1 total tags in treatment: 3460143 INFO @ Wed, 28 Jun 2017 05:09:27: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:27: #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 05:09:27: #1 tags after filtering in treatment: 3052289 INFO @ Wed, 28 Jun 2017 05:09:27: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:09:27: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:27: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 05:09:27: Too few paired peaks (29) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 28 Jun 2017 05:09:27: Process for pairing-model is terminated! cat: SRX1419793.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1419793.10_model.r': 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 `SRX1419793.10_*.xls': 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 `SRX1419793.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:09:34: 7000000 INFO @ Wed, 28 Jun 2017 05:09:34: 7000000 INFO @ Wed, 28 Jun 2017 05:09:34: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:09:34: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:09:34: #1 total tags in treatment: 3460143 INFO @ Wed, 28 Jun 2017 05:09:34: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:34: #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 05:09:34: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:09:34: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:09:34: #1 total tags in treatment: 3460143 INFO @ Wed, 28 Jun 2017 05:09:34: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:34: #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 05:09:34: #1 tags after filtering in treatment: 3052289 INFO @ Wed, 28 Jun 2017 05:09:34: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:09:34: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:34: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:34: #1 tags after filtering in treatment: 3052289 INFO @ Wed, 28 Jun 2017 05:09:34: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:09:34: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:34: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:35: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 05:09:35: Too few paired peaks (29) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 28 Jun 2017 05:09:35: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 05:09:35: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 05:09:35: Too few paired peaks (29) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 28 Jun 2017 05:09:35: Process for pairing-model is terminated! cat: SRX1419793.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1419793.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1419793.05_model.r': 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 `SRX1419793.05_*.xls': 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 `SRX1419793.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1419793.20_model.r': 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 `SRX1419793.20_*.xls': 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 `SRX1419793.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。