Job ID = 10609006 sra ファイルのダウンロード中... Completed: 234810K bytes transferred in 28 seconds (67357K bits/sec), in 1 file. 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 2732762 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3063094/SRR5901524.sra Written 2732762 spots total rm: cannot remove `[DSE]RX*': 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 `[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: 00:02:44 2732762 reads; of these: 2732762 (100.00%) were paired; of these: 144931 (5.30%) aligned concordantly 0 times 2219013 (81.20%) aligned concordantly exactly 1 time 368818 (13.50%) aligned concordantly >1 times ---- 144931 pairs aligned concordantly 0 times; of these: 32531 (22.45%) aligned discordantly 1 time ---- 112400 pairs aligned 0 times concordantly or discordantly; of these: 224800 mates make up the pairs; of these: 175499 (78.07%) aligned 0 times 32782 (14.58%) aligned exactly 1 time 16519 (7.35%) aligned >1 times 96.79% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 38321 / 2617990 = 0.0146 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 @ Thu, 03 May 2018 23:06:56: # Command line: callpeak -t SRX3063094.bam -f BAM -g 12100000 -n SRX3063094.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3063094.20 # format = BAM # ChIP-seq file = ['SRX3063094.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 @ Thu, 03 May 2018 23:06:56: # Command line: callpeak -t SRX3063094.bam -f BAM -g 12100000 -n SRX3063094.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3063094.05 # format = BAM # ChIP-seq file = ['SRX3063094.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 @ Thu, 03 May 2018 23:06:56: #1 read tag files... INFO @ Thu, 03 May 2018 23:06:56: #1 read tag files... INFO @ Thu, 03 May 2018 23:06:56: # Command line: callpeak -t SRX3063094.bam -f BAM -g 12100000 -n SRX3063094.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3063094.10 # format = BAM # ChIP-seq file = ['SRX3063094.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 @ Thu, 03 May 2018 23:06:56: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:06:56: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:06:56: #1 read tag files... INFO @ Thu, 03 May 2018 23:06:56: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:07:02: 1000000 INFO @ Thu, 03 May 2018 23:07:02: 1000000 INFO @ Thu, 03 May 2018 23:07:02: 1000000 INFO @ Thu, 03 May 2018 23:07:09: 2000000 INFO @ Thu, 03 May 2018 23:07:09: 2000000 INFO @ Thu, 03 May 2018 23:07:09: 2000000 INFO @ Thu, 03 May 2018 23:07:15: 3000000 INFO @ Thu, 03 May 2018 23:07:15: 3000000 INFO @ Thu, 03 May 2018 23:07:16: 3000000 INFO @ Thu, 03 May 2018 23:07:22: 4000000 INFO @ Thu, 03 May 2018 23:07:22: 4000000 INFO @ Thu, 03 May 2018 23:07:22: 4000000 INFO @ Thu, 03 May 2018 23:07:28: 5000000 INFO @ Thu, 03 May 2018 23:07:29: 5000000 INFO @ Thu, 03 May 2018 23:07:29: 5000000 INFO @ Thu, 03 May 2018 23:07:30: #1 tag size is determined as 79 bps INFO @ Thu, 03 May 2018 23:07:30: #1 tag size = 79 INFO @ Thu, 03 May 2018 23:07:30: #1 total tags in treatment: 2549672 INFO @ Thu, 03 May 2018 23:07:30: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:07:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:07:30: #1 tags after filtering in treatment: 2261183 INFO @ Thu, 03 May 2018 23:07:30: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 03 May 2018 23:07:30: #1 finished! INFO @ Thu, 03 May 2018 23:07:30: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:07:30: #2 number of paired peaks: 37 WARNING @ Thu, 03 May 2018 23:07:30: Too few paired peaks (37) 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 @ Thu, 03 May 2018 23:07:30: Process for pairing-model is terminated! cat: SRX3063094.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3063094.20_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 `SRX3063094.20_*.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 `SRX3063094.20_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 INFO @ Thu, 03 May 2018 23:07:30: #1 tag size is determined as 79 bps INFO @ Thu, 03 May 2018 23:07:30: #1 tag size = 79 INFO @ Thu, 03 May 2018 23:07:30: #1 total tags in treatment: 2549672 INFO @ Thu, 03 May 2018 23:07:30: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:07:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:07:30: #1 tag size is determined as 79 bps INFO @ Thu, 03 May 2018 23:07:30: #1 tag size = 79 INFO @ Thu, 03 May 2018 23:07:30: #1 total tags in treatment: 2549672 INFO @ Thu, 03 May 2018 23:07:30: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:07:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:07:30: #1 tags after filtering in treatment: 2261183 INFO @ Thu, 03 May 2018 23:07:30: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 03 May 2018 23:07:30: #1 finished! INFO @ Thu, 03 May 2018 23:07:30: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:07:30: #1 tags after filtering in treatment: 2261183 INFO @ Thu, 03 May 2018 23:07:30: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 03 May 2018 23:07:30: #1 finished! INFO @ Thu, 03 May 2018 23:07:30: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:07:30: #2 number of paired peaks: 37 WARNING @ Thu, 03 May 2018 23:07:30: Too few paired peaks (37) 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 @ Thu, 03 May 2018 23:07:30: Process for pairing-model is terminated! cat: SRX3063094.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3063094.05_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 `SRX3063094.05_*.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 `SRX3063094.05_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 INFO @ Thu, 03 May 2018 23:07:30: #2 number of paired peaks: 37 WARNING @ Thu, 03 May 2018 23:07:30: Too few paired peaks (37) 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 @ Thu, 03 May 2018 23:07:30: Process for pairing-model is terminated! cat: SRX3063094.10_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 `SRX3063094.10_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 `SRX3063094.10_*.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 `SRX3063094.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。