Job ID = 10609018 sra ファイルのダウンロード中... Completed: 402263K bytes transferred in 9 seconds (344203K 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 4129283 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3063105/SRR5901535.sra Written 4129283 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: 00:05:48 4129283 reads; of these: 4129283 (100.00%) were paired; of these: 370434 (8.97%) aligned concordantly 0 times 3227327 (78.16%) aligned concordantly exactly 1 time 531522 (12.87%) aligned concordantly >1 times ---- 370434 pairs aligned concordantly 0 times; of these: 141818 (38.28%) aligned discordantly 1 time ---- 228616 pairs aligned 0 times concordantly or discordantly; of these: 457232 mates make up the pairs; of these: 295874 (64.71%) aligned 0 times 96711 (21.15%) aligned exactly 1 time 64647 (14.14%) aligned >1 times 96.42% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 169558 / 3850578 = 0.0440 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 23:18:12: # Command line: callpeak -t SRX3063105.bam -f BAM -g 12100000 -n SRX3063105.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3063105.10 # format = BAM # ChIP-seq file = ['SRX3063105.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 23:18:12: #1 read tag files... INFO @ Thu, 03 May 2018 23:18:12: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:18:12: # Command line: callpeak -t SRX3063105.bam -f BAM -g 12100000 -n SRX3063105.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3063105.05 # format = BAM # ChIP-seq file = ['SRX3063105.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 23:18:12: #1 read tag files... INFO @ Thu, 03 May 2018 23:18:12: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:18:12: # Command line: callpeak -t SRX3063105.bam -f BAM -g 12100000 -n SRX3063105.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3063105.20 # format = BAM # ChIP-seq file = ['SRX3063105.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 23:18:12: #1 read tag files... INFO @ Thu, 03 May 2018 23:18:12: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:18:21: 1000000 INFO @ Thu, 03 May 2018 23:18:21: 1000000 INFO @ Thu, 03 May 2018 23:18:21: 1000000 INFO @ Thu, 03 May 2018 23:18:29: 2000000 INFO @ Thu, 03 May 2018 23:18:30: 2000000 INFO @ Thu, 03 May 2018 23:18:30: 2000000 INFO @ Thu, 03 May 2018 23:18:38: 3000000 INFO @ Thu, 03 May 2018 23:18:39: 3000000 INFO @ Thu, 03 May 2018 23:18:39: 3000000 INFO @ Thu, 03 May 2018 23:18:46: 4000000 INFO @ Thu, 03 May 2018 23:18:48: 4000000 INFO @ Thu, 03 May 2018 23:18:48: 4000000 INFO @ Thu, 03 May 2018 23:18:54: 5000000 INFO @ Thu, 03 May 2018 23:18:56: 5000000 INFO @ Thu, 03 May 2018 23:18:56: 5000000 INFO @ Thu, 03 May 2018 23:19:03: 6000000 INFO @ Thu, 03 May 2018 23:19:05: 6000000 INFO @ Thu, 03 May 2018 23:19:05: 6000000 INFO @ Thu, 03 May 2018 23:19:11: 7000000 INFO @ Thu, 03 May 2018 23:19:14: 7000000 INFO @ Thu, 03 May 2018 23:19:14: 7000000 INFO @ Thu, 03 May 2018 23:19:17: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:19:17: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:19:17: #1 total tags in treatment: 3591527 INFO @ Thu, 03 May 2018 23:19:17: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:19:17: #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 23:19:17: #1 tags after filtering in treatment: 3066223 INFO @ Thu, 03 May 2018 23:19:17: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 03 May 2018 23:19:17: #1 finished! INFO @ Thu, 03 May 2018 23:19:17: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:19:17: #2 number of paired peaks: 33 WARNING @ Thu, 03 May 2018 23:19:17: Too few paired peaks (33) 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 23:19:17: Process for pairing-model is terminated! cat: SRX3063105.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3063105.05_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 `SRX3063105.05_*.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 `SRX3063105.05_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 23:19:19: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:19:19: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:19:19: #1 total tags in treatment: 3591527 INFO @ Thu, 03 May 2018 23:19:19: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:19:19: #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 23:19:19: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:19:19: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:19:19: #1 total tags in treatment: 3591527 INFO @ Thu, 03 May 2018 23:19:19: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:19:19: #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 23:19:19: #1 tags after filtering in treatment: 3066223 INFO @ Thu, 03 May 2018 23:19:19: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 03 May 2018 23:19:19: #1 finished! INFO @ Thu, 03 May 2018 23:19:19: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:19:19: #1 tags after filtering in treatment: 3066223 INFO @ Thu, 03 May 2018 23:19:19: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 03 May 2018 23:19:19: #1 finished! INFO @ Thu, 03 May 2018 23:19:19: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:19:19: #2 number of paired peaks: 33 WARNING @ Thu, 03 May 2018 23:19:19: Too few paired peaks (33) 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 23:19:19: Process for pairing-model is terminated! INFO @ Thu, 03 May 2018 23:19:19: #2 number of paired peaks: 33 WARNING @ Thu, 03 May 2018 23:19:19: Too few paired peaks (33) 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 23:19:19: Process for pairing-model is terminated! cat: SRX3063105.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3063105.20_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 `SRX3063105.10_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 `SRX3063105.10_*.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 `SRX3063105.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3063105.20_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 `SRX3063105.20_*.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 `SRX3063105.20_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。