Job ID = 9162503 sra ファイルのダウンロード中... Completed: 166330K bytes transferred in 4 seconds (289332K 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 2718742 spots for /home/okishinya/chipatlas/results/sacCer3/SRX360895/SRR1003617.sra Written 2718742 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: 00:01:45 2718742 reads; of these: 2718742 (100.00%) were paired; of these: 1237447 (45.52%) aligned concordantly 0 times 1120379 (41.21%) aligned concordantly exactly 1 time 360916 (13.28%) aligned concordantly >1 times ---- 1237447 pairs aligned concordantly 0 times; of these: 11347 (0.92%) aligned discordantly 1 time ---- 1226100 pairs aligned 0 times concordantly or discordantly; of these: 2452200 mates make up the pairs; of these: 1967348 (80.23%) aligned 0 times 401564 (16.38%) aligned exactly 1 time 83288 (3.40%) aligned >1 times 63.82% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 1220299 / 1483178 = 0.8228 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 08:01:14: # Command line: callpeak -t SRX360895.bam -f BAM -g 12100000 -n SRX360895.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX360895.20 # format = BAM # ChIP-seq file = ['SRX360895.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 08:01:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:01:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:01:14: # Command line: callpeak -t SRX360895.bam -f BAM -g 12100000 -n SRX360895.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX360895.10 # format = BAM # ChIP-seq file = ['SRX360895.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 08:01:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:01:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:01:14: # Command line: callpeak -t SRX360895.bam -f BAM -g 12100000 -n SRX360895.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX360895.05 # format = BAM # ChIP-seq file = ['SRX360895.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 08:01:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:01:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:01:19: 1000000 INFO @ Wed, 28 Jun 2017 08:01:19: 1000000 INFO @ Wed, 28 Jun 2017 08:01:19: 1000000 INFO @ Wed, 28 Jun 2017 08:01:19: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:01:19: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:01:19: #1 total tags in treatment: 261551 INFO @ Wed, 28 Jun 2017 08:01:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:01:19: #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 08:01:19: #1 tags after filtering in treatment: 222181 INFO @ Wed, 28 Jun 2017 08:01:19: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 28 Jun 2017 08:01:19: #1 finished! INFO @ Wed, 28 Jun 2017 08:01:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:01:19: #2 number of paired peaks: 78 WARNING @ Wed, 28 Jun 2017 08:01:19: Too few paired peaks (78) 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 08:01:19: Process for pairing-model is terminated! cat: SRX360895.05_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 `SRX360895.05_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 `SRX360895.05_*.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 `SRX360895.05_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 @ Wed, 28 Jun 2017 08:01:19: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:01:19: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:01:19: #1 total tags in treatment: 261551 INFO @ Wed, 28 Jun 2017 08:01:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:01:19: #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 08:01:19: #1 tags after filtering in treatment: 222181 INFO @ Wed, 28 Jun 2017 08:01:19: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 28 Jun 2017 08:01:19: #1 finished! INFO @ Wed, 28 Jun 2017 08:01:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:01:19: #2 number of paired peaks: 78 WARNING @ Wed, 28 Jun 2017 08:01:19: Too few paired peaks (78) 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 08:01:19: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 08:01:19: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:01:19: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:01:19: #1 total tags in treatment: 261551 INFO @ Wed, 28 Jun 2017 08:01:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:01:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cat: SRX360895.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Wed, 28 Jun 2017 08:01:19: #1 tags after filtering in treatment: 222181 INFO @ Wed, 28 Jun 2017 08:01:19: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 28 Jun 2017 08:01:19: #1 finished! INFO @ Wed, 28 Jun 2017 08:01:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:01:19: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX360895.10_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 `SRX360895.10_*.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 `SRX360895.10_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 08:01:20: #2 number of paired peaks: 78 WARNING @ Wed, 28 Jun 2017 08:01:20: Too few paired peaks (78) 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 08:01:20: Process for pairing-model is terminated! cat: SRX360895.20_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 `SRX360895.20_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 `SRX360895.20_*.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 `SRX360895.20_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。