Job ID = 11192945 sra ファイルのダウンロード中... Completed: 627498K bytes transferred in 9 seconds (545519K 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... Read 17954395 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242060/SRR6129602.sra Written 17954395 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242060/SRR6129602.sra 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: 00:05:42 17954395 reads; of these: 17954395 (100.00%) were paired; of these: 15673105 (87.29%) aligned concordantly 0 times 2028372 (11.30%) aligned concordantly exactly 1 time 252918 (1.41%) aligned concordantly >1 times ---- 15673105 pairs aligned concordantly 0 times; of these: 589046 (3.76%) aligned discordantly 1 time ---- 15084059 pairs aligned 0 times concordantly or discordantly; of these: 30168118 mates make up the pairs; of these: 25539173 (84.66%) aligned 0 times 4165270 (13.81%) aligned exactly 1 time 463675 (1.54%) aligned >1 times 28.88% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 1680867 / 2845937 = 0.5906 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 @ Sat, 15 Sep 2018 10:44:08: # Command line: callpeak -t SRX3242060.bam -f BAM -g 12100000 -n SRX3242060.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242060.10 # format = BAM # ChIP-seq file = ['SRX3242060.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 @ Sat, 15 Sep 2018 10:44:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:44:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:44:08: # Command line: callpeak -t SRX3242060.bam -f BAM -g 12100000 -n SRX3242060.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242060.05 # format = BAM # ChIP-seq file = ['SRX3242060.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 @ Sat, 15 Sep 2018 10:44:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:44:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:44:08: # Command line: callpeak -t SRX3242060.bam -f BAM -g 12100000 -n SRX3242060.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242060.20 # format = BAM # ChIP-seq file = ['SRX3242060.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 @ Sat, 15 Sep 2018 10:44:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:44:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:44:13: 1000000 INFO @ Sat, 15 Sep 2018 10:44:13: 1000000 INFO @ Sat, 15 Sep 2018 10:44:13: 1000000 INFO @ Sat, 15 Sep 2018 10:44:17: 2000000 INFO @ Sat, 15 Sep 2018 10:44:18: 2000000 INFO @ Sat, 15 Sep 2018 10:44:18: 2000000 INFO @ Sat, 15 Sep 2018 10:44:22: 3000000 INFO @ Sat, 15 Sep 2018 10:44:22: 3000000 INFO @ Sat, 15 Sep 2018 10:44:22: 3000000 INFO @ Sat, 15 Sep 2018 10:44:26: 4000000 INFO @ Sat, 15 Sep 2018 10:44:27: 4000000 INFO @ Sat, 15 Sep 2018 10:44:27: 4000000 INFO @ Sat, 15 Sep 2018 10:44:31: 5000000 INFO @ Sat, 15 Sep 2018 10:44:31: 5000000 INFO @ Sat, 15 Sep 2018 10:44:32: 5000000 INFO @ Sat, 15 Sep 2018 10:44:36: 6000000 INFO @ Sat, 15 Sep 2018 10:44:36: 6000000 INFO @ Sat, 15 Sep 2018 10:44:36: 6000000 INFO @ Sat, 15 Sep 2018 10:44:40: 7000000 INFO @ Sat, 15 Sep 2018 10:44:40: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 10:44:40: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 10:44:40: #1 total tags in treatment: 949974 INFO @ Sat, 15 Sep 2018 10:44:40: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:44:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:44:40: #1 tags after filtering in treatment: 875673 INFO @ Sat, 15 Sep 2018 10:44:40: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:44:40: #1 finished! INFO @ Sat, 15 Sep 2018 10:44:40: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:44:40: #2 number of paired peaks: 93 WARNING @ Sat, 15 Sep 2018 10:44:40: Too few paired peaks (93) 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 @ Sat, 15 Sep 2018 10:44:40: Process for pairing-model is terminated! cat: SRX3242060.05_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 `SRX3242060.05_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 `SRX3242060.05_*.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 `SRX3242060.05_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 @ Sat, 15 Sep 2018 10:44:41: 7000000 INFO @ Sat, 15 Sep 2018 10:44:41: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 10:44:41: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 10:44:41: #1 total tags in treatment: 949974 INFO @ Sat, 15 Sep 2018 10:44:41: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:44:41: #1 tags after filtering in treatment: 875673 INFO @ Sat, 15 Sep 2018 10:44:41: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:44:41: #1 finished! INFO @ Sat, 15 Sep 2018 10:44:41: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:44:41: #2 number of paired peaks: 93 WARNING @ Sat, 15 Sep 2018 10:44:41: Too few paired peaks (93) 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 @ Sat, 15 Sep 2018 10:44:41: Process for pairing-model is terminated! cat: SRX3242060.10_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 `SRX3242060.10_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 `SRX3242060.10_*.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 `SRX3242060.10_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 @ Sat, 15 Sep 2018 10:44:41: 7000000 INFO @ Sat, 15 Sep 2018 10:44:41: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 10:44:41: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 10:44:41: #1 total tags in treatment: 949974 INFO @ Sat, 15 Sep 2018 10:44:41: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:44:41: #1 tags after filtering in treatment: 875673 INFO @ Sat, 15 Sep 2018 10:44:41: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:44:41: #1 finished! INFO @ Sat, 15 Sep 2018 10:44:41: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:44:41: #2 number of paired peaks: 93 WARNING @ Sat, 15 Sep 2018 10:44:41: Too few paired peaks (93) 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 @ Sat, 15 Sep 2018 10:44:41: Process for pairing-model is terminated! cat: SRX3242060.20_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 `SRX3242060.20_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 `SRX3242060.20_*.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 `SRX3242060.20_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。