Job ID = 11192678 sra ファイルのダウンロード中... Completed: 131048K bytes transferred in 4 seconds (222131K 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 4343211 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924799/SRR3824830.sra Written 4343211 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924799/SRR3824830.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: 00:02:31 4343211 reads; of these: 4343211 (100.00%) were paired; of these: 1545743 (35.59%) aligned concordantly 0 times 2614706 (60.20%) aligned concordantly exactly 1 time 182762 (4.21%) aligned concordantly >1 times ---- 1545743 pairs aligned concordantly 0 times; of these: 177443 (11.48%) aligned discordantly 1 time ---- 1368300 pairs aligned 0 times concordantly or discordantly; of these: 2736600 mates make up the pairs; of these: 1579191 (57.71%) aligned 0 times 1054197 (38.52%) aligned exactly 1 time 103212 (3.77%) aligned >1 times 81.82% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 1854796 / 2842452 = 0.6525 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 09:48:57: # Command line: callpeak -t SRX1924799.bam -f BAM -g 12100000 -n SRX1924799.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924799.10 # format = BAM # ChIP-seq file = ['SRX1924799.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 09:48:57: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:48:57: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:48:57: # Command line: callpeak -t SRX1924799.bam -f BAM -g 12100000 -n SRX1924799.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924799.05 # format = BAM # ChIP-seq file = ['SRX1924799.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 09:48:57: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:48:57: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:48:57: # Command line: callpeak -t SRX1924799.bam -f BAM -g 12100000 -n SRX1924799.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924799.20 # format = BAM # ChIP-seq file = ['SRX1924799.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 09:48:57: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:48:57: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:49:02: 1000000 INFO @ Sat, 15 Sep 2018 09:49:02: 1000000 INFO @ Sat, 15 Sep 2018 09:49:02: 1000000 INFO @ Sat, 15 Sep 2018 09:49:07: 2000000 INFO @ Sat, 15 Sep 2018 09:49:07: 2000000 INFO @ Sat, 15 Sep 2018 09:49:07: 2000000 INFO @ Sat, 15 Sep 2018 09:49:11: 3000000 INFO @ Sat, 15 Sep 2018 09:49:12: 3000000 INFO @ Sat, 15 Sep 2018 09:49:12: 3000000 INFO @ Sat, 15 Sep 2018 09:49:13: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 09:49:13: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 09:49:13: #1 total tags in treatment: 967409 INFO @ Sat, 15 Sep 2018 09:49:13: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:49:13: #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 09:49:13: #1 tags after filtering in treatment: 867930 INFO @ Sat, 15 Sep 2018 09:49:13: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 09:49:13: #1 finished! INFO @ Sat, 15 Sep 2018 09:49:13: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:49:13: #2 number of paired peaks: 14 WARNING @ Sat, 15 Sep 2018 09:49:13: Too few paired peaks (14) 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 09:49:13: Process for pairing-model is terminated! cat: SRX1924799.10_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 `SRX1924799.10_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 `SRX1924799.10_*.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 `SRX1924799.10_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 09:49:13: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 09:49:13: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 09:49:13: #1 total tags in treatment: 967409 INFO @ Sat, 15 Sep 2018 09:49:13: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:49:13: #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 09:49:14: #1 tags after filtering in treatment: 867930 INFO @ Sat, 15 Sep 2018 09:49:14: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 09:49:14: #1 finished! INFO @ Sat, 15 Sep 2018 09:49:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:49:14: #2 number of paired peaks: 14 WARNING @ Sat, 15 Sep 2018 09:49:14: Too few paired peaks (14) 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 09:49:14: Process for pairing-model is terminated! cat: SRX1924799.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Sat, 15 Sep 2018 09:49:14: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 09:49:14: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 09:49:14: #1 total tags in treatment: 967409 INFO @ Sat, 15 Sep 2018 09:49:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:49:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1924799.05_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 `SRX1924799.05_*.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 `SRX1924799.05_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 09:49:14: #1 tags after filtering in treatment: 867930 INFO @ Sat, 15 Sep 2018 09:49:14: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 09:49:14: #1 finished! INFO @ Sat, 15 Sep 2018 09:49:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:49:14: #2 number of paired peaks: 14 WARNING @ Sat, 15 Sep 2018 09:49:14: Too few paired peaks (14) 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 09:49:14: Process for pairing-model is terminated! cat: SRX1924799.20_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 `SRX1924799.20_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 `SRX1924799.20_*.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 `SRX1924799.20_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。