Job ID = 11192833 sra ファイルのダウンロード中... Completed: 641268K bytes transferred in 16 seconds (316122K 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 16796691 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1972001/SRR3946116.sra Written 16796691 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1972001/SRR3946116.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:08 16796691 reads; of these: 16796691 (100.00%) were paired; of these: 7791226 (46.39%) aligned concordantly 0 times 7807363 (46.48%) aligned concordantly exactly 1 time 1198102 (7.13%) aligned concordantly >1 times ---- 7791226 pairs aligned concordantly 0 times; of these: 109365 (1.40%) aligned discordantly 1 time ---- 7681861 pairs aligned 0 times concordantly or discordantly; of these: 15363722 mates make up the pairs; of these: 9356904 (60.90%) aligned 0 times 4816536 (31.35%) aligned exactly 1 time 1190282 (7.75%) aligned >1 times 72.15% overall alignment rate Time searching: 00:11:09 Overall time: 00:11:09 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_sort_core] merging from 8 files... [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] 5429967 / 9077645 = 0.5982 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 10:16:14: # Command line: callpeak -t SRX1972001.bam -f BAM -g 12100000 -n SRX1972001.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1972001.05 # format = BAM # ChIP-seq file = ['SRX1972001.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 10:16:14: # Command line: callpeak -t SRX1972001.bam -f BAM -g 12100000 -n SRX1972001.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1972001.10 # format = BAM # ChIP-seq file = ['SRX1972001.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 10:16:14: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:16:14: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:16:14: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:16:14: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:16:14: # Command line: callpeak -t SRX1972001.bam -f BAM -g 12100000 -n SRX1972001.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1972001.20 # format = BAM # ChIP-seq file = ['SRX1972001.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 10:16:14: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:16:14: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:16:20: 1000000 INFO @ Sat, 15 Sep 2018 10:16:20: 1000000 INFO @ Sat, 15 Sep 2018 10:16:20: 1000000 INFO @ Sat, 15 Sep 2018 10:16:26: 2000000 INFO @ Sat, 15 Sep 2018 10:16:26: 2000000 INFO @ Sat, 15 Sep 2018 10:16:26: 2000000 INFO @ Sat, 15 Sep 2018 10:16:32: 3000000 INFO @ Sat, 15 Sep 2018 10:16:32: 3000000 INFO @ Sat, 15 Sep 2018 10:16:32: 3000000 INFO @ Sat, 15 Sep 2018 10:16:38: 4000000 INFO @ Sat, 15 Sep 2018 10:16:38: 4000000 INFO @ Sat, 15 Sep 2018 10:16:38: 4000000 INFO @ Sat, 15 Sep 2018 10:16:44: 5000000 INFO @ Sat, 15 Sep 2018 10:16:44: 5000000 INFO @ Sat, 15 Sep 2018 10:16:44: 5000000 INFO @ Sat, 15 Sep 2018 10:16:50: 6000000 INFO @ Sat, 15 Sep 2018 10:16:50: 6000000 INFO @ Sat, 15 Sep 2018 10:16:50: 6000000 INFO @ Sat, 15 Sep 2018 10:16:56: 7000000 INFO @ Sat, 15 Sep 2018 10:16:56: 7000000 INFO @ Sat, 15 Sep 2018 10:16:56: 7000000 INFO @ Sat, 15 Sep 2018 10:17:02: 8000000 INFO @ Sat, 15 Sep 2018 10:17:02: 8000000 INFO @ Sat, 15 Sep 2018 10:17:02: 8000000 INFO @ Sat, 15 Sep 2018 10:17:08: 9000000 INFO @ Sat, 15 Sep 2018 10:17:08: 9000000 INFO @ Sat, 15 Sep 2018 10:17:08: 9000000 INFO @ Sat, 15 Sep 2018 10:17:14: 10000000 INFO @ Sat, 15 Sep 2018 10:17:14: 10000000 INFO @ Sat, 15 Sep 2018 10:17:14: 10000000 INFO @ Sat, 15 Sep 2018 10:17:20: 11000000 INFO @ Sat, 15 Sep 2018 10:17:21: 11000000 INFO @ Sat, 15 Sep 2018 10:17:21: 11000000 INFO @ Sat, 15 Sep 2018 10:17:27: 12000000 INFO @ Sat, 15 Sep 2018 10:17:27: 12000000 INFO @ Sat, 15 Sep 2018 10:17:27: 12000000 INFO @ Sat, 15 Sep 2018 10:17:32: 13000000 INFO @ Sat, 15 Sep 2018 10:17:32: 13000000 INFO @ Sat, 15 Sep 2018 10:17:33: 13000000 INFO @ Sat, 15 Sep 2018 10:17:35: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:17:35: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:17:35: #1 total tags in treatment: 3612498 INFO @ Sat, 15 Sep 2018 10:17:35: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:17:35: #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 10:17:35: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:17:35: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:17:35: #1 total tags in treatment: 3612498 INFO @ Sat, 15 Sep 2018 10:17:35: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:17:35: #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 10:17:35: #1 tags after filtering in treatment: 2482368 INFO @ Sat, 15 Sep 2018 10:17:35: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 10:17:35: #1 finished! INFO @ Sat, 15 Sep 2018 10:17:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:17:35: #1 tags after filtering in treatment: 2482368 INFO @ Sat, 15 Sep 2018 10:17:35: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 10:17:35: #1 finished! INFO @ Sat, 15 Sep 2018 10:17:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:17:35: #2 number of paired peaks: 32 WARNING @ Sat, 15 Sep 2018 10:17:35: Too few paired peaks (32) 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 10:17:35: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 10:17:35: #2 number of paired peaks: 32 WARNING @ Sat, 15 Sep 2018 10:17:35: Too few paired peaks (32) 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 10:17:35: Process for pairing-model is terminated! cat: cat: SRX1972001.10_peaks.narrowPeakSRX1972001.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません: 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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1972001.10_model.r'rm: cannot remove `SRX1972001.05_model.r': そのようなファイルやディレクトリはありません : 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 `SRX1972001.10_*.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 `SRX1972001.05_*.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 `SRX1972001.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1972001.05_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 CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:17:36: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:17:36: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:17:36: #1 total tags in treatment: 3612498 INFO @ Sat, 15 Sep 2018 10:17:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:17:36: #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 10:17:36: #1 tags after filtering in treatment: 2482368 INFO @ Sat, 15 Sep 2018 10:17:36: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 10:17:36: #1 finished! INFO @ Sat, 15 Sep 2018 10:17:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:17:36: #2 number of paired peaks: 32 WARNING @ Sat, 15 Sep 2018 10:17:36: Too few paired peaks (32) 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 10:17:36: Process for pairing-model is terminated! cat: SRX1972001.20_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 `SRX1972001.20_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 `SRX1972001.20_*.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 `SRX1972001.20_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。