Job ID = 11634723 sra ファイルのダウンロード中... Completed: 628874K bytes transferred in 12 seconds (410606K 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: SINGLE fastq に変換中... Read 35500507 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957458/SRR8136472.sra Written 35500507 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957458/SRR8136472.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: 00:06:18 35500507 reads; of these: 35500507 (100.00%) were unpaired; of these: 2496367 (7.03%) aligned 0 times 26448806 (74.50%) aligned exactly 1 time 6555334 (18.47%) aligned >1 times 92.97% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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 16 files... [bam_rmdupse_core] 29352402 / 33004140 = 0.8894 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 @ Fri, 15 Feb 2019 10:42:37: # Command line: callpeak -t SRX4957458.bam -f BAM -g 12100000 -n SRX4957458.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4957458.10 # format = BAM # ChIP-seq file = ['SRX4957458.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 @ Fri, 15 Feb 2019 10:42:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:42:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:42:37: # Command line: callpeak -t SRX4957458.bam -f BAM -g 12100000 -n SRX4957458.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4957458.05 # format = BAM # ChIP-seq file = ['SRX4957458.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 @ Fri, 15 Feb 2019 10:42:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:42:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:42:37: # Command line: callpeak -t SRX4957458.bam -f BAM -g 12100000 -n SRX4957458.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4957458.20 # format = BAM # ChIP-seq file = ['SRX4957458.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 @ Fri, 15 Feb 2019 10:42:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:42:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:42:43: 1000000 INFO @ Fri, 15 Feb 2019 10:42:44: 1000000 INFO @ Fri, 15 Feb 2019 10:42:44: 1000000 INFO @ Fri, 15 Feb 2019 10:42:49: 2000000 INFO @ Fri, 15 Feb 2019 10:42:51: 2000000 INFO @ Fri, 15 Feb 2019 10:42:51: 2000000 INFO @ Fri, 15 Feb 2019 10:42:55: 3000000 INFO @ Fri, 15 Feb 2019 10:42:57: 3000000 INFO @ Fri, 15 Feb 2019 10:42:57: 3000000 INFO @ Fri, 15 Feb 2019 10:42:59: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:42:59: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:42:59: #1 total tags in treatment: 3651738 INFO @ Fri, 15 Feb 2019 10:42:59: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:42:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:42:59: #1 tags after filtering in treatment: 3651738 INFO @ Fri, 15 Feb 2019 10:42:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:42:59: #1 finished! INFO @ Fri, 15 Feb 2019 10:42:59: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:42:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:42:59: #2 number of paired peaks: 38 WARNING @ Fri, 15 Feb 2019 10:42:59: Too few paired peaks (38) 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 @ Fri, 15 Feb 2019 10:42:59: Process for pairing-model is terminated! cat: SRX4957458.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4957458.20_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 `SRX4957458.20_*.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 `SRX4957458.20_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 INFO @ Fri, 15 Feb 2019 10:43:01: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:43:01: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:43:01: #1 total tags in treatment: 3651738 INFO @ Fri, 15 Feb 2019 10:43:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:43:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:43:01: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:43:01: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:43:01: #1 total tags in treatment: 3651738 INFO @ Fri, 15 Feb 2019 10:43:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:43:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:43:01: #1 tags after filtering in treatment: 3651738 INFO @ Fri, 15 Feb 2019 10:43:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:43:01: #1 finished! INFO @ Fri, 15 Feb 2019 10:43:01: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:43:01: #1 tags after filtering in treatment: 3651738 INFO @ Fri, 15 Feb 2019 10:43:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:43:01: #1 finished! INFO @ Fri, 15 Feb 2019 10:43:01: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:43:01: #2 number of paired peaks: 38 WARNING @ Fri, 15 Feb 2019 10:43:01: Too few paired peaks (38) 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 @ Fri, 15 Feb 2019 10:43:01: Process for pairing-model is terminated! cat: SRX4957458.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 15 Feb 2019 10:43:01: #2 number of paired peaks: 38 WARNING @ Fri, 15 Feb 2019 10:43:01: Too few paired peaks (38) 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 @ Fri, 15 Feb 2019 10:43:01: Process for pairing-model is terminated! rm: cannot remove `SRX4957458.10_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 `SRX4957458.10_*.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 `SRX4957458.10_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 cat: SRX4957458.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4957458.05_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 `SRX4957458.05_*.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 `SRX4957458.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。