Job ID = 11634704 sra ファイルのダウンロード中... Completed: 592657K bytes transferred in 10 seconds (456490K 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 32369583 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957440/SRR8136454.sra Written 32369583 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957440/SRR8136454.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: 00:05:23 32369583 reads; of these: 32369583 (100.00%) were unpaired; of these: 2093897 (6.47%) aligned 0 times 27437788 (84.76%) aligned exactly 1 time 2837898 (8.77%) aligned >1 times 93.53% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 19252772 / 30275686 = 0.6359 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 10:40:03: # Command line: callpeak -t SRX4957440.bam -f BAM -g 12100000 -n SRX4957440.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4957440.05 # format = BAM # ChIP-seq file = ['SRX4957440.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 10:40:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:03: # Command line: callpeak -t SRX4957440.bam -f BAM -g 12100000 -n SRX4957440.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4957440.10 # format = BAM # ChIP-seq file = ['SRX4957440.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 10:40:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:03: # Command line: callpeak -t SRX4957440.bam -f BAM -g 12100000 -n SRX4957440.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4957440.20 # format = BAM # ChIP-seq file = ['SRX4957440.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 10:40:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:40:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:40:10: 1000000 INFO @ Fri, 15 Feb 2019 10:40:10: 1000000 INFO @ Fri, 15 Feb 2019 10:40:10: 1000000 INFO @ Fri, 15 Feb 2019 10:40:16: 2000000 INFO @ Fri, 15 Feb 2019 10:40:17: 2000000 INFO @ Fri, 15 Feb 2019 10:40:17: 2000000 INFO @ Fri, 15 Feb 2019 10:40:23: 3000000 INFO @ Fri, 15 Feb 2019 10:40:23: 3000000 INFO @ Fri, 15 Feb 2019 10:40:23: 3000000 INFO @ Fri, 15 Feb 2019 10:40:30: 4000000 INFO @ Fri, 15 Feb 2019 10:40:30: 4000000 INFO @ Fri, 15 Feb 2019 10:40:30: 4000000 INFO @ Fri, 15 Feb 2019 10:40:36: 5000000 INFO @ Fri, 15 Feb 2019 10:40:37: 5000000 INFO @ Fri, 15 Feb 2019 10:40:37: 5000000 INFO @ Fri, 15 Feb 2019 10:40:43: 6000000 INFO @ Fri, 15 Feb 2019 10:40:43: 6000000 INFO @ Fri, 15 Feb 2019 10:40:44: 6000000 INFO @ Fri, 15 Feb 2019 10:40:49: 7000000 INFO @ Fri, 15 Feb 2019 10:40:50: 7000000 INFO @ Fri, 15 Feb 2019 10:40:50: 7000000 INFO @ Fri, 15 Feb 2019 10:40:56: 8000000 INFO @ Fri, 15 Feb 2019 10:40:57: 8000000 INFO @ Fri, 15 Feb 2019 10:40:57: 8000000 INFO @ Fri, 15 Feb 2019 10:41:03: 9000000 INFO @ Fri, 15 Feb 2019 10:41:04: 9000000 INFO @ Fri, 15 Feb 2019 10:41:04: 9000000 INFO @ Fri, 15 Feb 2019 10:41:09: 10000000 INFO @ Fri, 15 Feb 2019 10:41:10: 10000000 INFO @ Fri, 15 Feb 2019 10:41:11: 10000000 INFO @ Fri, 15 Feb 2019 10:41:15: 11000000 INFO @ Fri, 15 Feb 2019 10:41:16: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:41:16: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:41:16: #1 total tags in treatment: 11022914 INFO @ Fri, 15 Feb 2019 10:41:16: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:41:16: #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 10:41:16: #1 tags after filtering in treatment: 11022914 INFO @ Fri, 15 Feb 2019 10:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:41:16: #1 finished! INFO @ Fri, 15 Feb 2019 10:41:16: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:41:16: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:41:16: Too few paired peaks (0) 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 10:41:16: Process for pairing-model is terminated! cat: SRX4957440.10_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) rm: cannot remove `SRX4957440.10_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 `SRX4957440.10_*.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 `SRX4957440.10_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 @ Fri, 15 Feb 2019 10:41:17: 11000000 INFO @ Fri, 15 Feb 2019 10:41:17: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:41:17: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:41:17: #1 total tags in treatment: 11022914 INFO @ Fri, 15 Feb 2019 10:41:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:41:17: #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 10:41:17: 11000000 INFO @ Fri, 15 Feb 2019 10:41:17: #1 tags after filtering in treatment: 11022914 INFO @ Fri, 15 Feb 2019 10:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:41:17: #1 finished! INFO @ Fri, 15 Feb 2019 10:41:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:41:17: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:41:17: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:41:17: #1 total tags in treatment: 11022914 INFO @ Fri, 15 Feb 2019 10:41:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:41:17: #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 10:41:18: #1 tags after filtering in treatment: 11022914 INFO @ Fri, 15 Feb 2019 10:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:41:18: #1 finished! INFO @ Fri, 15 Feb 2019 10:41:18: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:41:18: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:41:18: Too few paired peaks (0) 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 10:41:18: Process for pairing-model is terminated! cat: SRX4957440.20_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4957440.20_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 `SRX4957440.20_*.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 `SRX4957440.20_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 10:41:18: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:41:18: Too few paired peaks (0) 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 10:41:18: Process for pairing-model is terminated! cat: SRX4957440.05_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 `SRX4957440.05_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 `SRX4957440.05_*.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 `SRX4957440.05_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。