Job ID = 11245116 sra ファイルのダウンロード中... Completed: 466338K bytes transferred in 7 seconds (490301K 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 25909140 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4668668/SRR7817166.sra Written 25909140 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4668668/SRR7817166.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: 00:04:47 25909140 reads; of these: 25909140 (100.00%) were unpaired; of these: 6400236 (24.70%) aligned 0 times 16267532 (62.79%) aligned exactly 1 time 3241372 (12.51%) aligned >1 times 75.30% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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_rmdupse_core] 15325555 / 19508904 = 0.7856 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 @ Tue, 09 Oct 2018 23:37:02: # Command line: callpeak -t SRX4668668.bam -f BAM -g 12100000 -n SRX4668668.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4668668.20 # format = BAM # ChIP-seq file = ['SRX4668668.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 @ Tue, 09 Oct 2018 23:37:02: # Command line: callpeak -t SRX4668668.bam -f BAM -g 12100000 -n SRX4668668.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4668668.10 # format = BAM # ChIP-seq file = ['SRX4668668.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 @ Tue, 09 Oct 2018 23:37:02: # Command line: callpeak -t SRX4668668.bam -f BAM -g 12100000 -n SRX4668668.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4668668.05 # format = BAM # ChIP-seq file = ['SRX4668668.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 @ Tue, 09 Oct 2018 23:37:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:08: 1000000 INFO @ Tue, 09 Oct 2018 23:37:08: 1000000 INFO @ Tue, 09 Oct 2018 23:37:09: 1000000 INFO @ Tue, 09 Oct 2018 23:37:15: 2000000 INFO @ Tue, 09 Oct 2018 23:37:15: 2000000 INFO @ Tue, 09 Oct 2018 23:37:16: 2000000 INFO @ Tue, 09 Oct 2018 23:37:22: 3000000 INFO @ Tue, 09 Oct 2018 23:37:22: 3000000 INFO @ Tue, 09 Oct 2018 23:37:23: 3000000 INFO @ Tue, 09 Oct 2018 23:37:29: 4000000 INFO @ Tue, 09 Oct 2018 23:37:29: 4000000 INFO @ Tue, 09 Oct 2018 23:37:30: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:37:30: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:37:30: #1 total tags in treatment: 4183349 INFO @ Tue, 09 Oct 2018 23:37:30: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:37:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:37:30: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:37:30: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:37:30: #1 total tags in treatment: 4183349 INFO @ Tue, 09 Oct 2018 23:37:30: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:37:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:37:30: #1 tags after filtering in treatment: 4183349 INFO @ Tue, 09 Oct 2018 23:37:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 23:37:30: #1 finished! INFO @ Tue, 09 Oct 2018 23:37:30: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:37:30: #1 tags after filtering in treatment: 4183349 INFO @ Tue, 09 Oct 2018 23:37:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 23:37:30: #1 finished! INFO @ Tue, 09 Oct 2018 23:37:30: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:37:30: 4000000 INFO @ Tue, 09 Oct 2018 23:37:31: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 23:37:31: Too few paired peaks (28) 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 @ Tue, 09 Oct 2018 23:37:31: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:37:31: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 23:37:31: Too few paired peaks (28) 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 @ Tue, 09 Oct 2018 23:37:31: Process for pairing-model is terminated! cat: SRX4668668.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4668668.20_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) pass1 - making usageList (0 chroms): 1 millis rm: cannot remove `SRX4668668.05_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 `SRX4668668.05_*.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 `SRX4668668.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling rm: cannot remove `SRX4668668.20_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 `SRX4668668.20_*.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 `SRX4668668.20_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 @ Tue, 09 Oct 2018 23:37:31: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:37:31: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:37:31: #1 total tags in treatment: 4183349 INFO @ Tue, 09 Oct 2018 23:37:31: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:37:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:37:32: #1 tags after filtering in treatment: 4183349 INFO @ Tue, 09 Oct 2018 23:37:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 23:37:32: #1 finished! INFO @ Tue, 09 Oct 2018 23:37:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:37:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:37:32: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 23:37:32: Too few paired peaks (28) 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 @ Tue, 09 Oct 2018 23:37:32: Process for pairing-model is terminated! cat: SRX4668668.10_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 `SRX4668668.10_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 `SRX4668668.10_*.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 `SRX4668668.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。