Job ID = 10924626 sra ファイルのダウンロード中... Completed: 516255K bytes transferred in 9 seconds (427181K 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 15654495 spots for /home/okishinya/chipatlas/results/dm3/SRX3989971/SRR7059012.sra Written 15654495 spots for /home/okishinya/chipatlas/results/dm3/SRX3989971/SRR7059012.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: 00:05:41 15654495 reads; of these: 15654495 (100.00%) were unpaired; of these: 1411135 (9.01%) aligned 0 times 11606722 (74.14%) aligned exactly 1 time 2636638 (16.84%) aligned >1 times 90.99% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2815627 / 14243360 = 0.1977 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 @ Mon, 06 Aug 2018 10:36:48: # Command line: callpeak -t SRX3989971.bam -f BAM -g dm -n SRX3989971.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3989971.10 # format = BAM # ChIP-seq file = ['SRX3989971.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 06 Aug 2018 10:36:48: # Command line: callpeak -t SRX3989971.bam -f BAM -g dm -n SRX3989971.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3989971.20 # format = BAM # ChIP-seq file = ['SRX3989971.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 06 Aug 2018 10:36:48: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:48: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:48: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:36:48: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:36:48: # Command line: callpeak -t SRX3989971.bam -f BAM -g dm -n SRX3989971.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3989971.05 # format = BAM # ChIP-seq file = ['SRX3989971.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 06 Aug 2018 10:36:48: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:48: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:36:55: 1000000 INFO @ Mon, 06 Aug 2018 10:36:55: 1000000 INFO @ Mon, 06 Aug 2018 10:36:55: 1000000 INFO @ Mon, 06 Aug 2018 10:37:02: 2000000 INFO @ Mon, 06 Aug 2018 10:37:02: 2000000 INFO @ Mon, 06 Aug 2018 10:37:02: 2000000 INFO @ Mon, 06 Aug 2018 10:37:09: 3000000 INFO @ Mon, 06 Aug 2018 10:37:09: 3000000 INFO @ Mon, 06 Aug 2018 10:37:09: 3000000 INFO @ Mon, 06 Aug 2018 10:37:16: 4000000 INFO @ Mon, 06 Aug 2018 10:37:16: 4000000 INFO @ Mon, 06 Aug 2018 10:37:17: 4000000 INFO @ Mon, 06 Aug 2018 10:37:23: 5000000 INFO @ Mon, 06 Aug 2018 10:37:23: 5000000 INFO @ Mon, 06 Aug 2018 10:37:24: 5000000 INFO @ Mon, 06 Aug 2018 10:37:30: 6000000 INFO @ Mon, 06 Aug 2018 10:37:30: 6000000 INFO @ Mon, 06 Aug 2018 10:37:31: 6000000 INFO @ Mon, 06 Aug 2018 10:37:37: 7000000 INFO @ Mon, 06 Aug 2018 10:37:37: 7000000 INFO @ Mon, 06 Aug 2018 10:37:39: 7000000 INFO @ Mon, 06 Aug 2018 10:37:44: 8000000 INFO @ Mon, 06 Aug 2018 10:37:44: 8000000 INFO @ Mon, 06 Aug 2018 10:37:46: 8000000 INFO @ Mon, 06 Aug 2018 10:37:51: 9000000 INFO @ Mon, 06 Aug 2018 10:37:51: 9000000 INFO @ Mon, 06 Aug 2018 10:37:53: 9000000 INFO @ Mon, 06 Aug 2018 10:37:57: 10000000 INFO @ Mon, 06 Aug 2018 10:37:58: 10000000 INFO @ Mon, 06 Aug 2018 10:38:01: 10000000 INFO @ Mon, 06 Aug 2018 10:38:04: 11000000 INFO @ Mon, 06 Aug 2018 10:38:05: 11000000 INFO @ Mon, 06 Aug 2018 10:38:07: #1 tag size is determined as 49 bps INFO @ Mon, 06 Aug 2018 10:38:07: #1 tag size = 49 INFO @ Mon, 06 Aug 2018 10:38:07: #1 total tags in treatment: 11427733 INFO @ Mon, 06 Aug 2018 10:38:07: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:38:07: #1 tags after filtering in treatment: 11427733 INFO @ Mon, 06 Aug 2018 10:38:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:38:07: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:07: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:08: 11000000 INFO @ Mon, 06 Aug 2018 10:38:08: #2 number of paired peaks: 16 WARNING @ Mon, 06 Aug 2018 10:38:08: Too few paired peaks (16) 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 @ Mon, 06 Aug 2018 10:38:08: Process for pairing-model is terminated! cat: SRX3989971.05_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): 1 millis INFO @ Mon, 06 Aug 2018 10:38:08: #1 tag size is determined as 49 bps INFO @ Mon, 06 Aug 2018 10:38:08: #1 tag size = 49 INFO @ Mon, 06 Aug 2018 10:38:08: #1 total tags in treatment: 11427733 INFO @ Mon, 06 Aug 2018 10:38:08: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3989971.05_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 `SRX3989971.05_*.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 `SRX3989971.05_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 @ Mon, 06 Aug 2018 10:38:09: #1 tags after filtering in treatment: 11427733 INFO @ Mon, 06 Aug 2018 10:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:38:09: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:09: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:09: #2 number of paired peaks: 16 WARNING @ Mon, 06 Aug 2018 10:38:09: Too few paired peaks (16) 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 @ Mon, 06 Aug 2018 10:38:09: Process for pairing-model is terminated! cat: SRX3989971.10_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 `SRX3989971.10_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 `SRX3989971.10_*.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 `SRX3989971.10_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 @ Mon, 06 Aug 2018 10:38:11: #1 tag size is determined as 49 bps INFO @ Mon, 06 Aug 2018 10:38:11: #1 tag size = 49 INFO @ Mon, 06 Aug 2018 10:38:11: #1 total tags in treatment: 11427733 INFO @ Mon, 06 Aug 2018 10:38:11: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:38:11: #1 tags after filtering in treatment: 11427733 INFO @ Mon, 06 Aug 2018 10:38:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:38:11: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:11: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:12: #2 number of paired peaks: 16 WARNING @ Mon, 06 Aug 2018 10:38:12: Too few paired peaks (16) 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 @ Mon, 06 Aug 2018 10:38:12: Process for pairing-model is terminated! cat: SRX3989971.20_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 `SRX3989971.20_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 `SRX3989971.20_*.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 `SRX3989971.20_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。