Job ID = 11296953 sra ファイルのダウンロード中... Completed: 228591K bytes transferred in 6 seconds (303087K 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 11622486 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856375/SRR6908193.sra Written 11622486 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856375/SRR6908193.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: 00:02:04 11622486 reads; of these: 11622486 (100.00%) were unpaired; of these: 433195 (3.73%) aligned 0 times 9402346 (80.90%) aligned exactly 1 time 1786945 (15.37%) aligned >1 times 96.27% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 3360090 / 11189291 = 0.3003 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, 05 Nov 2018 18:05:15: # Command line: callpeak -t SRX3856375.bam -f BAM -g 12100000 -n SRX3856375.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856375.05 # format = BAM # ChIP-seq file = ['SRX3856375.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 @ Mon, 05 Nov 2018 18:05:15: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:15: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:15: # Command line: callpeak -t SRX3856375.bam -f BAM -g 12100000 -n SRX3856375.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856375.10 # format = BAM # ChIP-seq file = ['SRX3856375.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 @ Mon, 05 Nov 2018 18:05:15: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:15: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:15: # Command line: callpeak -t SRX3856375.bam -f BAM -g 12100000 -n SRX3856375.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856375.20 # format = BAM # ChIP-seq file = ['SRX3856375.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 @ Mon, 05 Nov 2018 18:05:15: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:15: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:22: 1000000 INFO @ Mon, 05 Nov 2018 18:05:24: 1000000 INFO @ Mon, 05 Nov 2018 18:05:24: 1000000 INFO @ Mon, 05 Nov 2018 18:05:29: 2000000 INFO @ Mon, 05 Nov 2018 18:05:32: 2000000 INFO @ Mon, 05 Nov 2018 18:05:32: 2000000 INFO @ Mon, 05 Nov 2018 18:05:36: 3000000 INFO @ Mon, 05 Nov 2018 18:05:41: 3000000 INFO @ Mon, 05 Nov 2018 18:05:41: 3000000 INFO @ Mon, 05 Nov 2018 18:05:43: 4000000 INFO @ Mon, 05 Nov 2018 18:05:50: 5000000 INFO @ Mon, 05 Nov 2018 18:05:50: 4000000 INFO @ Mon, 05 Nov 2018 18:05:50: 4000000 INFO @ Mon, 05 Nov 2018 18:05:56: 6000000 INFO @ Mon, 05 Nov 2018 18:05:57: 5000000 INFO @ Mon, 05 Nov 2018 18:05:57: 5000000 INFO @ Mon, 05 Nov 2018 18:06:04: 7000000 INFO @ Mon, 05 Nov 2018 18:06:04: 6000000 INFO @ Mon, 05 Nov 2018 18:06:04: 6000000 INFO @ Mon, 05 Nov 2018 18:06:09: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:06:09: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:06:09: #1 total tags in treatment: 7829201 INFO @ Mon, 05 Nov 2018 18:06:09: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:06:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:06:09: #1 tags after filtering in treatment: 7829201 INFO @ Mon, 05 Nov 2018 18:06:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:06:09: #1 finished! INFO @ Mon, 05 Nov 2018 18:06:09: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:06:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:06:10: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:06:10: 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 @ Mon, 05 Nov 2018 18:06:10: Process for pairing-model is terminated! cat: SRX3856375.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856375.05_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 `SRX3856375.05_*.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 `SRX3856375.05_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, 05 Nov 2018 18:06:11: 7000000 INFO @ Mon, 05 Nov 2018 18:06:11: 7000000 INFO @ Mon, 05 Nov 2018 18:06:17: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:06:17: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:06:17: #1 total tags in treatment: 7829201 INFO @ Mon, 05 Nov 2018 18:06:17: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:06:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:06:17: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:06:17: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:06:17: #1 total tags in treatment: 7829201 INFO @ Mon, 05 Nov 2018 18:06:17: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:06:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:06:17: #1 tags after filtering in treatment: 7829201 INFO @ Mon, 05 Nov 2018 18:06:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:06:17: #1 tags after filtering in treatment: 7829201 INFO @ Mon, 05 Nov 2018 18:06:17: #1 finished! INFO @ Mon, 05 Nov 2018 18:06:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:06:17: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:06:17: #1 finished! INFO @ Mon, 05 Nov 2018 18:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:06:17: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:06:18: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:06:18: 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 @ Mon, 05 Nov 2018 18:06:18: Process for pairing-model is terminated! INFO @ Mon, 05 Nov 2018 18:06:18: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:06:18: 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 @ Mon, 05 Nov 2018 18:06:18: Process for pairing-model is terminated! cat: SRX3856375.20_peaks.narrowPeakcat: SRX3856375.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません : 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 `SRX3856375.20_model.r'rm: cannot remove `SRX3856375.10_model.r': そのようなファイルやディレクトリはありません : 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 `SRX3856375.20_*.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 `SRX3856375.10_*.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 `SRX3856375.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX3856375.10_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 CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。