Job ID = 11296933 sra ファイルのダウンロード中... Completed: 332656K bytes transferred in 6 seconds (444543K 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 16163670 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856348/SRR6908165.sra Written 16163670 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856348/SRR6908165.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: 00:03:21 16163670 reads; of these: 16163670 (100.00%) were unpaired; of these: 994308 (6.15%) aligned 0 times 12730022 (78.76%) aligned exactly 1 time 2439340 (15.09%) aligned >1 times 93.85% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 5021375 / 15169362 = 0.3310 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 18:04:30: # Command line: callpeak -t SRX3856348.bam -f BAM -g 12100000 -n SRX3856348.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856348.10 # format = BAM # ChIP-seq file = ['SRX3856348.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 18:04:30: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:04:30: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:04:30: # Command line: callpeak -t SRX3856348.bam -f BAM -g 12100000 -n SRX3856348.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856348.05 # format = BAM # ChIP-seq file = ['SRX3856348.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 18:04:30: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:04:30: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:04:30: # Command line: callpeak -t SRX3856348.bam -f BAM -g 12100000 -n SRX3856348.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856348.20 # format = BAM # ChIP-seq file = ['SRX3856348.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 18:04:30: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:04:30: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:04:37: 1000000 INFO @ Mon, 05 Nov 2018 18:04:37: 1000000 INFO @ Mon, 05 Nov 2018 18:04:38: 1000000 INFO @ Mon, 05 Nov 2018 18:04:44: 2000000 INFO @ Mon, 05 Nov 2018 18:04:45: 2000000 INFO @ Mon, 05 Nov 2018 18:04:45: 2000000 INFO @ Mon, 05 Nov 2018 18:04:52: 3000000 INFO @ Mon, 05 Nov 2018 18:04:52: 3000000 INFO @ Mon, 05 Nov 2018 18:04:53: 3000000 INFO @ Mon, 05 Nov 2018 18:04:59: 4000000 INFO @ Mon, 05 Nov 2018 18:04:59: 4000000 INFO @ Mon, 05 Nov 2018 18:05:02: 4000000 INFO @ Mon, 05 Nov 2018 18:05:06: 5000000 INFO @ Mon, 05 Nov 2018 18:05:06: 5000000 INFO @ Mon, 05 Nov 2018 18:05:10: 5000000 INFO @ Mon, 05 Nov 2018 18:05:13: 6000000 INFO @ Mon, 05 Nov 2018 18:05:13: 6000000 INFO @ Mon, 05 Nov 2018 18:05:18: 6000000 INFO @ Mon, 05 Nov 2018 18:05:20: 7000000 INFO @ Mon, 05 Nov 2018 18:05:20: 7000000 INFO @ Mon, 05 Nov 2018 18:05:26: 7000000 INFO @ Mon, 05 Nov 2018 18:05:28: 8000000 INFO @ Mon, 05 Nov 2018 18:05:28: 8000000 INFO @ Mon, 05 Nov 2018 18:05:35: 9000000 INFO @ Mon, 05 Nov 2018 18:05:35: 8000000 INFO @ Mon, 05 Nov 2018 18:05:37: 9000000 INFO @ Mon, 05 Nov 2018 18:05:43: 10000000 INFO @ Mon, 05 Nov 2018 18:05:44: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:05:44: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:05:44: #1 total tags in treatment: 10147987 INFO @ Mon, 05 Nov 2018 18:05:44: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:44: #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 18:05:44: 9000000 INFO @ Mon, 05 Nov 2018 18:05:44: #1 tags after filtering in treatment: 10147987 INFO @ Mon, 05 Nov 2018 18:05:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:44: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:44: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:45: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:05:45: 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 18:05:45: Process for pairing-model is terminated! cat: SRX3856348.05_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 `SRX3856348.05_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 `SRX3856348.05_*.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 `SRX3856348.05_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 18:05:46: 10000000 INFO @ Mon, 05 Nov 2018 18:05:47: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:05:47: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:05:47: #1 total tags in treatment: 10147987 INFO @ Mon, 05 Nov 2018 18:05:47: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:47: #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 18:05:47: #1 tags after filtering in treatment: 10147987 INFO @ Mon, 05 Nov 2018 18:05:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:47: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:47: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:48: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:05:48: 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 18:05:48: Process for pairing-model is terminated! cat: SRX3856348.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856348.10_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 `SRX3856348.10_*.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 `SRX3856348.10_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, 05 Nov 2018 18:05:53: 10000000 INFO @ Mon, 05 Nov 2018 18:05:54: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:05:54: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:05:54: #1 total tags in treatment: 10147987 INFO @ Mon, 05 Nov 2018 18:05:54: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:54: #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 18:05:54: #1 tags after filtering in treatment: 10147987 INFO @ Mon, 05 Nov 2018 18:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:54: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:54: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:55: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:05:55: 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 18:05:55: Process for pairing-model is terminated! cat: SRX3856348.20_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 `SRX3856348.20_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 `SRX3856348.20_*.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 `SRX3856348.20_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。