Job ID = 10937465 sra ファイルのダウンロード中... Completed: 340482K bytes transferred in 5 seconds (465115K 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: PAIRED fastq に変換中... Read 6243108 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198737/SRR4304467.sra Written 6243108 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198737/SRR4304467.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: 00:04:41 6243108 reads; of these: 6243108 (100.00%) were paired; of these: 1803843 (28.89%) aligned concordantly 0 times 3466836 (55.53%) aligned concordantly exactly 1 time 972429 (15.58%) aligned concordantly >1 times ---- 1803843 pairs aligned concordantly 0 times; of these: 39325 (2.18%) aligned discordantly 1 time ---- 1764518 pairs aligned 0 times concordantly or discordantly; of these: 3529036 mates make up the pairs; of these: 3351090 (94.96%) aligned 0 times 48579 (1.38%) aligned exactly 1 time 129367 (3.67%) aligned >1 times 73.16% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 287597 / 4466417 = 0.0644 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, 10 Aug 2018 02:23:35: # Command line: callpeak -t SRX2198737.bam -f BAM -g 12100000 -n SRX2198737.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198737.05 # format = BAM # ChIP-seq file = ['SRX2198737.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, 10 Aug 2018 02:23:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:23:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:23:35: # Command line: callpeak -t SRX2198737.bam -f BAM -g 12100000 -n SRX2198737.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198737.20 # format = BAM # ChIP-seq file = ['SRX2198737.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, 10 Aug 2018 02:23:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:23:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:23:35: # Command line: callpeak -t SRX2198737.bam -f BAM -g 12100000 -n SRX2198737.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198737.10 # format = BAM # ChIP-seq file = ['SRX2198737.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, 10 Aug 2018 02:23:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:23:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:23:40: 1000000 INFO @ Fri, 10 Aug 2018 02:23:40: 1000000 INFO @ Fri, 10 Aug 2018 02:23:41: 1000000 INFO @ Fri, 10 Aug 2018 02:23:45: 2000000 INFO @ Fri, 10 Aug 2018 02:23:45: 2000000 INFO @ Fri, 10 Aug 2018 02:23:47: 2000000 INFO @ Fri, 10 Aug 2018 02:23:49: 3000000 INFO @ Fri, 10 Aug 2018 02:23:50: 3000000 INFO @ Fri, 10 Aug 2018 02:23:52: 3000000 INFO @ Fri, 10 Aug 2018 02:23:54: 4000000 INFO @ Fri, 10 Aug 2018 02:23:55: 4000000 INFO @ Fri, 10 Aug 2018 02:23:58: 4000000 INFO @ Fri, 10 Aug 2018 02:23:59: 5000000 INFO @ Fri, 10 Aug 2018 02:24:00: 5000000 INFO @ Fri, 10 Aug 2018 02:24:04: 6000000 INFO @ Fri, 10 Aug 2018 02:24:04: 5000000 INFO @ Fri, 10 Aug 2018 02:24:05: 6000000 INFO @ Fri, 10 Aug 2018 02:24:09: 7000000 INFO @ Fri, 10 Aug 2018 02:24:10: 7000000 INFO @ Fri, 10 Aug 2018 02:24:10: 6000000 INFO @ Fri, 10 Aug 2018 02:24:14: 8000000 INFO @ Fri, 10 Aug 2018 02:24:15: 8000000 INFO @ Fri, 10 Aug 2018 02:24:16: 7000000 INFO @ Fri, 10 Aug 2018 02:24:17: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:24:17: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:24:17: #1 total tags in treatment: 4152001 INFO @ Fri, 10 Aug 2018 02:24:17: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:24:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:24:17: #1 tags after filtering in treatment: 2401282 INFO @ Fri, 10 Aug 2018 02:24:17: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 10 Aug 2018 02:24:17: #1 finished! INFO @ Fri, 10 Aug 2018 02:24:17: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:24:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:24:17: #2 number of paired peaks: 19 WARNING @ Fri, 10 Aug 2018 02:24:17: Too few paired peaks (19) 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, 10 Aug 2018 02:24:17: Process for pairing-model is terminated! cat: SRX2198737.05_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 `SRX2198737.05_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 `SRX2198737.05_*.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 `SRX2198737.05_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 @ Fri, 10 Aug 2018 02:24:17: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:24:17: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:24:17: #1 total tags in treatment: 4152001 INFO @ Fri, 10 Aug 2018 02:24:17: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:24:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:24:18: #1 tags after filtering in treatment: 2401282 INFO @ Fri, 10 Aug 2018 02:24:18: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 10 Aug 2018 02:24:18: #1 finished! INFO @ Fri, 10 Aug 2018 02:24:18: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:24:18: #2 number of paired peaks: 19 WARNING @ Fri, 10 Aug 2018 02:24:18: Too few paired peaks (19) 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, 10 Aug 2018 02:24:18: Process for pairing-model is terminated! cat: SRX2198737.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198737.20_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 `SRX2198737.20_*.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 `SRX2198737.20_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, 10 Aug 2018 02:24:21: 8000000 INFO @ Fri, 10 Aug 2018 02:24:24: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:24:24: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:24:24: #1 total tags in treatment: 4152001 INFO @ Fri, 10 Aug 2018 02:24:24: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:24:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:24:24: #1 tags after filtering in treatment: 2401282 INFO @ Fri, 10 Aug 2018 02:24:24: #1 Redundant rate of treatment: 0.42 INFO @ Fri, 10 Aug 2018 02:24:24: #1 finished! INFO @ Fri, 10 Aug 2018 02:24:24: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:24:25: #2 number of paired peaks: 19 WARNING @ Fri, 10 Aug 2018 02:24:25: Too few paired peaks (19) 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, 10 Aug 2018 02:24:25: Process for pairing-model is terminated! cat: SRX2198737.10_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 `SRX2198737.10_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 `SRX2198737.10_*.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 `SRX2198737.10_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。