Job ID = 11192886 sra ファイルのダウンロード中... Completed: 823095K bytes transferred in 34 seconds (193472K 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 15000928 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771764/SRR5488919.sra Written 15000928 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771764/SRR5488919.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: 00:16:07 15000928 reads; of these: 15000928 (100.00%) were paired; of these: 979473 (6.53%) aligned concordantly 0 times 12151039 (81.00%) aligned concordantly exactly 1 time 1870416 (12.47%) aligned concordantly >1 times ---- 979473 pairs aligned concordantly 0 times; of these: 71411 (7.29%) aligned discordantly 1 time ---- 908062 pairs aligned 0 times concordantly or discordantly; of these: 1816124 mates make up the pairs; of these: 1509517 (83.12%) aligned 0 times 231783 (12.76%) aligned exactly 1 time 74824 (4.12%) aligned >1 times 94.97% overall alignment rate Time searching: 00:16:07 Overall time: 00:16:07 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 12 files... [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] 621988 / 14080668 = 0.0442 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 @ Sat, 15 Sep 2018 10:42:37: # Command line: callpeak -t SRX2771764.bam -f BAM -g 12100000 -n SRX2771764.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2771764.05 # format = BAM # ChIP-seq file = ['SRX2771764.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 @ Sat, 15 Sep 2018 10:42:37: # Command line: callpeak -t SRX2771764.bam -f BAM -g 12100000 -n SRX2771764.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2771764.20 # format = BAM # ChIP-seq file = ['SRX2771764.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 @ Sat, 15 Sep 2018 10:42:37: # Command line: callpeak -t SRX2771764.bam -f BAM -g 12100000 -n SRX2771764.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2771764.10 # format = BAM # ChIP-seq file = ['SRX2771764.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 @ Sat, 15 Sep 2018 10:42:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:42:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:42:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:42:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:42:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:42:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:42:46: 1000000 INFO @ Sat, 15 Sep 2018 10:42:46: 1000000 INFO @ Sat, 15 Sep 2018 10:42:46: 1000000 INFO @ Sat, 15 Sep 2018 10:42:56: 2000000 INFO @ Sat, 15 Sep 2018 10:42:56: 2000000 INFO @ Sat, 15 Sep 2018 10:42:56: 2000000 INFO @ Sat, 15 Sep 2018 10:43:06: 3000000 INFO @ Sat, 15 Sep 2018 10:43:06: 3000000 INFO @ Sat, 15 Sep 2018 10:43:06: 3000000 INFO @ Sat, 15 Sep 2018 10:43:15: 4000000 INFO @ Sat, 15 Sep 2018 10:43:15: 4000000 INFO @ Sat, 15 Sep 2018 10:43:15: 4000000 INFO @ Sat, 15 Sep 2018 10:43:23: 5000000 INFO @ Sat, 15 Sep 2018 10:43:23: 5000000 INFO @ Sat, 15 Sep 2018 10:43:23: 5000000 INFO @ Sat, 15 Sep 2018 10:43:31: 6000000 INFO @ Sat, 15 Sep 2018 10:43:31: 6000000 INFO @ Sat, 15 Sep 2018 10:43:31: 6000000 INFO @ Sat, 15 Sep 2018 10:43:40: 7000000 INFO @ Sat, 15 Sep 2018 10:43:40: 7000000 INFO @ Sat, 15 Sep 2018 10:43:40: 7000000 INFO @ Sat, 15 Sep 2018 10:43:49: 8000000 INFO @ Sat, 15 Sep 2018 10:43:49: 8000000 INFO @ Sat, 15 Sep 2018 10:43:49: 8000000 INFO @ Sat, 15 Sep 2018 10:43:58: 9000000 INFO @ Sat, 15 Sep 2018 10:43:58: 9000000 INFO @ Sat, 15 Sep 2018 10:43:58: 9000000 INFO @ Sat, 15 Sep 2018 10:44:07: 10000000 INFO @ Sat, 15 Sep 2018 10:44:07: 10000000 INFO @ Sat, 15 Sep 2018 10:44:07: 10000000 INFO @ Sat, 15 Sep 2018 10:44:16: 11000000 INFO @ Sat, 15 Sep 2018 10:44:16: 11000000 INFO @ Sat, 15 Sep 2018 10:44:16: 11000000 INFO @ Sat, 15 Sep 2018 10:44:25: 12000000 INFO @ Sat, 15 Sep 2018 10:44:25: 12000000 INFO @ Sat, 15 Sep 2018 10:44:25: 12000000 INFO @ Sat, 15 Sep 2018 10:44:34: 13000000 INFO @ Sat, 15 Sep 2018 10:44:34: 13000000 INFO @ Sat, 15 Sep 2018 10:44:34: 13000000 INFO @ Sat, 15 Sep 2018 10:44:42: 14000000 INFO @ Sat, 15 Sep 2018 10:44:42: 14000000 INFO @ Sat, 15 Sep 2018 10:44:42: 14000000 INFO @ Sat, 15 Sep 2018 10:44:50: 15000000 INFO @ Sat, 15 Sep 2018 10:44:50: 15000000 INFO @ Sat, 15 Sep 2018 10:44:51: 15000000 INFO @ Sat, 15 Sep 2018 10:44:58: 16000000 INFO @ Sat, 15 Sep 2018 10:44:58: 16000000 INFO @ Sat, 15 Sep 2018 10:45:00: 16000000 INFO @ Sat, 15 Sep 2018 10:45:06: 17000000 INFO @ Sat, 15 Sep 2018 10:45:06: 17000000 INFO @ Sat, 15 Sep 2018 10:45:09: 17000000 INFO @ Sat, 15 Sep 2018 10:45:14: 18000000 INFO @ Sat, 15 Sep 2018 10:45:14: 18000000 INFO @ Sat, 15 Sep 2018 10:45:18: 18000000 INFO @ Sat, 15 Sep 2018 10:45:22: 19000000 INFO @ Sat, 15 Sep 2018 10:45:22: 19000000 INFO @ Sat, 15 Sep 2018 10:45:26: 19000000 INFO @ Sat, 15 Sep 2018 10:45:31: 20000000 INFO @ Sat, 15 Sep 2018 10:45:31: 20000000 INFO @ Sat, 15 Sep 2018 10:45:34: 20000000 INFO @ Sat, 15 Sep 2018 10:45:40: 21000000 INFO @ Sat, 15 Sep 2018 10:45:40: 21000000 INFO @ Sat, 15 Sep 2018 10:45:42: 21000000 INFO @ Sat, 15 Sep 2018 10:45:48: 22000000 INFO @ Sat, 15 Sep 2018 10:45:48: 22000000 INFO @ Sat, 15 Sep 2018 10:45:51: 22000000 INFO @ Sat, 15 Sep 2018 10:45:57: 23000000 INFO @ Sat, 15 Sep 2018 10:45:57: 23000000 INFO @ Sat, 15 Sep 2018 10:45:59: 23000000 INFO @ Sat, 15 Sep 2018 10:46:05: 24000000 INFO @ Sat, 15 Sep 2018 10:46:05: 24000000 INFO @ Sat, 15 Sep 2018 10:46:08: 24000000 INFO @ Sat, 15 Sep 2018 10:46:13: 25000000 INFO @ Sat, 15 Sep 2018 10:46:13: 25000000 INFO @ Sat, 15 Sep 2018 10:46:17: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Sep 2018 10:46:22: 26000000 INFO @ Sat, 15 Sep 2018 10:46:22: 26000000 INFO @ Sat, 15 Sep 2018 10:46:26: 26000000 INFO @ Sat, 15 Sep 2018 10:46:30: 27000000 INFO @ Sat, 15 Sep 2018 10:46:30: 27000000 INFO @ Sat, 15 Sep 2018 10:46:33: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:46:33: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:46:33: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:46:33: #1 total tags in treatment: 13400593 INFO @ Sat, 15 Sep 2018 10:46:33: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:46:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:46:33: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:46:33: #1 total tags in treatment: 13400593 INFO @ Sat, 15 Sep 2018 10:46:33: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:46:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:46:33: #1 tags after filtering in treatment: 9250036 INFO @ Sat, 15 Sep 2018 10:46:33: #1 tags after filtering in treatment: 9250036 INFO @ Sat, 15 Sep 2018 10:46:33: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 10:46:33: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 10:46:33: #1 finished! INFO @ Sat, 15 Sep 2018 10:46:33: #1 finished! INFO @ Sat, 15 Sep 2018 10:46:33: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:46:33: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:46:34: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:46:34: 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 @ Sat, 15 Sep 2018 10:46:34: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 10:46:34: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:46:34: 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 @ Sat, 15 Sep 2018 10:46:34: Process for pairing-model is terminated! cat: SRX2771764.10_peaks.narrowPeakcat: SRX2771764.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません : 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): 13 millis pass1 - making usageList (0 chroms): 14 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2771764.10_model.r'rm: cannot remove `SRX2771764.05_model.r': そのようなファイルやディレクトリはありません : 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 `SRX2771764.10_*.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 `SRX2771764.05_*.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 `SRX2771764.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2771764.05_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 CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:46:34: 27000000 BigWig に変換しました。 INFO @ Sat, 15 Sep 2018 10:46:36: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:46:36: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:46:36: #1 total tags in treatment: 13400593 INFO @ Sat, 15 Sep 2018 10:46:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:46:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:46:37: #1 tags after filtering in treatment: 9250036 INFO @ Sat, 15 Sep 2018 10:46:37: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 10:46:37: #1 finished! INFO @ Sat, 15 Sep 2018 10:46:37: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:46:37: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:46:37: 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 @ Sat, 15 Sep 2018 10:46:37: Process for pairing-model is terminated! cat: SRX2771764.20_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 `SRX2771764.20_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 `SRX2771764.20_*.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 `SRX2771764.20_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