Job ID = 11245166 sra ファイルのダウンロード中... Completed: 319001K bytes transferred in 6 seconds (417732K 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 6515398 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669613/SRR7818196.sra Written 6515398 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669613/SRR7818196.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: 00:04:31 6515398 reads; of these: 6515398 (100.00%) were paired; of these: 666076 (10.22%) aligned concordantly 0 times 5095438 (78.21%) aligned concordantly exactly 1 time 753884 (11.57%) aligned concordantly >1 times ---- 666076 pairs aligned concordantly 0 times; of these: 32820 (4.93%) aligned discordantly 1 time ---- 633256 pairs aligned 0 times concordantly or discordantly; of these: 1266512 mates make up the pairs; of these: 1025437 (80.97%) aligned 0 times 164779 (13.01%) aligned exactly 1 time 76296 (6.02%) aligned >1 times 92.13% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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_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] 74668 / 5866104 = 0.0127 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 @ Tue, 09 Oct 2018 23:47:46: # Command line: callpeak -t SRX4669613.bam -f BAM -g 12100000 -n SRX4669613.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669613.10 # format = BAM # ChIP-seq file = ['SRX4669613.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 @ Tue, 09 Oct 2018 23:47:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:47:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:47:46: # Command line: callpeak -t SRX4669613.bam -f BAM -g 12100000 -n SRX4669613.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669613.20 # format = BAM # ChIP-seq file = ['SRX4669613.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 @ Tue, 09 Oct 2018 23:47:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:47:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:47:46: # Command line: callpeak -t SRX4669613.bam -f BAM -g 12100000 -n SRX4669613.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669613.05 # format = BAM # ChIP-seq file = ['SRX4669613.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 @ Tue, 09 Oct 2018 23:47:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:47:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:47:52: 1000000 INFO @ Tue, 09 Oct 2018 23:47:52: 1000000 INFO @ Tue, 09 Oct 2018 23:47:52: 1000000 INFO @ Tue, 09 Oct 2018 23:47:57: 2000000 INFO @ Tue, 09 Oct 2018 23:47:57: 2000000 INFO @ Tue, 09 Oct 2018 23:47:58: 2000000 INFO @ Tue, 09 Oct 2018 23:48:03: 3000000 INFO @ Tue, 09 Oct 2018 23:48:03: 3000000 INFO @ Tue, 09 Oct 2018 23:48:03: 3000000 INFO @ Tue, 09 Oct 2018 23:48:08: 4000000 INFO @ Tue, 09 Oct 2018 23:48:09: 4000000 INFO @ Tue, 09 Oct 2018 23:48:09: 4000000 INFO @ Tue, 09 Oct 2018 23:48:14: 5000000 INFO @ Tue, 09 Oct 2018 23:48:15: 5000000 INFO @ Tue, 09 Oct 2018 23:48:16: 5000000 INFO @ Tue, 09 Oct 2018 23:48:20: 6000000 INFO @ Tue, 09 Oct 2018 23:48:21: 6000000 INFO @ Tue, 09 Oct 2018 23:48:22: 6000000 INFO @ Tue, 09 Oct 2018 23:48:25: 7000000 INFO @ Tue, 09 Oct 2018 23:48:27: 7000000 INFO @ Tue, 09 Oct 2018 23:48:28: 7000000 INFO @ Tue, 09 Oct 2018 23:48:31: 8000000 INFO @ Tue, 09 Oct 2018 23:48:32: 8000000 INFO @ Tue, 09 Oct 2018 23:48:34: 8000000 INFO @ Tue, 09 Oct 2018 23:48:36: 9000000 INFO @ Tue, 09 Oct 2018 23:48:38: 9000000 INFO @ Tue, 09 Oct 2018 23:48:40: 9000000 INFO @ Tue, 09 Oct 2018 23:48:42: 10000000 INFO @ Tue, 09 Oct 2018 23:48:44: 10000000 INFO @ Tue, 09 Oct 2018 23:48:46: 10000000 INFO @ Tue, 09 Oct 2018 23:48:47: 11000000 INFO @ Tue, 09 Oct 2018 23:48:50: 11000000 INFO @ Tue, 09 Oct 2018 23:48:52: 11000000 INFO @ Tue, 09 Oct 2018 23:48:52: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:48:52: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:48:52: #1 total tags in treatment: 5774927 INFO @ Tue, 09 Oct 2018 23:48:52: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:48:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:48:53: #1 tags after filtering in treatment: 4709552 INFO @ Tue, 09 Oct 2018 23:48:53: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:48:53: #1 finished! INFO @ Tue, 09 Oct 2018 23:48:53: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:48:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:48:53: #2 number of paired peaks: 24 WARNING @ Tue, 09 Oct 2018 23:48:53: Too few paired peaks (24) 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 @ Tue, 09 Oct 2018 23:48:53: Process for pairing-model is terminated! cat: SRX4669613.05_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 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669613.05_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 `SRX4669613.05_*.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 `SRX4669613.05_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 @ Tue, 09 Oct 2018 23:48:55: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:48:55: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:48:55: #1 total tags in treatment: 5774927 INFO @ Tue, 09 Oct 2018 23:48:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:48:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:48:55: #1 tags after filtering in treatment: 4709552 INFO @ Tue, 09 Oct 2018 23:48:55: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:48:55: #1 finished! INFO @ Tue, 09 Oct 2018 23:48:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:48:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:48:55: #2 number of paired peaks: 24 WARNING @ Tue, 09 Oct 2018 23:48:55: Too few paired peaks (24) 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 @ Tue, 09 Oct 2018 23:48:55: Process for pairing-model is terminated! cat: SRX4669613.20_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 `SRX4669613.20_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 `SRX4669613.20_*.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 `SRX4669613.20_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 @ Tue, 09 Oct 2018 23:48:57: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:48:57: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:48:57: #1 total tags in treatment: 5774927 INFO @ Tue, 09 Oct 2018 23:48:57: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:48:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:48:57: #1 tags after filtering in treatment: 4709552 INFO @ Tue, 09 Oct 2018 23:48:57: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:48:57: #1 finished! INFO @ Tue, 09 Oct 2018 23:48:57: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:48:58: #2 number of paired peaks: 24 WARNING @ Tue, 09 Oct 2018 23:48:58: Too few paired peaks (24) 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 @ Tue, 09 Oct 2018 23:48:58: Process for pairing-model is terminated! cat: SRX4669613.10_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 `SRX4669613.10_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 `SRX4669613.10_*.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 `SRX4669613.10_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。