Job ID = 11245136 sra ファイルのダウンロード中... Completed: 513241K bytes transferred in 7 seconds (527089K 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 9151681 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669587/SRR7818161.sra Written 9151681 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669587/SRR7818161.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: 00:08:02 9151681 reads; of these: 9151681 (100.00%) were paired; of these: 926034 (10.12%) aligned concordantly 0 times 7239558 (79.11%) aligned concordantly exactly 1 time 986089 (10.77%) aligned concordantly >1 times ---- 926034 pairs aligned concordantly 0 times; of these: 21442 (2.32%) aligned discordantly 1 time ---- 904592 pairs aligned 0 times concordantly or discordantly; of these: 1809184 mates make up the pairs; of these: 1613495 (89.18%) aligned 0 times 99818 (5.52%) aligned exactly 1 time 95871 (5.30%) aligned >1 times 91.18% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 1106999 / 8244544 = 0.1343 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 23:44:16: # Command line: callpeak -t SRX4669587.bam -f BAM -g 12100000 -n SRX4669587.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669587.10 # format = BAM # ChIP-seq file = ['SRX4669587.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 23:44:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:44:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:44:16: # Command line: callpeak -t SRX4669587.bam -f BAM -g 12100000 -n SRX4669587.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669587.20 # format = BAM # ChIP-seq file = ['SRX4669587.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 23:44:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:44:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:44:16: # Command line: callpeak -t SRX4669587.bam -f BAM -g 12100000 -n SRX4669587.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669587.05 # format = BAM # ChIP-seq file = ['SRX4669587.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 23:44:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:44:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:44:22: 1000000 INFO @ Tue, 09 Oct 2018 23:44:22: 1000000 INFO @ Tue, 09 Oct 2018 23:44:22: 1000000 INFO @ Tue, 09 Oct 2018 23:44:29: 2000000 INFO @ Tue, 09 Oct 2018 23:44:29: 2000000 INFO @ Tue, 09 Oct 2018 23:44:29: 2000000 INFO @ Tue, 09 Oct 2018 23:44:35: 3000000 INFO @ Tue, 09 Oct 2018 23:44:35: 3000000 INFO @ Tue, 09 Oct 2018 23:44:35: 3000000 INFO @ Tue, 09 Oct 2018 23:44:41: 4000000 INFO @ Tue, 09 Oct 2018 23:44:42: 4000000 INFO @ Tue, 09 Oct 2018 23:44:42: 4000000 INFO @ Tue, 09 Oct 2018 23:44:48: 5000000 INFO @ Tue, 09 Oct 2018 23:44:48: 5000000 INFO @ Tue, 09 Oct 2018 23:44:48: 5000000 INFO @ Tue, 09 Oct 2018 23:44:54: 6000000 INFO @ Tue, 09 Oct 2018 23:44:55: 6000000 INFO @ Tue, 09 Oct 2018 23:44:55: 6000000 INFO @ Tue, 09 Oct 2018 23:45:01: 7000000 INFO @ Tue, 09 Oct 2018 23:45:01: 7000000 INFO @ Tue, 09 Oct 2018 23:45:01: 7000000 INFO @ Tue, 09 Oct 2018 23:45:07: 8000000 INFO @ Tue, 09 Oct 2018 23:45:08: 8000000 INFO @ Tue, 09 Oct 2018 23:45:08: 8000000 INFO @ Tue, 09 Oct 2018 23:45:14: 9000000 INFO @ Tue, 09 Oct 2018 23:45:14: 9000000 INFO @ Tue, 09 Oct 2018 23:45:14: 9000000 INFO @ Tue, 09 Oct 2018 23:45:20: 10000000 INFO @ Tue, 09 Oct 2018 23:45:21: 10000000 INFO @ Tue, 09 Oct 2018 23:45:21: 10000000 INFO @ Tue, 09 Oct 2018 23:45:27: 11000000 INFO @ Tue, 09 Oct 2018 23:45:28: 11000000 INFO @ Tue, 09 Oct 2018 23:45:28: 11000000 INFO @ Tue, 09 Oct 2018 23:45:34: 12000000 INFO @ Tue, 09 Oct 2018 23:45:35: 12000000 INFO @ Tue, 09 Oct 2018 23:45:35: 12000000 INFO @ Tue, 09 Oct 2018 23:45:41: 13000000 INFO @ Tue, 09 Oct 2018 23:45:42: 13000000 INFO @ Tue, 09 Oct 2018 23:45:43: 13000000 INFO @ Tue, 09 Oct 2018 23:45:48: 14000000 INFO @ Tue, 09 Oct 2018 23:45:49: 14000000 INFO @ Tue, 09 Oct 2018 23:45:52: 14000000 INFO @ Tue, 09 Oct 2018 23:45:52: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:45:52: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:45:52: #1 total tags in treatment: 7120519 INFO @ Tue, 09 Oct 2018 23:45:52: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:45:52: #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 23:45:52: #1 tags after filtering in treatment: 5624916 INFO @ Tue, 09 Oct 2018 23:45:52: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:45:52: #1 finished! INFO @ Tue, 09 Oct 2018 23:45:52: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:45:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:45:52: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:45:52: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:45:52: #1 total tags in treatment: 7120519 INFO @ Tue, 09 Oct 2018 23:45:52: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:45:52: #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 23:45:52: #1 tags after filtering in treatment: 5624916 INFO @ Tue, 09 Oct 2018 23:45:52: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:45:52: #1 finished! INFO @ Tue, 09 Oct 2018 23:45:52: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:45:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:45:52: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:45:52: 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 @ Tue, 09 Oct 2018 23:45:52: Process for pairing-model is terminated! cat: SRX4669587.05_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 `SRX4669587.05_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 `SRX4669587.05_*.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 `SRX4669587.05_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 23:45:53: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:45:53: 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 @ Tue, 09 Oct 2018 23:45:53: Process for pairing-model is terminated! cat: SRX4669587.10_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 `SRX4669587.10_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 `SRX4669587.10_*.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 `SRX4669587.10_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 @ Tue, 09 Oct 2018 23:45:55: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:45:55: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:45:55: #1 total tags in treatment: 7120519 INFO @ Tue, 09 Oct 2018 23:45:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:45:55: #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 23:45:55: #1 tags after filtering in treatment: 5624916 INFO @ Tue, 09 Oct 2018 23:45:55: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:45:55: #1 finished! INFO @ Tue, 09 Oct 2018 23:45:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:45:56: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:45:56: 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 @ Tue, 09 Oct 2018 23:45:56: Process for pairing-model is terminated! cat: SRX4669587.20_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 `SRX4669587.20_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 `SRX4669587.20_*.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 `SRX4669587.20_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。