Job ID = 11245017 sra ファイルのダウンロード中... Completed: 311829K bytes transferred in 8 seconds (305223K 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 10217658 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554731/SRR7696403.sra Written 10217658 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554731/SRR7696403.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: 00:05:10 10217658 reads; of these: 10217658 (100.00%) were paired; of these: 5162708 (50.53%) aligned concordantly 0 times 4841446 (47.38%) aligned concordantly exactly 1 time 213504 (2.09%) aligned concordantly >1 times ---- 5162708 pairs aligned concordantly 0 times; of these: 10256 (0.20%) aligned discordantly 1 time ---- 5152452 pairs aligned 0 times concordantly or discordantly; of these: 10304904 mates make up the pairs; of these: 6026497 (58.48%) aligned 0 times 4064911 (39.45%) aligned exactly 1 time 213496 (2.07%) aligned >1 times 70.51% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 246626 / 5064508 = 0.0487 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 23:17:23: # Command line: callpeak -t SRX4554731.bam -f BAM -g 12100000 -n SRX4554731.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554731.05 # format = BAM # ChIP-seq file = ['SRX4554731.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 23:17:23: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:23: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:17:23: # Command line: callpeak -t SRX4554731.bam -f BAM -g 12100000 -n SRX4554731.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554731.10 # format = BAM # ChIP-seq file = ['SRX4554731.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 23:17:23: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:23: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:17:23: # Command line: callpeak -t SRX4554731.bam -f BAM -g 12100000 -n SRX4554731.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554731.20 # format = BAM # ChIP-seq file = ['SRX4554731.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 23:17:23: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:23: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:17:28: 1000000 INFO @ Tue, 09 Oct 2018 23:17:28: 1000000 INFO @ Tue, 09 Oct 2018 23:17:28: 1000000 INFO @ Tue, 09 Oct 2018 23:17:33: 2000000 INFO @ Tue, 09 Oct 2018 23:17:34: 2000000 INFO @ Tue, 09 Oct 2018 23:17:34: 2000000 INFO @ Tue, 09 Oct 2018 23:17:39: 3000000 INFO @ Tue, 09 Oct 2018 23:17:39: 3000000 INFO @ Tue, 09 Oct 2018 23:17:39: 3000000 INFO @ Tue, 09 Oct 2018 23:17:44: 4000000 INFO @ Tue, 09 Oct 2018 23:17:45: 4000000 INFO @ Tue, 09 Oct 2018 23:17:45: 4000000 INFO @ Tue, 09 Oct 2018 23:17:50: 5000000 INFO @ Tue, 09 Oct 2018 23:17:50: 5000000 INFO @ Tue, 09 Oct 2018 23:17:50: 5000000 INFO @ Tue, 09 Oct 2018 23:17:55: 6000000 INFO @ Tue, 09 Oct 2018 23:17:56: 6000000 INFO @ Tue, 09 Oct 2018 23:17:56: 6000000 INFO @ Tue, 09 Oct 2018 23:18:00: 7000000 INFO @ Tue, 09 Oct 2018 23:18:01: 7000000 INFO @ Tue, 09 Oct 2018 23:18:02: 7000000 INFO @ Tue, 09 Oct 2018 23:18:05: 8000000 INFO @ Tue, 09 Oct 2018 23:18:07: 8000000 INFO @ Tue, 09 Oct 2018 23:18:07: 8000000 INFO @ Tue, 09 Oct 2018 23:18:10: 9000000 INFO @ Tue, 09 Oct 2018 23:18:13: 9000000 INFO @ Tue, 09 Oct 2018 23:18:13: 9000000 INFO @ Tue, 09 Oct 2018 23:18:16: 10000000 INFO @ Tue, 09 Oct 2018 23:18:18: 10000000 INFO @ Tue, 09 Oct 2018 23:18:19: 10000000 INFO @ Tue, 09 Oct 2018 23:18:21: 11000000 INFO @ Tue, 09 Oct 2018 23:18:24: 11000000 INFO @ Tue, 09 Oct 2018 23:18:24: 11000000 INFO @ Tue, 09 Oct 2018 23:18:26: 12000000 INFO @ Tue, 09 Oct 2018 23:18:30: 12000000 INFO @ Tue, 09 Oct 2018 23:18:30: 12000000 INFO @ Tue, 09 Oct 2018 23:18:31: 13000000 INFO @ Tue, 09 Oct 2018 23:18:35: 13000000 INFO @ Tue, 09 Oct 2018 23:18:36: 13000000 INFO @ Tue, 09 Oct 2018 23:18:36: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:36: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:36: #1 total tags in treatment: 4808381 INFO @ Tue, 09 Oct 2018 23:18:36: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:36: #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 23:18:36: #1 tags after filtering in treatment: 2787576 INFO @ Tue, 09 Oct 2018 23:18:36: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:18:36: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:36: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:36: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:18:36: 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 23:18:36: Process for pairing-model is terminated! cat: SRX4554731.05_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 `SRX4554731.05_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 `SRX4554731.05_*.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 `SRX4554731.05_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 23:18:40: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:40: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:40: #1 total tags in treatment: 4808381 INFO @ Tue, 09 Oct 2018 23:18:40: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:40: #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 23:18:40: #1 tags after filtering in treatment: 2787576 INFO @ Tue, 09 Oct 2018 23:18:40: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:18:40: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:40: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:40: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:40: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:40: #1 total tags in treatment: 4808381 INFO @ Tue, 09 Oct 2018 23:18:40: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:40: #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 23:18:40: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:18:40: 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 23:18:40: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:18:40: #1 tags after filtering in treatment: 2787576 INFO @ Tue, 09 Oct 2018 23:18:40: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:18:40: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:40: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:40: #2 looking for paired plus/minus strand peaks... cat: SRX4554731.10_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 `SRX4554731.10_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 `SRX4554731.10_*.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 `SRX4554731.10_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 23:18:41: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:18:41: 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 23:18:41: Process for pairing-model is terminated! cat: SRX4554731.20_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 `SRX4554731.20_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 `SRX4554731.20_*.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 `SRX4554731.20_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。