Job ID = 11244985 sra ファイルのダウンロード中... Completed: 271279K bytes transferred in 7 seconds (313385K 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 8528576 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554697/SRR7696369.sra Written 8528576 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554697/SRR7696369.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: 00:03:56 8528576 reads; of these: 8528576 (100.00%) were paired; of these: 5488373 (64.35%) aligned concordantly 0 times 2923177 (34.28%) aligned concordantly exactly 1 time 117026 (1.37%) aligned concordantly >1 times ---- 5488373 pairs aligned concordantly 0 times; of these: 2967 (0.05%) aligned discordantly 1 time ---- 5485406 pairs aligned 0 times concordantly or discordantly; of these: 10970812 mates make up the pairs; of these: 6344084 (57.83%) aligned 0 times 4420336 (40.29%) aligned exactly 1 time 206392 (1.88%) aligned >1 times 62.81% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 84837 / 3042783 = 0.0279 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 23:07:23: # Command line: callpeak -t SRX4554697.bam -f BAM -g 12100000 -n SRX4554697.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554697.10 # format = BAM # ChIP-seq file = ['SRX4554697.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 23:07:23: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:07:23: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:07:23: # Command line: callpeak -t SRX4554697.bam -f BAM -g 12100000 -n SRX4554697.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554697.20 # format = BAM # ChIP-seq file = ['SRX4554697.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 23:07:23: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:07:23: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:07:23: # Command line: callpeak -t SRX4554697.bam -f BAM -g 12100000 -n SRX4554697.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554697.05 # format = BAM # ChIP-seq file = ['SRX4554697.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 23:07:23: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:07:23: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:07:28: 1000000 INFO @ Tue, 09 Oct 2018 23:07:28: 1000000 INFO @ Tue, 09 Oct 2018 23:07:28: 1000000 INFO @ Tue, 09 Oct 2018 23:07:33: 2000000 INFO @ Tue, 09 Oct 2018 23:07:33: 2000000 INFO @ Tue, 09 Oct 2018 23:07:33: 2000000 INFO @ Tue, 09 Oct 2018 23:07:37: 3000000 INFO @ Tue, 09 Oct 2018 23:07:37: 3000000 INFO @ Tue, 09 Oct 2018 23:07:38: 3000000 INFO @ Tue, 09 Oct 2018 23:07:42: 4000000 INFO @ Tue, 09 Oct 2018 23:07:42: 4000000 INFO @ Tue, 09 Oct 2018 23:07:43: 4000000 INFO @ Tue, 09 Oct 2018 23:07:47: 5000000 INFO @ Tue, 09 Oct 2018 23:07:47: 5000000 INFO @ Tue, 09 Oct 2018 23:07:48: 5000000 INFO @ Tue, 09 Oct 2018 23:07:51: 6000000 INFO @ Tue, 09 Oct 2018 23:07:53: 6000000 INFO @ Tue, 09 Oct 2018 23:07:53: 6000000 INFO @ Tue, 09 Oct 2018 23:07:56: 7000000 INFO @ Tue, 09 Oct 2018 23:07:58: 7000000 INFO @ Tue, 09 Oct 2018 23:07:59: 7000000 INFO @ Tue, 09 Oct 2018 23:08:01: 8000000 INFO @ Tue, 09 Oct 2018 23:08:03: 8000000 INFO @ Tue, 09 Oct 2018 23:08:04: 8000000 INFO @ Tue, 09 Oct 2018 23:08:05: 9000000 INFO @ Tue, 09 Oct 2018 23:08:08: 9000000 INFO @ Tue, 09 Oct 2018 23:08:09: 9000000 INFO @ Tue, 09 Oct 2018 23:08:10: 10000000 INFO @ Tue, 09 Oct 2018 23:08:13: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:08:13: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:08:13: #1 total tags in treatment: 2955369 INFO @ Tue, 09 Oct 2018 23:08:13: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:08:13: #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 23:08:13: #1 tags after filtering in treatment: 1959026 INFO @ Tue, 09 Oct 2018 23:08:13: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:08:13: #1 finished! INFO @ Tue, 09 Oct 2018 23:08:13: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:08:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:08:13: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:08:13: 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 23:08:13: Process for pairing-model is terminated! cat: SRX4554697.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Tue, 09 Oct 2018 23:08:13: 10000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554697.05_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 `SRX4554697.05_*.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 `SRX4554697.05_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 23:08:14: 10000000 INFO @ Tue, 09 Oct 2018 23:08:16: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:08:16: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:08:16: #1 total tags in treatment: 2955369 INFO @ Tue, 09 Oct 2018 23:08:16: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:08:16: #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 23:08:16: #1 tags after filtering in treatment: 1959026 INFO @ Tue, 09 Oct 2018 23:08:16: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:08:16: #1 finished! INFO @ Tue, 09 Oct 2018 23:08:16: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:08:16: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:08:16: 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 23:08:16: Process for pairing-model is terminated! cat: SRX4554697.20_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 `SRX4554697.20_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 `SRX4554697.20_*.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 `SRX4554697.20_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 23:08:17: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:08:17: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:08:17: #1 total tags in treatment: 2955369 INFO @ Tue, 09 Oct 2018 23:08:17: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:08:17: #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 23:08:17: #1 tags after filtering in treatment: 1959026 INFO @ Tue, 09 Oct 2018 23:08:17: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:08:17: #1 finished! INFO @ Tue, 09 Oct 2018 23:08:17: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:08:17: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:08:17: 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 23:08:17: Process for pairing-model is terminated! cat: SRX4554697.10_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 `SRX4554697.10_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 `SRX4554697.10_*.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 `SRX4554697.10_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。