Job ID = 11245049 sra ファイルのダウンロード中... Completed: 245298K bytes transferred in 8 seconds (223391K 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 7870745 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554761/SRR7696434.sra Written 7870745 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554761/SRR7696434.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: 00:03:23 7870745 reads; of these: 7870745 (100.00%) were paired; of these: 5040459 (64.04%) aligned concordantly 0 times 2074282 (26.35%) aligned concordantly exactly 1 time 756004 (9.61%) aligned concordantly >1 times ---- 5040459 pairs aligned concordantly 0 times; of these: 7718 (0.15%) aligned discordantly 1 time ---- 5032741 pairs aligned 0 times concordantly or discordantly; of these: 10065482 mates make up the pairs; of these: 8347408 (82.93%) aligned 0 times 1252441 (12.44%) aligned exactly 1 time 465633 (4.63%) aligned >1 times 46.97% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 354929 / 2837329 = 0.1251 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 23:19:01: # Command line: callpeak -t SRX4554761.bam -f BAM -g 12100000 -n SRX4554761.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554761.10 # format = BAM # ChIP-seq file = ['SRX4554761.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 23:19:01: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:19:01: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:19:01: # Command line: callpeak -t SRX4554761.bam -f BAM -g 12100000 -n SRX4554761.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554761.20 # format = BAM # ChIP-seq file = ['SRX4554761.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 23:19:01: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:19:01: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:19:01: # Command line: callpeak -t SRX4554761.bam -f BAM -g 12100000 -n SRX4554761.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554761.05 # format = BAM # ChIP-seq file = ['SRX4554761.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 23:19:01: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:19:01: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:19:06: 1000000 INFO @ Tue, 09 Oct 2018 23:19:06: 1000000 INFO @ Tue, 09 Oct 2018 23:19:06: 1000000 INFO @ Tue, 09 Oct 2018 23:19:11: 2000000 INFO @ Tue, 09 Oct 2018 23:19:11: 2000000 INFO @ Tue, 09 Oct 2018 23:19:11: 2000000 INFO @ Tue, 09 Oct 2018 23:19:16: 3000000 INFO @ Tue, 09 Oct 2018 23:19:16: 3000000 INFO @ Tue, 09 Oct 2018 23:19:17: 3000000 INFO @ Tue, 09 Oct 2018 23:19:21: 4000000 INFO @ Tue, 09 Oct 2018 23:19:21: 4000000 INFO @ Tue, 09 Oct 2018 23:19:22: 4000000 INFO @ Tue, 09 Oct 2018 23:19:26: 5000000 INFO @ Tue, 09 Oct 2018 23:19:26: 5000000 INFO @ Tue, 09 Oct 2018 23:19:27: 5000000 INFO @ Tue, 09 Oct 2018 23:19:31: 6000000 INFO @ Tue, 09 Oct 2018 23:19:32: 6000000 INFO @ Tue, 09 Oct 2018 23:19:32: 6000000 INFO @ Tue, 09 Oct 2018 23:19:34: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:34: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:34: #1 total tags in treatment: 2475402 INFO @ Tue, 09 Oct 2018 23:19:34: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:34: #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 23:19:34: #1 tags after filtering in treatment: 1642409 INFO @ Tue, 09 Oct 2018 23:19:34: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:19:34: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:34: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:34: #2 number of paired peaks: 44 WARNING @ Tue, 09 Oct 2018 23:19:34: Too few paired peaks (44) 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 23:19:34: Process for pairing-model is terminated! cat: SRX4554761.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554761.10_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 `SRX4554761.10_*.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 `SRX4554761.10_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 23:19:35: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:35: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:35: #1 total tags in treatment: 2475402 INFO @ Tue, 09 Oct 2018 23:19:35: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:35: #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 23:19:35: #1 tags after filtering in treatment: 1642409 INFO @ Tue, 09 Oct 2018 23:19:35: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:19:35: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:35: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:35: #2 number of paired peaks: 44 WARNING @ Tue, 09 Oct 2018 23:19:35: Too few paired peaks (44) 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 23:19:35: Process for pairing-model is terminated! cat: SRX4554761.05_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 `SRX4554761.05_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 `SRX4554761.05_*.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 `SRX4554761.05_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 23:19:36: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:36: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:36: #1 total tags in treatment: 2475402 INFO @ Tue, 09 Oct 2018 23:19:36: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:36: #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 23:19:36: #1 tags after filtering in treatment: 1642409 INFO @ Tue, 09 Oct 2018 23:19:36: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:19:36: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:36: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:36: #2 number of paired peaks: 44 WARNING @ Tue, 09 Oct 2018 23:19:36: Too few paired peaks (44) 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 23:19:36: Process for pairing-model is terminated! cat: SRX4554761.20_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 `SRX4554761.20_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 `SRX4554761.20_*.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 `SRX4554761.20_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。