Job ID = 11244993 sra ファイルのダウンロード中... Completed: 198764K bytes transferred in 7 seconds (214568K 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 5943055 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554707/SRR7696380.sra Written 5943055 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554707/SRR7696380.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: 00:03:34 5943055 reads; of these: 5943055 (100.00%) were paired; of these: 2998379 (50.45%) aligned concordantly 0 times 1717036 (28.89%) aligned concordantly exactly 1 time 1227640 (20.66%) aligned concordantly >1 times ---- 2998379 pairs aligned concordantly 0 times; of these: 978 (0.03%) aligned discordantly 1 time ---- 2997401 pairs aligned 0 times concordantly or discordantly; of these: 5994802 mates make up the pairs; of these: 3911905 (65.25%) aligned 0 times 1308206 (21.82%) aligned exactly 1 time 774691 (12.92%) aligned >1 times 67.09% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 814871 / 2945359 = 0.2767 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 23:07:12: # Command line: callpeak -t SRX4554707.bam -f BAM -g 12100000 -n SRX4554707.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554707.05 # format = BAM # ChIP-seq file = ['SRX4554707.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 23:07:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:07:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:07:12: # Command line: callpeak -t SRX4554707.bam -f BAM -g 12100000 -n SRX4554707.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554707.20 # format = BAM # ChIP-seq file = ['SRX4554707.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 23:07:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:07:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:07:12: # Command line: callpeak -t SRX4554707.bam -f BAM -g 12100000 -n SRX4554707.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554707.10 # format = BAM # ChIP-seq file = ['SRX4554707.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 23:07:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:07:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:07:18: 1000000 INFO @ Tue, 09 Oct 2018 23:07:18: 1000000 INFO @ Tue, 09 Oct 2018 23:07:18: 1000000 INFO @ Tue, 09 Oct 2018 23:07:23: 2000000 INFO @ Tue, 09 Oct 2018 23:07:24: 2000000 INFO @ Tue, 09 Oct 2018 23:07:24: 2000000 INFO @ Tue, 09 Oct 2018 23:07:28: 3000000 INFO @ Tue, 09 Oct 2018 23:07:30: 3000000 INFO @ Tue, 09 Oct 2018 23:07:30: 3000000 INFO @ Tue, 09 Oct 2018 23:07:33: 4000000 INFO @ Tue, 09 Oct 2018 23:07:35: 4000000 INFO @ Tue, 09 Oct 2018 23:07:35: 4000000 INFO @ Tue, 09 Oct 2018 23:07:37: 5000000 INFO @ Tue, 09 Oct 2018 23:07:40: 5000000 INFO @ Tue, 09 Oct 2018 23:07:40: 5000000 INFO @ Tue, 09 Oct 2018 23:07:43: 6000000 INFO @ Tue, 09 Oct 2018 23:07:44: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:07:44: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:07:44: #1 total tags in treatment: 2129811 INFO @ Tue, 09 Oct 2018 23:07:44: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:07:44: #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 23:07:44: #1 tags after filtering in treatment: 1277023 INFO @ Tue, 09 Oct 2018 23:07:44: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 23:07:44: #1 finished! INFO @ Tue, 09 Oct 2018 23:07:44: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:07:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:07:45: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 23:07:45: Too few paired peaks (28) 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 23:07:45: Process for pairing-model is terminated! cat: SRX4554707.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554707.05_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 `SRX4554707.05_*.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 `SRX4554707.05_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 23:07:46: 6000000 INFO @ Tue, 09 Oct 2018 23:07:46: 6000000 INFO @ Tue, 09 Oct 2018 23:07:48: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:07:48: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:07:48: #1 total tags in treatment: 2129811 INFO @ Tue, 09 Oct 2018 23:07:48: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:07:48: #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 23:07:48: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:07:48: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:07:48: #1 total tags in treatment: 2129811 INFO @ Tue, 09 Oct 2018 23:07:48: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:07:48: #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 23:07:48: #1 tags after filtering in treatment: 1277023 INFO @ Tue, 09 Oct 2018 23:07:48: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 23:07:48: #1 finished! INFO @ Tue, 09 Oct 2018 23:07:48: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:07:48: #1 tags after filtering in treatment: 1277023 INFO @ Tue, 09 Oct 2018 23:07:48: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 23:07:48: #1 finished! INFO @ Tue, 09 Oct 2018 23:07:48: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:07:48: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 23:07:48: Too few paired peaks (28) 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 23:07:48: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:07:48: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 23:07:48: Too few paired peaks (28) 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 23:07:48: Process for pairing-model is terminated! cat: SRX4554707.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4554707.20_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 `SRX4554707.10_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 `SRX4554707.10_*.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 `SRX4554707.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554707.20_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 `SRX4554707.20_*.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 `SRX4554707.20_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。