Job ID = 10937503 sra ファイルのダウンロード中... Completed: 427118K bytes transferred in 20 seconds (166673K 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 4550175 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010310/SRR5833303.sra Written 4550175 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010310/SRR5833303.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: 00:05:32 4550175 reads; of these: 4550175 (100.00%) were paired; of these: 336116 (7.39%) aligned concordantly 0 times 3353500 (73.70%) aligned concordantly exactly 1 time 860559 (18.91%) aligned concordantly >1 times ---- 336116 pairs aligned concordantly 0 times; of these: 47217 (14.05%) aligned discordantly 1 time ---- 288899 pairs aligned 0 times concordantly or discordantly; of these: 577798 mates make up the pairs; of these: 487780 (84.42%) aligned 0 times 52005 (9.00%) aligned exactly 1 time 38013 (6.58%) aligned >1 times 94.64% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 126833 / 4239952 = 0.0299 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 @ Fri, 10 Aug 2018 02:31:43: # Command line: callpeak -t SRX3010310.bam -f BAM -g 12100000 -n SRX3010310.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010310.20 # format = BAM # ChIP-seq file = ['SRX3010310.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 @ Fri, 10 Aug 2018 02:31:43: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:43: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:43: # Command line: callpeak -t SRX3010310.bam -f BAM -g 12100000 -n SRX3010310.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010310.05 # format = BAM # ChIP-seq file = ['SRX3010310.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 @ Fri, 10 Aug 2018 02:31:43: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:43: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:43: # Command line: callpeak -t SRX3010310.bam -f BAM -g 12100000 -n SRX3010310.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010310.10 # format = BAM # ChIP-seq file = ['SRX3010310.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 @ Fri, 10 Aug 2018 02:31:43: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:43: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:50: 1000000 INFO @ Fri, 10 Aug 2018 02:31:51: 1000000 INFO @ Fri, 10 Aug 2018 02:31:51: 1000000 INFO @ Fri, 10 Aug 2018 02:31:58: 2000000 INFO @ Fri, 10 Aug 2018 02:31:58: 2000000 INFO @ Fri, 10 Aug 2018 02:31:59: 2000000 INFO @ Fri, 10 Aug 2018 02:32:05: 3000000 INFO @ Fri, 10 Aug 2018 02:32:06: 3000000 INFO @ Fri, 10 Aug 2018 02:32:06: 3000000 INFO @ Fri, 10 Aug 2018 02:32:13: 4000000 INFO @ Fri, 10 Aug 2018 02:32:14: 4000000 INFO @ Fri, 10 Aug 2018 02:32:14: 4000000 INFO @ Fri, 10 Aug 2018 02:32:20: 5000000 INFO @ Fri, 10 Aug 2018 02:32:22: 5000000 INFO @ Fri, 10 Aug 2018 02:32:23: 5000000 INFO @ Fri, 10 Aug 2018 02:32:27: 6000000 INFO @ Fri, 10 Aug 2018 02:32:30: 6000000 INFO @ Fri, 10 Aug 2018 02:32:31: 6000000 INFO @ Fri, 10 Aug 2018 02:32:35: 7000000 INFO @ Fri, 10 Aug 2018 02:32:39: 7000000 INFO @ Fri, 10 Aug 2018 02:32:40: 7000000 INFO @ Fri, 10 Aug 2018 02:32:42: 8000000 INFO @ Fri, 10 Aug 2018 02:32:45: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:45: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:45: #1 total tags in treatment: 4087370 INFO @ Fri, 10 Aug 2018 02:32:45: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:32:45: #1 tags after filtering in treatment: 3260020 INFO @ Fri, 10 Aug 2018 02:32:45: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Aug 2018 02:32:45: #1 finished! INFO @ Fri, 10 Aug 2018 02:32:45: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:32:45: #2 number of paired peaks: 50 WARNING @ Fri, 10 Aug 2018 02:32:45: Too few paired peaks (50) 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 @ Fri, 10 Aug 2018 02:32:45: Process for pairing-model is terminated! cat: SRX3010310.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010310.05_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 `SRX3010310.05_*.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 `SRX3010310.05_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 @ Fri, 10 Aug 2018 02:32:47: 8000000 INFO @ Fri, 10 Aug 2018 02:32:48: 8000000 INFO @ Fri, 10 Aug 2018 02:32:49: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:49: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:49: #1 total tags in treatment: 4087370 INFO @ Fri, 10 Aug 2018 02:32:49: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:32:49: #1 tags after filtering in treatment: 3260020 INFO @ Fri, 10 Aug 2018 02:32:49: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Aug 2018 02:32:49: #1 finished! INFO @ Fri, 10 Aug 2018 02:32:49: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:32:50: #2 number of paired peaks: 50 WARNING @ Fri, 10 Aug 2018 02:32:50: Too few paired peaks (50) 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 @ Fri, 10 Aug 2018 02:32:50: Process for pairing-model is terminated! cat: SRX3010310.10_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 `SRX3010310.10_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 `SRX3010310.10_*.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 `SRX3010310.10_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 @ Fri, 10 Aug 2018 02:32:51: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:51: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:51: #1 total tags in treatment: 4087370 INFO @ Fri, 10 Aug 2018 02:32:51: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:32:51: #1 tags after filtering in treatment: 3260020 INFO @ Fri, 10 Aug 2018 02:32:51: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Aug 2018 02:32:51: #1 finished! INFO @ Fri, 10 Aug 2018 02:32:51: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:32:51: #2 number of paired peaks: 50 WARNING @ Fri, 10 Aug 2018 02:32:51: Too few paired peaks (50) 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 @ Fri, 10 Aug 2018 02:32:51: Process for pairing-model is terminated! cat: SRX3010310.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010310.20_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 `SRX3010310.20_*.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 `SRX3010310.20_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。