Job ID = 11162629 sra ファイルのダウンロード中... Completed: 114416K bytes transferred in 5 seconds (164392K 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 2670756 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709365/SRR6736417.sra Written 2670756 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709365/SRR6736417.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:25 2670756 reads; of these: 2670756 (100.00%) were paired; of these: 679807 (25.45%) aligned concordantly 0 times 1732378 (64.86%) aligned concordantly exactly 1 time 258571 (9.68%) aligned concordantly >1 times ---- 679807 pairs aligned concordantly 0 times; of these: 3346 (0.49%) aligned discordantly 1 time ---- 676461 pairs aligned 0 times concordantly or discordantly; of these: 1352922 mates make up the pairs; of these: 1236602 (91.40%) aligned 0 times 98485 (7.28%) aligned exactly 1 time 17835 (1.32%) aligned >1 times 76.85% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 422335 / 1992734 = 0.2119 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 @ Wed, 05 Sep 2018 10:38:45: # Command line: callpeak -t SRX3709365.bam -f BAM -g 12100000 -n SRX3709365.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3709365.10 # format = BAM # ChIP-seq file = ['SRX3709365.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 @ Wed, 05 Sep 2018 10:38:45: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:38:45: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:38:45: # Command line: callpeak -t SRX3709365.bam -f BAM -g 12100000 -n SRX3709365.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3709365.20 # format = BAM # ChIP-seq file = ['SRX3709365.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 @ Wed, 05 Sep 2018 10:38:45: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:38:45: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:38:45: # Command line: callpeak -t SRX3709365.bam -f BAM -g 12100000 -n SRX3709365.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3709365.05 # format = BAM # ChIP-seq file = ['SRX3709365.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 @ Wed, 05 Sep 2018 10:38:45: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:38:45: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:38:52: 1000000 INFO @ Wed, 05 Sep 2018 10:38:53: 1000000 INFO @ Wed, 05 Sep 2018 10:38:53: 1000000 INFO @ Wed, 05 Sep 2018 10:38:59: 2000000 INFO @ Wed, 05 Sep 2018 10:39:01: 2000000 INFO @ Wed, 05 Sep 2018 10:39:01: 2000000 INFO @ Wed, 05 Sep 2018 10:39:06: 3000000 INFO @ Wed, 05 Sep 2018 10:39:08: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:39:08: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:39:08: #1 total tags in treatment: 1569285 INFO @ Wed, 05 Sep 2018 10:39:08: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:39:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:39:08: #1 tags after filtering in treatment: 1433997 INFO @ Wed, 05 Sep 2018 10:39:08: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 05 Sep 2018 10:39:08: #1 finished! INFO @ Wed, 05 Sep 2018 10:39:08: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:39:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:39:08: #2 number of paired peaks: 38 WARNING @ Wed, 05 Sep 2018 10:39:08: Too few paired peaks (38) 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 @ Wed, 05 Sep 2018 10:39:08: Process for pairing-model is terminated! cat: SRX3709365.10_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 `SRX3709365.10_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 `SRX3709365.10_*.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 `SRX3709365.10_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 @ Wed, 05 Sep 2018 10:39:09: 3000000 INFO @ Wed, 05 Sep 2018 10:39:09: 3000000 INFO @ Wed, 05 Sep 2018 10:39:11: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:39:11: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:39:11: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:39:11: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:39:11: #1 total tags in treatment: 1569285 INFO @ Wed, 05 Sep 2018 10:39:11: #1 total tags in treatment: 1569285 INFO @ Wed, 05 Sep 2018 10:39:11: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:39:11: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:39:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:39:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:39:11: #1 tags after filtering in treatment: 1433997 INFO @ Wed, 05 Sep 2018 10:39:11: #1 tags after filtering in treatment: 1433997 INFO @ Wed, 05 Sep 2018 10:39:11: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 05 Sep 2018 10:39:11: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 05 Sep 2018 10:39:11: #1 finished! INFO @ Wed, 05 Sep 2018 10:39:11: #1 finished! INFO @ Wed, 05 Sep 2018 10:39:11: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:39:11: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:39:11: #2 number of paired peaks: 38 INFO @ Wed, 05 Sep 2018 10:39:11: #2 number of paired peaks: 38 WARNING @ Wed, 05 Sep 2018 10:39:11: Too few paired peaks (38) 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 @ Wed, 05 Sep 2018 10:39:11: Too few paired peaks (38) 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 @ Wed, 05 Sep 2018 10:39:11: Process for pairing-model is terminated! WARNING @ Wed, 05 Sep 2018 10:39:11: Process for pairing-model is terminated! cat: SRX3709365.20_peaks.narrowPeakcat: SRX3709365.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません : 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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3709365.20_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 `SRX3709365.05_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 `SRX3709365.20_*.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 `SRX3709365.05_*.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 `SRX3709365.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX3709365.05_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 CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。