Job ID = 11193195 sra ファイルのダウンロード中... Completed: 360141K bytes transferred in 10 seconds (275695K 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 8247581 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876285/SRR1802388.sra Written 8247581 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876285/SRR1802388.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: 00:03:52 8247581 reads; of these: 8247581 (100.00%) were paired; of these: 4073134 (49.39%) aligned concordantly 0 times 3506321 (42.51%) aligned concordantly exactly 1 time 668126 (8.10%) aligned concordantly >1 times ---- 4073134 pairs aligned concordantly 0 times; of these: 105177 (2.58%) aligned discordantly 1 time ---- 3967957 pairs aligned 0 times concordantly or discordantly; of these: 7935914 mates make up the pairs; of these: 7727011 (97.37%) aligned 0 times 131192 (1.65%) aligned exactly 1 time 77711 (0.98%) aligned >1 times 53.16% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 2096359 / 4250696 = 0.4932 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 @ Sat, 15 Sep 2018 11:13:26: # Command line: callpeak -t SRX876285.bam -f BAM -g 12100000 -n SRX876285.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876285.10 # format = BAM # ChIP-seq file = ['SRX876285.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 @ Sat, 15 Sep 2018 11:13:26: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:26: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:26: # Command line: callpeak -t SRX876285.bam -f BAM -g 12100000 -n SRX876285.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876285.20 # format = BAM # ChIP-seq file = ['SRX876285.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 @ Sat, 15 Sep 2018 11:13:26: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:26: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:26: # Command line: callpeak -t SRX876285.bam -f BAM -g 12100000 -n SRX876285.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876285.05 # format = BAM # ChIP-seq file = ['SRX876285.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 @ Sat, 15 Sep 2018 11:13:26: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:26: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:35: 1000000 INFO @ Sat, 15 Sep 2018 11:13:35: 1000000 INFO @ Sat, 15 Sep 2018 11:13:35: 1000000 INFO @ Sat, 15 Sep 2018 11:13:42: 2000000 INFO @ Sat, 15 Sep 2018 11:13:43: 2000000 INFO @ Sat, 15 Sep 2018 11:13:43: 2000000 INFO @ Sat, 15 Sep 2018 11:13:50: 3000000 INFO @ Sat, 15 Sep 2018 11:13:51: 3000000 INFO @ Sat, 15 Sep 2018 11:13:51: 3000000 INFO @ Sat, 15 Sep 2018 11:13:57: 4000000 INFO @ Sat, 15 Sep 2018 11:13:59: 4000000 INFO @ Sat, 15 Sep 2018 11:13:59: 4000000 INFO @ Sat, 15 Sep 2018 11:14:02: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:14:02: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:14:02: #1 total tags in treatment: 2125741 INFO @ Sat, 15 Sep 2018 11:14:02: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:14:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:14:02: #1 tags after filtering in treatment: 1741123 INFO @ Sat, 15 Sep 2018 11:14:02: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Sep 2018 11:14:02: #1 finished! INFO @ Sat, 15 Sep 2018 11:14:02: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:14:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:14:02: #2 number of paired peaks: 38 WARNING @ Sat, 15 Sep 2018 11:14:02: 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 @ Sat, 15 Sep 2018 11:14:02: Process for pairing-model is terminated! cat: SRX876285.05_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 `SRX876285.05_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 `SRX876285.05_*.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 `SRX876285.05_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 @ Sat, 15 Sep 2018 11:14:04: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:14:04: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:14:04: #1 total tags in treatment: 2125741 INFO @ Sat, 15 Sep 2018 11:14:04: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:14:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:14:04: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:14:04: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:14:04: #1 total tags in treatment: 2125741 INFO @ Sat, 15 Sep 2018 11:14:04: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:14:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:14:04: #1 tags after filtering in treatment: 1741123 INFO @ Sat, 15 Sep 2018 11:14:04: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Sep 2018 11:14:04: #1 finished! INFO @ Sat, 15 Sep 2018 11:14:04: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:14:04: #1 tags after filtering in treatment: 1741123 INFO @ Sat, 15 Sep 2018 11:14:04: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Sep 2018 11:14:04: #1 finished! INFO @ Sat, 15 Sep 2018 11:14:04: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:14:04: #2 number of paired peaks: 38 WARNING @ Sat, 15 Sep 2018 11:14:04: 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 @ Sat, 15 Sep 2018 11:14:04: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 11:14:04: #2 number of paired peaks: 38 WARNING @ Sat, 15 Sep 2018 11:14:04: 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 @ Sat, 15 Sep 2018 11:14:04: Process for pairing-model is terminated! cat: SRX876285.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX876285.10_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) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX876285.20_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 `SRX876285.20_*.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 `SRX876285.20_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 rm: cannot remove `SRX876285.10_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 `SRX876285.10_*.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 `SRX876285.10_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。