Job ID = 11245001 sra ファイルのダウンロード中... Completed: 265572K bytes transferred in 8 seconds (268657K 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 7881965 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554713/SRR7696386.sra Written 7881965 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554713/SRR7696386.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: 00:04:31 7881965 reads; of these: 7881965 (100.00%) were paired; of these: 4410363 (55.96%) aligned concordantly 0 times 2116711 (26.86%) aligned concordantly exactly 1 time 1354891 (17.19%) aligned concordantly >1 times ---- 4410363 pairs aligned concordantly 0 times; of these: 1348 (0.03%) aligned discordantly 1 time ---- 4409015 pairs aligned 0 times concordantly or discordantly; of these: 8818030 mates make up the pairs; of these: 5784341 (65.60%) aligned 0 times 1970073 (22.34%) aligned exactly 1 time 1063616 (12.06%) aligned >1 times 63.31% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 870215 / 3472488 = 0.2506 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 23:11:02: # Command line: callpeak -t SRX4554713.bam -f BAM -g 12100000 -n SRX4554713.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554713.05 # format = BAM # ChIP-seq file = ['SRX4554713.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 23:11:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:11:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:11:02: # Command line: callpeak -t SRX4554713.bam -f BAM -g 12100000 -n SRX4554713.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554713.20 # format = BAM # ChIP-seq file = ['SRX4554713.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 23:11:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:11:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:11:02: # Command line: callpeak -t SRX4554713.bam -f BAM -g 12100000 -n SRX4554713.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554713.10 # format = BAM # ChIP-seq file = ['SRX4554713.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 23:11:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:11:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:11:07: 1000000 INFO @ Tue, 09 Oct 2018 23:11:07: 1000000 INFO @ Tue, 09 Oct 2018 23:11:07: 1000000 INFO @ Tue, 09 Oct 2018 23:11:13: 2000000 INFO @ Tue, 09 Oct 2018 23:11:13: 2000000 INFO @ Tue, 09 Oct 2018 23:11:13: 2000000 INFO @ Tue, 09 Oct 2018 23:11:18: 3000000 INFO @ Tue, 09 Oct 2018 23:11:18: 3000000 INFO @ Tue, 09 Oct 2018 23:11:19: 3000000 INFO @ Tue, 09 Oct 2018 23:11:23: 4000000 INFO @ Tue, 09 Oct 2018 23:11:24: 4000000 INFO @ Tue, 09 Oct 2018 23:11:24: 4000000 INFO @ Tue, 09 Oct 2018 23:11:28: 5000000 INFO @ Tue, 09 Oct 2018 23:11:29: 5000000 INFO @ Tue, 09 Oct 2018 23:11:29: 5000000 INFO @ Tue, 09 Oct 2018 23:11:34: 6000000 INFO @ Tue, 09 Oct 2018 23:11:34: 6000000 INFO @ Tue, 09 Oct 2018 23:11:34: 6000000 INFO @ Tue, 09 Oct 2018 23:11:39: 7000000 INFO @ Tue, 09 Oct 2018 23:11:40: 7000000 INFO @ Tue, 09 Oct 2018 23:11:40: 7000000 INFO @ Tue, 09 Oct 2018 23:11:45: 8000000 INFO @ Tue, 09 Oct 2018 23:11:45: 8000000 INFO @ Tue, 09 Oct 2018 23:11:45: 8000000 INFO @ Tue, 09 Oct 2018 23:11:46: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:46: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:46: #1 total tags in treatment: 2601394 INFO @ Tue, 09 Oct 2018 23:11:46: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:46: #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 23:11:46: #1 tags after filtering in treatment: 1538601 INFO @ Tue, 09 Oct 2018 23:11:46: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:11:46: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:46: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:46: #2 number of paired peaks: 32 WARNING @ Tue, 09 Oct 2018 23:11:46: Too few paired peaks (32) 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 23:11:46: Process for pairing-model is terminated! cat: SRX4554713.20_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 `SRX4554713.20_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 `SRX4554713.20_*.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 `SRX4554713.20_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 INFO @ Tue, 09 Oct 2018 23:11:47: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:47: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:47: #1 total tags in treatment: 2601394 INFO @ Tue, 09 Oct 2018 23:11:47: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:47: #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 23:11:47: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:47: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:47: #1 total tags in treatment: 2601394 INFO @ Tue, 09 Oct 2018 23:11:47: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:47: #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 23:11:47: #1 tags after filtering in treatment: 1538601 INFO @ Tue, 09 Oct 2018 23:11:47: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:11:47: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:47: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:47: #1 tags after filtering in treatment: 1538601 INFO @ Tue, 09 Oct 2018 23:11:47: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:11:47: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:47: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:47: #2 number of paired peaks: 32 WARNING @ Tue, 09 Oct 2018 23:11:47: Too few paired peaks (32) 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 23:11:47: Process for pairing-model is terminated! cat: SRX4554713.05_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 `SRX4554713.05_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 `SRX4554713.05_*.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 `SRX4554713.05_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 23:11:47: #2 number of paired peaks: 32 WARNING @ Tue, 09 Oct 2018 23:11:47: Too few paired peaks (32) 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 23:11:47: Process for pairing-model is terminated! cat: SRX4554713.10_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 `SRX4554713.10_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 `SRX4554713.10_*.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 `SRX4554713.10_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。