Job ID = 11193159 sra ファイルのダウンロード中... Completed: 281659K bytes transferred in 5 seconds (402501K 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 7801564 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337751/SRR7467852.sra Written 7801564 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337751/SRR7467852.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: 00:01:40 7801564 reads; of these: 7801564 (100.00%) were paired; of these: 7374618 (94.53%) aligned concordantly 0 times 344251 (4.41%) aligned concordantly exactly 1 time 82695 (1.06%) aligned concordantly >1 times ---- 7374618 pairs aligned concordantly 0 times; of these: 137846 (1.87%) aligned discordantly 1 time ---- 7236772 pairs aligned 0 times concordantly or discordantly; of these: 14473544 mates make up the pairs; of these: 13520964 (93.42%) aligned 0 times 789059 (5.45%) aligned exactly 1 time 163521 (1.13%) aligned >1 times 13.34% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 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] 158373 / 557290 = 0.2842 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 11:05:05: # Command line: callpeak -t SRX4337751.bam -f BAM -g 12100000 -n SRX4337751.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337751.10 # format = BAM # ChIP-seq file = ['SRX4337751.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 11:05:05: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:05:05: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:05:05: # Command line: callpeak -t SRX4337751.bam -f BAM -g 12100000 -n SRX4337751.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337751.05 # format = BAM # ChIP-seq file = ['SRX4337751.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 11:05:05: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:05:05: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:05:05: # Command line: callpeak -t SRX4337751.bam -f BAM -g 12100000 -n SRX4337751.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337751.20 # format = BAM # ChIP-seq file = ['SRX4337751.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 11:05:05: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:05:05: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:05:11: 1000000 INFO @ Sat, 15 Sep 2018 11:05:11: 1000000 INFO @ Sat, 15 Sep 2018 11:05:11: 1000000 INFO @ Sat, 15 Sep 2018 11:05:15: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:05:15: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:05:15: #1 total tags in treatment: 315444 INFO @ Sat, 15 Sep 2018 11:05:15: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:15: #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 11:05:15: #1 tags after filtering in treatment: 291172 INFO @ Sat, 15 Sep 2018 11:05:15: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 11:05:15: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:15: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:15: #2 number of paired peaks: 65 WARNING @ Sat, 15 Sep 2018 11:05:15: Too few paired peaks (65) 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 11:05:15: Process for pairing-model is terminated! cat: SRX4337751.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4337751.10_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 `SRX4337751.10_*.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 `SRX4337751.10_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 @ Sat, 15 Sep 2018 11:05:15: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:05:15: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:05:15: #1 total tags in treatment: 315444 INFO @ Sat, 15 Sep 2018 11:05:15: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:15: #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 11:05:15: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:05:15: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:05:15: #1 total tags in treatment: 315444 INFO @ Sat, 15 Sep 2018 11:05:15: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:15: #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 11:05:15: #1 tags after filtering in treatment: 291172 INFO @ Sat, 15 Sep 2018 11:05:15: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 11:05:15: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:15: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:15: #1 tags after filtering in treatment: 291172 INFO @ Sat, 15 Sep 2018 11:05:15: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 11:05:15: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:15: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:15: #2 number of paired peaks: 65 WARNING @ Sat, 15 Sep 2018 11:05:15: Too few paired peaks (65) 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 11:05:15: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 11:05:15: #2 number of paired peaks: 65 WARNING @ Sat, 15 Sep 2018 11:05:15: Too few paired peaks (65) 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 11:05:15: Process for pairing-model is terminated! cat: SRX4337751.20_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: SRX4337751.05_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) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4337751.20_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 `SRX4337751.20_*.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 `SRX4337751.20_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 `SRX4337751.05_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 `SRX4337751.05_*.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 `SRX4337751.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。