Job ID = 9160041 sra ファイルのダウンロード中... Completed: 43021K bytes transferred in 3 seconds (94388K bits/sec), in 1 file, 2 directories. 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... Written 1534983 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2574978/SRR5270927.sra Written 1534983 spots total 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: 00:00:48 1534983 reads; of these: 1534983 (100.00%) were paired; of these: 90782 (5.91%) aligned concordantly 0 times 1253703 (81.68%) aligned concordantly exactly 1 time 190498 (12.41%) aligned concordantly >1 times ---- 90782 pairs aligned concordantly 0 times; of these: 11562 (12.74%) aligned discordantly 1 time ---- 79220 pairs aligned 0 times concordantly or discordantly; of these: 158440 mates make up the pairs; of these: 117570 (74.20%) aligned 0 times 31780 (20.06%) aligned exactly 1 time 9090 (5.74%) aligned >1 times 96.17% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 17336 / 1449989 = 0.0120 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, 28 Jun 2017 01:45:56: # Command line: callpeak -t SRX2574978.bam -f BAM -g 12100000 -n SRX2574978.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2574978.10 # format = BAM # ChIP-seq file = ['SRX2574978.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, 28 Jun 2017 01:45:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:56: # Command line: callpeak -t SRX2574978.bam -f BAM -g 12100000 -n SRX2574978.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2574978.20 # format = BAM # ChIP-seq file = ['SRX2574978.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, 28 Jun 2017 01:45:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:56: # Command line: callpeak -t SRX2574978.bam -f BAM -g 12100000 -n SRX2574978.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2574978.05 # format = BAM # ChIP-seq file = ['SRX2574978.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, 28 Jun 2017 01:45:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:46:01: 1000000 INFO @ Wed, 28 Jun 2017 01:46:01: 1000000 INFO @ Wed, 28 Jun 2017 01:46:02: 1000000 INFO @ Wed, 28 Jun 2017 01:46:07: 2000000 INFO @ Wed, 28 Jun 2017 01:46:07: 2000000 INFO @ Wed, 28 Jun 2017 01:46:07: 2000000 INFO @ Wed, 28 Jun 2017 01:46:11: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:46:11: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:46:11: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:46:11: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:46:11: #1 total tags in treatment: 1426883 INFO @ Wed, 28 Jun 2017 01:46:11: #1 total tags in treatment: 1426883 INFO @ Wed, 28 Jun 2017 01:46:11: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:46:11: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:46:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:46:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:46:11: #1 tags after filtering in treatment: 1325169 INFO @ Wed, 28 Jun 2017 01:46:11: #1 tags after filtering in treatment: 1325169 INFO @ Wed, 28 Jun 2017 01:46:11: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:46:11: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:46:11: #1 finished! INFO @ Wed, 28 Jun 2017 01:46:11: #1 finished! INFO @ Wed, 28 Jun 2017 01:46:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:46:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:46:11: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 01:46:11: Too few paired peaks (39) 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, 28 Jun 2017 01:46:11: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 01:46:11: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 01:46:11: Too few paired peaks (39) 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, 28 Jun 2017 01:46:11: Process for pairing-model is terminated! cat: SRX2574978.20_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: SRX2574978.10_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 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 `SRX2574978.10_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 `SRX2574978.10_*.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 `SRX2574978.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2574978.20_model.r': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling rm: cannot remove `SRX2574978.20_*.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 `SRX2574978.20_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 @ Wed, 28 Jun 2017 01:46:12: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:46:12: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:46:12: #1 total tags in treatment: 1426883 INFO @ Wed, 28 Jun 2017 01:46:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:46:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:46:12: #1 tags after filtering in treatment: 1325169 INFO @ Wed, 28 Jun 2017 01:46:12: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:46:12: #1 finished! INFO @ Wed, 28 Jun 2017 01:46:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:46:12: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 01:46:12: Too few paired peaks (39) 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, 28 Jun 2017 01:46:12: Process for pairing-model is terminated! cat: SRX2574978.05_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 `SRX2574978.05_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 `SRX2574978.05_*.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 `SRX2574978.05_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。