Job ID = 9162121 sra ファイルのダウンロード中... Completed: 404050K bytes transferred in 6 seconds (539092K 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 2800710 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1639660/SRR3234023.sra Written 2800710 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: 00:03:27 2800710 reads; of these: 2800710 (100.00%) were paired; of these: 976725 (34.87%) aligned concordantly 0 times 1447722 (51.69%) aligned concordantly exactly 1 time 376263 (13.43%) aligned concordantly >1 times ---- 976725 pairs aligned concordantly 0 times; of these: 16637 (1.70%) aligned discordantly 1 time ---- 960088 pairs aligned 0 times concordantly or discordantly; of these: 1920176 mates make up the pairs; of these: 1888605 (98.36%) aligned 0 times 18515 (0.96%) aligned exactly 1 time 13056 (0.68%) aligned >1 times 66.28% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 132759 / 756301 = 0.1755 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 06:02:10: # Command line: callpeak -t SRX1639660.bam -f BAM -g 12100000 -n SRX1639660.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1639660.20 # format = BAM # ChIP-seq file = ['SRX1639660.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 06:02:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:02:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:02:10: # Command line: callpeak -t SRX1639660.bam -f BAM -g 12100000 -n SRX1639660.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1639660.10 # format = BAM # ChIP-seq file = ['SRX1639660.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 06:02:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:02:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:02:10: # Command line: callpeak -t SRX1639660.bam -f BAM -g 12100000 -n SRX1639660.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1639660.05 # format = BAM # ChIP-seq file = ['SRX1639660.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 06:02:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:02:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:02:19: 1000000 INFO @ Wed, 28 Jun 2017 06:02:23: 1000000 INFO @ Wed, 28 Jun 2017 06:02:24: 1000000 INFO @ Wed, 28 Jun 2017 06:02:27: 2000000 INFO @ Wed, 28 Jun 2017 06:02:35: 2000000 INFO @ Wed, 28 Jun 2017 06:02:35: 3000000 INFO @ Wed, 28 Jun 2017 06:02:35: 2000000 INFO @ Wed, 28 Jun 2017 06:02:39: #1 tag size is determined as 138 bps INFO @ Wed, 28 Jun 2017 06:02:39: #1 tag size = 138 INFO @ Wed, 28 Jun 2017 06:02:39: #1 total tags in treatment: 1691808 INFO @ Wed, 28 Jun 2017 06:02:39: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:02:39: #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 06:02:39: #1 tags after filtering in treatment: 1295585 INFO @ Wed, 28 Jun 2017 06:02:39: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 06:02:39: #1 finished! INFO @ Wed, 28 Jun 2017 06:02:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:02:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:02:39: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 06:02:39: 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 06:02:39: Process for pairing-model is terminated! cat: SRX1639660.05_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 `SRX1639660.05_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 `SRX1639660.05_*.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 `SRX1639660.05_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 @ Wed, 28 Jun 2017 06:02:46: 3000000 INFO @ Wed, 28 Jun 2017 06:02:46: 3000000 INFO @ Wed, 28 Jun 2017 06:02:50: #1 tag size is determined as 138 bps INFO @ Wed, 28 Jun 2017 06:02:50: #1 tag size = 138 INFO @ Wed, 28 Jun 2017 06:02:50: #1 total tags in treatment: 1691808 INFO @ Wed, 28 Jun 2017 06:02:50: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:02:50: #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 06:02:50: #1 tags after filtering in treatment: 1295585 INFO @ Wed, 28 Jun 2017 06:02:50: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 06:02:50: #1 finished! INFO @ Wed, 28 Jun 2017 06:02:50: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:02:50: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 06:02:50: 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 06:02:50: Process for pairing-model is terminated! cat: SRX1639660.10_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 `SRX1639660.10_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 `SRX1639660.10_*.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 `SRX1639660.10_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, 28 Jun 2017 06:02:50: #1 tag size is determined as 138 bps INFO @ Wed, 28 Jun 2017 06:02:50: #1 tag size = 138 INFO @ Wed, 28 Jun 2017 06:02:50: #1 total tags in treatment: 1691808 INFO @ Wed, 28 Jun 2017 06:02:50: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:02:50: #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 06:02:50: #1 tags after filtering in treatment: 1295585 INFO @ Wed, 28 Jun 2017 06:02:50: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 06:02:50: #1 finished! INFO @ Wed, 28 Jun 2017 06:02:50: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:02:50: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 06:02:50: 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 06:02:50: Process for pairing-model is terminated! cat: SRX1639660.20_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 `SRX1639660.20_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 `SRX1639660.20_*.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 `SRX1639660.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。