Job ID = 9163652 sra ファイルのダウンロード中... Completed: 409051K bytes transferred in 6 seconds (514934K 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 6075568 spots for /home/okishinya/chipatlas/results/sacCer3/SRX997168/SRR1976200.sra Written 6075568 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: 00:04:13 6075568 reads; of these: 6075568 (100.00%) were paired; of these: 868681 (14.30%) aligned concordantly 0 times 3799234 (62.53%) aligned concordantly exactly 1 time 1407653 (23.17%) aligned concordantly >1 times ---- 868681 pairs aligned concordantly 0 times; of these: 53772 (6.19%) aligned discordantly 1 time ---- 814909 pairs aligned 0 times concordantly or discordantly; of these: 1629818 mates make up the pairs; of these: 1435848 (88.10%) aligned 0 times 114001 (6.99%) aligned exactly 1 time 79969 (4.91%) aligned >1 times 88.18% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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_sort_core] merging from 8 files... [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] 1005629 / 5213078 = 0.1929 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 11:19:00: # Command line: callpeak -t SRX997168.bam -f BAM -g 12100000 -n SRX997168.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997168.05 # format = BAM # ChIP-seq file = ['SRX997168.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 11:19:00: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:19:00: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:19:00: # Command line: callpeak -t SRX997168.bam -f BAM -g 12100000 -n SRX997168.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997168.20 # format = BAM # ChIP-seq file = ['SRX997168.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 11:19:00: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:19:00: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:19:00: # Command line: callpeak -t SRX997168.bam -f BAM -g 12100000 -n SRX997168.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997168.10 # format = BAM # ChIP-seq file = ['SRX997168.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 11:19:00: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:19:00: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:19:07: 1000000 INFO @ Wed, 28 Jun 2017 11:19:07: 1000000 INFO @ Wed, 28 Jun 2017 11:19:07: 1000000 INFO @ Wed, 28 Jun 2017 11:19:13: 2000000 INFO @ Wed, 28 Jun 2017 11:19:14: 2000000 INFO @ Wed, 28 Jun 2017 11:19:14: 2000000 INFO @ Wed, 28 Jun 2017 11:19:19: 3000000 INFO @ Wed, 28 Jun 2017 11:19:20: 3000000 INFO @ Wed, 28 Jun 2017 11:19:20: 3000000 INFO @ Wed, 28 Jun 2017 11:19:26: 4000000 INFO @ Wed, 28 Jun 2017 11:19:27: 4000000 INFO @ Wed, 28 Jun 2017 11:19:27: 4000000 INFO @ Wed, 28 Jun 2017 11:19:32: 5000000 INFO @ Wed, 28 Jun 2017 11:19:34: 5000000 INFO @ Wed, 28 Jun 2017 11:19:34: 5000000 INFO @ Wed, 28 Jun 2017 11:19:38: 6000000 INFO @ Wed, 28 Jun 2017 11:19:40: 6000000 INFO @ Wed, 28 Jun 2017 11:19:41: 6000000 INFO @ Wed, 28 Jun 2017 11:19:45: 7000000 INFO @ Wed, 28 Jun 2017 11:19:47: 7000000 INFO @ Wed, 28 Jun 2017 11:19:48: 7000000 INFO @ Wed, 28 Jun 2017 11:19:52: 8000000 INFO @ Wed, 28 Jun 2017 11:19:53: 8000000 INFO @ Wed, 28 Jun 2017 11:19:55: 8000000 INFO @ Wed, 28 Jun 2017 11:19:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:19:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:19:57: #1 total tags in treatment: 4201312 INFO @ Wed, 28 Jun 2017 11:19:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:19:57: #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 11:19:57: #1 tags after filtering in treatment: 2739959 INFO @ Wed, 28 Jun 2017 11:19:57: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 28 Jun 2017 11:19:57: #1 finished! INFO @ Wed, 28 Jun 2017 11:19:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:19:57: #2 number of paired peaks: 30 WARNING @ Wed, 28 Jun 2017 11:19:57: Too few paired peaks (30) 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 11:19:57: Process for pairing-model is terminated! cat: SRX997168.10_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 `SRX997168.10_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 `SRX997168.10_*.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 `SRX997168.10_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 11:19:58: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:19:58: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:19:58: #1 total tags in treatment: 4201312 INFO @ Wed, 28 Jun 2017 11:19:58: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:19:58: #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 11:19:58: #1 tags after filtering in treatment: 2739959 INFO @ Wed, 28 Jun 2017 11:19:58: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 28 Jun 2017 11:19:58: #1 finished! INFO @ Wed, 28 Jun 2017 11:19:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:19:58: #2 number of paired peaks: 30 WARNING @ Wed, 28 Jun 2017 11:19:58: Too few paired peaks (30) 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 11:19:58: Process for pairing-model is terminated! cat: SRX997168.20_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 `SRX997168.20_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 `SRX997168.20_*.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 `SRX997168.20_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 11:20:00: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:20:00: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:20:00: #1 total tags in treatment: 4201312 INFO @ Wed, 28 Jun 2017 11:20:00: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:20:00: #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 11:20:00: #1 tags after filtering in treatment: 2739959 INFO @ Wed, 28 Jun 2017 11:20:00: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 28 Jun 2017 11:20:00: #1 finished! INFO @ Wed, 28 Jun 2017 11:20:00: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:20:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:20:00: #2 number of paired peaks: 30 WARNING @ Wed, 28 Jun 2017 11:20:00: Too few paired peaks (30) 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 11:20:00: Process for pairing-model is terminated! cat: SRX997168.05_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 `SRX997168.05_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 `SRX997168.05_*.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 `SRX997168.05_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。