Job ID = 9161937 sra ファイルのダウンロード中... Completed: 260887K bytes transferred in 5 seconds (406799K 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 3898868 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1419788/SRR2927537.sra Written 3898868 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: 00:04:24 3898868 reads; of these: 3898868 (100.00%) were paired; of these: 169497 (4.35%) aligned concordantly 0 times 3308528 (84.86%) aligned concordantly exactly 1 time 420843 (10.79%) aligned concordantly >1 times ---- 169497 pairs aligned concordantly 0 times; of these: 35356 (20.86%) aligned discordantly 1 time ---- 134141 pairs aligned 0 times concordantly or discordantly; of these: 268282 mates make up the pairs; of these: 230328 (85.85%) aligned 0 times 21624 (8.06%) aligned exactly 1 time 16330 (6.09%) aligned >1 times 97.05% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 89319 / 3751563 = 0.0238 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 05:08:09: # Command line: callpeak -t SRX1419788.bam -f BAM -g 12100000 -n SRX1419788.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1419788.20 # format = BAM # ChIP-seq file = ['SRX1419788.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 05:08:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:08:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:08:09: # Command line: callpeak -t SRX1419788.bam -f BAM -g 12100000 -n SRX1419788.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1419788.05 # format = BAM # ChIP-seq file = ['SRX1419788.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 05:08:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:08:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:08:09: # Command line: callpeak -t SRX1419788.bam -f BAM -g 12100000 -n SRX1419788.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1419788.10 # format = BAM # ChIP-seq file = ['SRX1419788.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 05:08:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:08:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:08:19: 1000000 INFO @ Wed, 28 Jun 2017 05:08:19: 1000000 INFO @ Wed, 28 Jun 2017 05:08:21: 1000000 INFO @ Wed, 28 Jun 2017 05:08:28: 2000000 INFO @ Wed, 28 Jun 2017 05:08:28: 2000000 INFO @ Wed, 28 Jun 2017 05:08:32: 2000000 INFO @ Wed, 28 Jun 2017 05:08:38: 3000000 INFO @ Wed, 28 Jun 2017 05:08:38: 3000000 INFO @ Wed, 28 Jun 2017 05:08:44: 3000000 INFO @ Wed, 28 Jun 2017 05:08:48: 4000000 INFO @ Wed, 28 Jun 2017 05:08:48: 4000000 INFO @ Wed, 28 Jun 2017 05:08:54: 4000000 INFO @ Wed, 28 Jun 2017 05:08:56: 5000000 INFO @ Wed, 28 Jun 2017 05:08:56: 5000000 INFO @ Wed, 28 Jun 2017 05:09:03: 5000000 INFO @ Wed, 28 Jun 2017 05:09:04: 6000000 INFO @ Wed, 28 Jun 2017 05:09:04: 6000000 INFO @ Wed, 28 Jun 2017 05:09:12: 6000000 INFO @ Wed, 28 Jun 2017 05:09:12: 7000000 INFO @ Wed, 28 Jun 2017 05:09:12: 7000000 INFO @ Wed, 28 Jun 2017 05:09:15: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:09:15: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:09:15: #1 total tags in treatment: 3640317 INFO @ Wed, 28 Jun 2017 05:09:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:15: #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 05:09:15: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:09:15: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:09:15: #1 total tags in treatment: 3640317 INFO @ Wed, 28 Jun 2017 05:09:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:15: #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 05:09:15: #1 tags after filtering in treatment: 3197995 INFO @ Wed, 28 Jun 2017 05:09:15: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:09:15: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:15: #1 tags after filtering in treatment: 3197995 INFO @ Wed, 28 Jun 2017 05:09:15: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:09:15: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:16: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 05:09:16: Too few paired peaks (29) 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 05:09:16: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 05:09:16: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 05:09:16: Too few paired peaks (29) 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. cat: SRX1419788.05_peaks.narrowPeakWARNING @ Wed, 28 Jun 2017 05:09:16: Process for pairing-model is terminated! : 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 cat: SRX1419788.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1419788.05_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 `SRX1419788.05_*.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 `SRX1419788.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1419788.20_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 `SRX1419788.20_*.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 `SRX1419788.20_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 05:09:21: 7000000 INFO @ Wed, 28 Jun 2017 05:09:24: #1 tag size is determined as 92 bps INFO @ Wed, 28 Jun 2017 05:09:24: #1 tag size = 92 INFO @ Wed, 28 Jun 2017 05:09:24: #1 total tags in treatment: 3640317 INFO @ Wed, 28 Jun 2017 05:09:24: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:24: #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 05:09:24: #1 tags after filtering in treatment: 3197995 INFO @ Wed, 28 Jun 2017 05:09:24: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 28 Jun 2017 05:09:24: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:24: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:24: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 05:09:24: Too few paired peaks (29) 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 05:09:24: Process for pairing-model is terminated! cat: SRX1419788.10_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 `SRX1419788.10_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 `SRX1419788.10_*.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 `SRX1419788.10_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。