Job ID = 9162413 sra ファイルのダウンロード中... Completed: 914778K bytes transferred in 13 seconds (544025K 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 10709037 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2457693/SRR5138808.sra Written 10709037 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: 00:12:50 10709037 reads; of these: 10709037 (100.00%) were paired; of these: 808844 (7.55%) aligned concordantly 0 times 9259060 (86.46%) aligned concordantly exactly 1 time 641133 (5.99%) aligned concordantly >1 times ---- 808844 pairs aligned concordantly 0 times; of these: 489044 (60.46%) aligned discordantly 1 time ---- 319800 pairs aligned 0 times concordantly or discordantly; of these: 639600 mates make up the pairs; of these: 487242 (76.18%) aligned 0 times 82814 (12.95%) aligned exactly 1 time 69544 (10.87%) aligned >1 times 97.73% overall alignment rate Time searching: 00:12:50 Overall time: 00:12:50 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 12 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] 1131859 / 10312115 = 0.1098 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 08:03:48: # Command line: callpeak -t SRX2457693.bam -f BAM -g 12100000 -n SRX2457693.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2457693.05 # format = BAM # ChIP-seq file = ['SRX2457693.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 08:03:48: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:03:48: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:03:48: # Command line: callpeak -t SRX2457693.bam -f BAM -g 12100000 -n SRX2457693.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2457693.10 # format = BAM # ChIP-seq file = ['SRX2457693.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 08:03:48: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:03:48: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:03:48: # Command line: callpeak -t SRX2457693.bam -f BAM -g 12100000 -n SRX2457693.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2457693.20 # format = BAM # ChIP-seq file = ['SRX2457693.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 08:03:48: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:03:48: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:03:58: 1000000 INFO @ Wed, 28 Jun 2017 08:03:58: 1000000 INFO @ Wed, 28 Jun 2017 08:03:58: 1000000 INFO @ Wed, 28 Jun 2017 08:04:08: 2000000 INFO @ Wed, 28 Jun 2017 08:04:08: 2000000 INFO @ Wed, 28 Jun 2017 08:04:08: 2000000 INFO @ Wed, 28 Jun 2017 08:04:18: 3000000 INFO @ Wed, 28 Jun 2017 08:04:18: 3000000 INFO @ Wed, 28 Jun 2017 08:04:18: 3000000 INFO @ Wed, 28 Jun 2017 08:04:28: 4000000 INFO @ Wed, 28 Jun 2017 08:04:28: 4000000 INFO @ Wed, 28 Jun 2017 08:04:28: 4000000 INFO @ Wed, 28 Jun 2017 08:04:38: 5000000 INFO @ Wed, 28 Jun 2017 08:04:38: 5000000 INFO @ Wed, 28 Jun 2017 08:04:38: 5000000 INFO @ Wed, 28 Jun 2017 08:04:48: 6000000 INFO @ Wed, 28 Jun 2017 08:04:48: 6000000 INFO @ Wed, 28 Jun 2017 08:04:48: 6000000 INFO @ Wed, 28 Jun 2017 08:04:59: 7000000 INFO @ Wed, 28 Jun 2017 08:04:59: 7000000 INFO @ Wed, 28 Jun 2017 08:04:59: 7000000 INFO @ Wed, 28 Jun 2017 08:05:09: 8000000 INFO @ Wed, 28 Jun 2017 08:05:09: 8000000 INFO @ Wed, 28 Jun 2017 08:05:09: 8000000 INFO @ Wed, 28 Jun 2017 08:05:19: 9000000 INFO @ Wed, 28 Jun 2017 08:05:19: 9000000 INFO @ Wed, 28 Jun 2017 08:05:19: 9000000 INFO @ Wed, 28 Jun 2017 08:05:29: 10000000 INFO @ Wed, 28 Jun 2017 08:05:29: 10000000 INFO @ Wed, 28 Jun 2017 08:05:29: 10000000 INFO @ Wed, 28 Jun 2017 08:05:39: 11000000 INFO @ Wed, 28 Jun 2017 08:05:39: 11000000 INFO @ Wed, 28 Jun 2017 08:05:39: 11000000 INFO @ Wed, 28 Jun 2017 08:05:49: 12000000 INFO @ Wed, 28 Jun 2017 08:05:49: 12000000 INFO @ Wed, 28 Jun 2017 08:05:49: 12000000 INFO @ Wed, 28 Jun 2017 08:05:59: 13000000 INFO @ Wed, 28 Jun 2017 08:05:59: 13000000 INFO @ Wed, 28 Jun 2017 08:05:59: 13000000 INFO @ Wed, 28 Jun 2017 08:06:09: 14000000 INFO @ Wed, 28 Jun 2017 08:06:09: 14000000 INFO @ Wed, 28 Jun 2017 08:06:09: 14000000 INFO @ Wed, 28 Jun 2017 08:06:19: 15000000 INFO @ Wed, 28 Jun 2017 08:06:19: 15000000 INFO @ Wed, 28 Jun 2017 08:06:19: 15000000 INFO @ Wed, 28 Jun 2017 08:06:29: 16000000 INFO @ Wed, 28 Jun 2017 08:06:29: 16000000 INFO @ Wed, 28 Jun 2017 08:06:29: 16000000 INFO @ Wed, 28 Jun 2017 08:06:39: 17000000 INFO @ Wed, 28 Jun 2017 08:06:39: 17000000 INFO @ Wed, 28 Jun 2017 08:06:39: 17000000 INFO @ Wed, 28 Jun 2017 08:06:49: 18000000 INFO @ Wed, 28 Jun 2017 08:06:49: 18000000 INFO @ Wed, 28 Jun 2017 08:06:49: 18000000 INFO @ Wed, 28 Jun 2017 08:06:56: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 08:06:56: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 08:06:56: #1 total tags in treatment: 8791887 INFO @ Wed, 28 Jun 2017 08:06:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:06:56: #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 08:06:56: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 08:06:56: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 08:06:56: #1 total tags in treatment: 8791887 INFO @ Wed, 28 Jun 2017 08:06:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:06:56: #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 08:06:56: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 08:06:56: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 08:06:56: #1 total tags in treatment: 8791887 INFO @ Wed, 28 Jun 2017 08:06:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:06:56: #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 08:06:56: #1 tags after filtering in treatment: 5069237 INFO @ Wed, 28 Jun 2017 08:06:56: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 28 Jun 2017 08:06:56: #1 finished! INFO @ Wed, 28 Jun 2017 08:06:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:06:56: #1 tags after filtering in treatment: 5069237 INFO @ Wed, 28 Jun 2017 08:06:56: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 28 Jun 2017 08:06:56: #1 finished! INFO @ Wed, 28 Jun 2017 08:06:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:06:56: #1 tags after filtering in treatment: 5069237 INFO @ Wed, 28 Jun 2017 08:06:56: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 28 Jun 2017 08:06:56: #1 finished! INFO @ Wed, 28 Jun 2017 08:06:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:06:57: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:06:57: Too few paired peaks (0) 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 08:06:57: Process for pairing-model is terminated! cat: SRX2457693.10_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 `SRX2457693.10_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 `SRX2457693.10_*.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 `SRX2457693.10_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 08:06:57: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:06:57: Too few paired peaks (0) 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 08:06:57: Process for pairing-model is terminated! cat: SRX2457693.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Wed, 28 Jun 2017 08:06:57: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:06:57: Too few paired peaks (0) 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 08:06:57: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2457693.05_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 `SRX2457693.05_*.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 `SRX2457693.05_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 cat: SRX2457693.20_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 `SRX2457693.20_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 `SRX2457693.20_*.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 `SRX2457693.20_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。