Job ID = 9160176 sra ファイルのダウンロード中... Completed: 702098K bytes transferred in 55 seconds (103051K 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 16171375 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2831023/SRR5572339.sra Written 16171375 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: 00:12:19 16171375 reads; of these: 16171375 (100.00%) were paired; of these: 956772 (5.92%) aligned concordantly 0 times 13032055 (80.59%) aligned concordantly exactly 1 time 2182548 (13.50%) aligned concordantly >1 times ---- 956772 pairs aligned concordantly 0 times; of these: 277421 (29.00%) aligned discordantly 1 time ---- 679351 pairs aligned 0 times concordantly or discordantly; of these: 1358702 mates make up the pairs; of these: 1081510 (79.60%) aligned 0 times 148808 (10.95%) aligned exactly 1 time 128384 (9.45%) aligned >1 times 96.66% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 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 16 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] 1771712 / 15333066 = 0.1155 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 02:21:31: # Command line: callpeak -t SRX2831023.bam -f BAM -g 12100000 -n SRX2831023.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2831023.05 # format = BAM # ChIP-seq file = ['SRX2831023.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 02:21:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 02:21:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 02:21:31: # Command line: callpeak -t SRX2831023.bam -f BAM -g 12100000 -n SRX2831023.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2831023.20 # format = BAM # ChIP-seq file = ['SRX2831023.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 02:21:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 02:21:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 02:21:31: # Command line: callpeak -t SRX2831023.bam -f BAM -g 12100000 -n SRX2831023.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2831023.10 # format = BAM # ChIP-seq file = ['SRX2831023.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 02:21:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 02:21:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 02:21:37: 1000000 INFO @ Wed, 28 Jun 2017 02:21:38: 1000000 INFO @ Wed, 28 Jun 2017 02:21:38: 1000000 INFO @ Wed, 28 Jun 2017 02:21:43: 2000000 INFO @ Wed, 28 Jun 2017 02:21:44: 2000000 INFO @ Wed, 28 Jun 2017 02:21:44: 2000000 INFO @ Wed, 28 Jun 2017 02:21:48: 3000000 INFO @ Wed, 28 Jun 2017 02:21:51: 3000000 INFO @ Wed, 28 Jun 2017 02:21:51: 3000000 INFO @ Wed, 28 Jun 2017 02:21:54: 4000000 INFO @ Wed, 28 Jun 2017 02:21:57: 4000000 INFO @ Wed, 28 Jun 2017 02:21:57: 4000000 INFO @ Wed, 28 Jun 2017 02:22:00: 5000000 INFO @ Wed, 28 Jun 2017 02:22:04: 5000000 INFO @ Wed, 28 Jun 2017 02:22:04: 5000000 INFO @ Wed, 28 Jun 2017 02:22:06: 6000000 INFO @ Wed, 28 Jun 2017 02:22:11: 6000000 INFO @ Wed, 28 Jun 2017 02:22:11: 6000000 INFO @ Wed, 28 Jun 2017 02:22:12: 7000000 INFO @ Wed, 28 Jun 2017 02:22:17: 7000000 INFO @ Wed, 28 Jun 2017 02:22:17: 7000000 INFO @ Wed, 28 Jun 2017 02:22:18: 8000000 INFO @ Wed, 28 Jun 2017 02:22:23: 8000000 INFO @ Wed, 28 Jun 2017 02:22:23: 8000000 INFO @ Wed, 28 Jun 2017 02:22:24: 9000000 INFO @ Wed, 28 Jun 2017 02:22:29: 10000000 INFO @ Wed, 28 Jun 2017 02:22:30: 9000000 INFO @ Wed, 28 Jun 2017 02:22:30: 9000000 INFO @ Wed, 28 Jun 2017 02:22:35: 11000000 INFO @ Wed, 28 Jun 2017 02:22:36: 10000000 INFO @ Wed, 28 Jun 2017 02:22:36: 10000000 INFO @ Wed, 28 Jun 2017 02:22:41: 12000000 INFO @ Wed, 28 Jun 2017 02:22:43: 11000000 INFO @ Wed, 28 Jun 2017 02:22:43: 11000000 INFO @ Wed, 28 Jun 2017 02:22:47: 13000000 INFO @ Wed, 28 Jun 2017 02:22:50: 12000000 INFO @ Wed, 28 Jun 2017 02:22:50: 12000000 INFO @ Wed, 28 Jun 2017 02:22:53: 14000000 INFO @ Wed, 28 Jun 2017 02:22:56: 13000000 INFO @ Wed, 28 Jun 2017 02:22:56: 13000000 INFO @ Wed, 28 Jun 2017 02:22:58: 15000000 INFO @ Wed, 28 Jun 2017 02:23:03: 14000000 INFO @ Wed, 28 Jun 2017 02:23:03: 14000000 INFO @ Wed, 28 Jun 2017 02:23:04: 16000000 INFO @ Wed, 28 Jun 2017 02:23:09: 15000000 INFO @ Wed, 28 Jun 2017 02:23:09: 15000000 INFO @ Wed, 28 Jun 2017 02:23:10: 17000000 INFO @ Wed, 28 Jun 2017 02:23:15: 16000000 INFO @ Wed, 28 Jun 2017 02:23:15: 16000000 INFO @ Wed, 28 Jun 2017 02:23:15: 18000000 INFO @ Wed, 28 Jun 2017 02:23:21: 17000000 INFO @ Wed, 28 Jun 2017 02:23:21: 17000000 INFO @ Wed, 28 Jun 2017 02:23:21: 19000000 INFO @ Wed, 28 Jun 2017 02:23:27: 20000000 INFO @ Wed, 28 Jun 2017 02:23:27: 18000000 INFO @ Wed, 28 Jun 2017 02:23:27: 18000000 INFO @ Wed, 28 Jun 2017 02:23:32: 21000000 INFO @ Wed, 28 Jun 2017 02:23:33: 19000000 INFO @ Wed, 28 Jun 2017 02:23:33: 19000000 INFO @ Wed, 28 Jun 2017 02:23:38: 22000000 INFO @ Wed, 28 Jun 2017 02:23:40: 20000000 INFO @ Wed, 28 Jun 2017 02:23:40: 20000000 INFO @ Wed, 28 Jun 2017 02:23:44: 23000000 INFO @ Wed, 28 Jun 2017 02:23:47: 21000000 INFO @ Wed, 28 Jun 2017 02:23:47: 21000000 INFO @ Wed, 28 Jun 2017 02:23:49: 24000000 INFO @ Wed, 28 Jun 2017 02:23:53: 22000000 INFO @ Wed, 28 Jun 2017 02:23:53: 22000000 INFO @ Wed, 28 Jun 2017 02:23:55: 25000000 INFO @ Wed, 28 Jun 2017 02:23:59: 23000000 INFO @ Wed, 28 Jun 2017 02:23:59: 23000000 INFO @ Wed, 28 Jun 2017 02:24:01: 26000000 INFO @ Wed, 28 Jun 2017 02:24:05: 24000000 INFO @ Wed, 28 Jun 2017 02:24:05: 24000000 INFO @ Wed, 28 Jun 2017 02:24:06: 27000000 INFO @ Wed, 28 Jun 2017 02:24:10: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 02:24:10: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 02:24:10: #1 total tags in treatment: 13449769 INFO @ Wed, 28 Jun 2017 02:24:10: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:24:10: #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 02:24:11: #1 tags after filtering in treatment: 8961990 INFO @ Wed, 28 Jun 2017 02:24:11: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 02:24:11: #1 finished! INFO @ Wed, 28 Jun 2017 02:24:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:24:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:24:11: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:24:11: 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 02:24:11: Process for pairing-model is terminated! cat: SRX2831023.10_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 `SRX2831023.10_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 `SRX2831023.10_*.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 `SRX2831023.10_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 02:24:11: 25000000 INFO @ Wed, 28 Jun 2017 02:24:11: 25000000 INFO @ Wed, 28 Jun 2017 02:24:17: 26000000 INFO @ Wed, 28 Jun 2017 02:24:17: 26000000 INFO @ Wed, 28 Jun 2017 02:24:23: 27000000 INFO @ Wed, 28 Jun 2017 02:24:23: 27000000 INFO @ Wed, 28 Jun 2017 02:24:28: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 02:24:28: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 02:24:28: #1 total tags in treatment: 13449769 INFO @ Wed, 28 Jun 2017 02:24:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:24:28: #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 02:24:28: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 02:24:28: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 02:24:28: #1 total tags in treatment: 13449769 INFO @ Wed, 28 Jun 2017 02:24:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:24:28: #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 02:24:28: #1 tags after filtering in treatment: 8961990 INFO @ Wed, 28 Jun 2017 02:24:28: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 02:24:28: #1 finished! INFO @ Wed, 28 Jun 2017 02:24:28: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:24:28: #1 tags after filtering in treatment: 8961990 INFO @ Wed, 28 Jun 2017 02:24:28: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 02:24:28: #1 finished! INFO @ Wed, 28 Jun 2017 02:24:28: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:24:29: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:24:29: 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 02:24:29: Process for pairing-model is terminated! cat: SRX2831023.20_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 `SRX2831023.20_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 `SRX2831023.20_*.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 `SRX2831023.20_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 02:24:29: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:24:29: 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 02:24:29: Process for pairing-model is terminated! cat: SRX2831023.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2831023.05_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 `SRX2831023.05_*.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 `SRX2831023.05_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。