Job ID = 9732092 sra ファイルのダウンロード中... Completed: 374532K bytes transferred in 13 seconds (224068K 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 16235850 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675882/SRR5380659.sra Written 16235850 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: 00:07:18 16235850 reads; of these: 16235850 (100.00%) were paired; of these: 4591305 (28.28%) aligned concordantly 0 times 10247714 (63.12%) aligned concordantly exactly 1 time 1396831 (8.60%) aligned concordantly >1 times ---- 4591305 pairs aligned concordantly 0 times; of these: 636941 (13.87%) aligned discordantly 1 time ---- 3954364 pairs aligned 0 times concordantly or discordantly; of these: 7908728 mates make up the pairs; of these: 7156415 (90.49%) aligned 0 times 501058 (6.34%) aligned exactly 1 time 251255 (3.18%) aligned >1 times 77.96% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:18 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] 1674036 / 12022880 = 0.1392 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 @ Sun, 03 Sep 2017 19:43:50: # Command line: callpeak -t SRX2675882.bam -f BAM -g 12100000 -n SRX2675882.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675882.20 # format = BAM # ChIP-seq file = ['SRX2675882.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 @ Sun, 03 Sep 2017 19:43:50: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:50: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:50: # Command line: callpeak -t SRX2675882.bam -f BAM -g 12100000 -n SRX2675882.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675882.10 # format = BAM # ChIP-seq file = ['SRX2675882.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 @ Sun, 03 Sep 2017 19:43:50: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:50: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:50: # Command line: callpeak -t SRX2675882.bam -f BAM -g 12100000 -n SRX2675882.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675882.05 # format = BAM # ChIP-seq file = ['SRX2675882.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 @ Sun, 03 Sep 2017 19:43:50: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:50: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:56: 1000000 INFO @ Sun, 03 Sep 2017 19:43:56: 1000000 INFO @ Sun, 03 Sep 2017 19:43:56: 1000000 INFO @ Sun, 03 Sep 2017 19:44:01: 2000000 INFO @ Sun, 03 Sep 2017 19:44:01: 2000000 INFO @ Sun, 03 Sep 2017 19:44:01: 2000000 INFO @ Sun, 03 Sep 2017 19:44:07: 3000000 INFO @ Sun, 03 Sep 2017 19:44:07: 3000000 INFO @ Sun, 03 Sep 2017 19:44:07: 3000000 INFO @ Sun, 03 Sep 2017 19:44:12: 4000000 INFO @ Sun, 03 Sep 2017 19:44:12: 4000000 INFO @ Sun, 03 Sep 2017 19:44:12: 4000000 INFO @ Sun, 03 Sep 2017 19:44:18: 5000000 INFO @ Sun, 03 Sep 2017 19:44:18: 5000000 INFO @ Sun, 03 Sep 2017 19:44:18: 5000000 INFO @ Sun, 03 Sep 2017 19:44:23: 6000000 INFO @ Sun, 03 Sep 2017 19:44:24: 6000000 INFO @ Sun, 03 Sep 2017 19:44:24: 6000000 INFO @ Sun, 03 Sep 2017 19:44:29: 7000000 INFO @ Sun, 03 Sep 2017 19:44:29: 7000000 INFO @ Sun, 03 Sep 2017 19:44:29: 7000000 INFO @ Sun, 03 Sep 2017 19:44:35: 8000000 INFO @ Sun, 03 Sep 2017 19:44:35: 8000000 INFO @ Sun, 03 Sep 2017 19:44:35: 8000000 INFO @ Sun, 03 Sep 2017 19:44:40: 9000000 INFO @ Sun, 03 Sep 2017 19:44:41: 9000000 INFO @ Sun, 03 Sep 2017 19:44:41: 9000000 INFO @ Sun, 03 Sep 2017 19:44:46: 10000000 INFO @ Sun, 03 Sep 2017 19:44:47: 10000000 INFO @ Sun, 03 Sep 2017 19:44:47: 10000000 INFO @ Sun, 03 Sep 2017 19:44:52: 11000000 INFO @ Sun, 03 Sep 2017 19:44:53: 11000000 INFO @ Sun, 03 Sep 2017 19:44:53: 11000000 INFO @ Sun, 03 Sep 2017 19:44:58: 12000000 INFO @ Sun, 03 Sep 2017 19:44:58: 12000000 INFO @ Sun, 03 Sep 2017 19:44:59: 12000000 INFO @ Sun, 03 Sep 2017 19:45:04: 13000000 INFO @ Sun, 03 Sep 2017 19:45:04: 13000000 INFO @ Sun, 03 Sep 2017 19:45:05: 13000000 INFO @ Sun, 03 Sep 2017 19:45:09: 14000000 INFO @ Sun, 03 Sep 2017 19:45:10: 14000000 INFO @ Sun, 03 Sep 2017 19:45:10: 14000000 INFO @ Sun, 03 Sep 2017 19:45:15: 15000000 INFO @ Sun, 03 Sep 2017 19:45:16: 15000000 INFO @ Sun, 03 Sep 2017 19:45:16: 15000000 INFO @ Sun, 03 Sep 2017 19:45:21: 16000000 INFO @ Sun, 03 Sep 2017 19:45:22: 16000000 INFO @ Sun, 03 Sep 2017 19:45:23: 16000000 INFO @ Sun, 03 Sep 2017 19:45:27: 17000000 INFO @ Sun, 03 Sep 2017 19:45:28: 17000000 INFO @ Sun, 03 Sep 2017 19:45:29: 17000000 INFO @ Sun, 03 Sep 2017 19:45:33: 18000000 INFO @ Sun, 03 Sep 2017 19:45:34: 18000000 INFO @ Sun, 03 Sep 2017 19:45:35: 18000000 INFO @ Sun, 03 Sep 2017 19:45:39: 19000000 INFO @ Sun, 03 Sep 2017 19:45:40: 19000000 INFO @ Sun, 03 Sep 2017 19:45:41: 19000000 INFO @ Sun, 03 Sep 2017 19:45:45: 20000000 INFO @ Sun, 03 Sep 2017 19:45:46: 20000000 INFO @ Sun, 03 Sep 2017 19:45:47: 20000000 INFO @ Sun, 03 Sep 2017 19:45:51: 21000000 INFO @ Sun, 03 Sep 2017 19:45:52: 21000000 INFO @ Sun, 03 Sep 2017 19:45:53: 21000000 INFO @ Sun, 03 Sep 2017 19:45:56: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:56: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:56: #1 total tags in treatment: 9979122 INFO @ Sun, 03 Sep 2017 19:45:56: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:57: #1 tags after filtering in treatment: 4802746 INFO @ Sun, 03 Sep 2017 19:45:57: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:45:57: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:57: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:57: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:57: 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 @ Sun, 03 Sep 2017 19:45:57: Process for pairing-model is terminated! cat: SRX2675882.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675882.10_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 `SRX2675882.10_*.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 `SRX2675882.10_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 @ Sun, 03 Sep 2017 19:45:58: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:58: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:58: #1 total tags in treatment: 9979122 INFO @ Sun, 03 Sep 2017 19:45:58: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:58: #1 tags after filtering in treatment: 4802746 INFO @ Sun, 03 Sep 2017 19:45:58: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:45:58: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:58: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:58: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:58: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:58: #1 total tags in treatment: 9979122 INFO @ Sun, 03 Sep 2017 19:45:58: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:58: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:58: 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 @ Sun, 03 Sep 2017 19:45:58: Process for pairing-model is terminated! cat: SRX2675882.20_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 `SRX2675882.20_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 `SRX2675882.20_*.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 `SRX2675882.20_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 @ Sun, 03 Sep 2017 19:45:58: #1 tags after filtering in treatment: 4802746 INFO @ Sun, 03 Sep 2017 19:45:58: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:45:58: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:58: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:59: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:59: 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 @ Sun, 03 Sep 2017 19:45:59: Process for pairing-model is terminated! cat: SRX2675882.05_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 `SRX2675882.05_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 `SRX2675882.05_*.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 `SRX2675882.05_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。