Job ID = 9161916 sra ファイルのダウンロード中... Completed: 2455976K bytes transferred in 21 seconds (941503K 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 19208111 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1406632/SRR2889257.sra Written 19208111 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: 00:15:00 19208111 reads; of these: 19208111 (100.00%) were paired; of these: 9305708 (48.45%) aligned concordantly 0 times 8067346 (42.00%) aligned concordantly exactly 1 time 1835057 (9.55%) aligned concordantly >1 times ---- 9305708 pairs aligned concordantly 0 times; of these: 25242 (0.27%) aligned discordantly 1 time ---- 9280466 pairs aligned 0 times concordantly or discordantly; of these: 18560932 mates make up the pairs; of these: 18284245 (98.51%) aligned 0 times 203717 (1.10%) aligned exactly 1 time 72970 (0.39%) aligned >1 times 52.40% overall alignment rate Time searching: 00:15:00 Overall time: 00:15:00 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] 605417 / 9922634 = 0.0610 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 05:23:31: # Command line: callpeak -t SRX1406632.bam -f BAM -g 12100000 -n SRX1406632.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1406632.05 # format = BAM # ChIP-seq file = ['SRX1406632.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 05:23:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:23:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:23:31: # Command line: callpeak -t SRX1406632.bam -f BAM -g 12100000 -n SRX1406632.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1406632.10 # format = BAM # ChIP-seq file = ['SRX1406632.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 05:23:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:23:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:23:31: # Command line: callpeak -t SRX1406632.bam -f BAM -g 12100000 -n SRX1406632.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1406632.20 # format = BAM # ChIP-seq file = ['SRX1406632.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 05:23:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:23:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:23:41: 1000000 INFO @ Wed, 28 Jun 2017 05:23:41: 1000000 INFO @ Wed, 28 Jun 2017 05:23:41: 1000000 INFO @ Wed, 28 Jun 2017 05:23:50: 2000000 INFO @ Wed, 28 Jun 2017 05:23:51: 2000000 INFO @ Wed, 28 Jun 2017 05:23:51: 2000000 INFO @ Wed, 28 Jun 2017 05:23:59: 3000000 INFO @ Wed, 28 Jun 2017 05:24:01: 3000000 INFO @ Wed, 28 Jun 2017 05:24:01: 3000000 INFO @ Wed, 28 Jun 2017 05:24:09: 4000000 INFO @ Wed, 28 Jun 2017 05:24:11: 4000000 INFO @ Wed, 28 Jun 2017 05:24:11: 4000000 INFO @ Wed, 28 Jun 2017 05:24:18: 5000000 INFO @ Wed, 28 Jun 2017 05:24:21: 5000000 INFO @ Wed, 28 Jun 2017 05:24:21: 5000000 INFO @ Wed, 28 Jun 2017 05:24:27: 6000000 INFO @ Wed, 28 Jun 2017 05:24:30: 6000000 INFO @ Wed, 28 Jun 2017 05:24:31: 6000000 INFO @ Wed, 28 Jun 2017 05:24:36: 7000000 INFO @ Wed, 28 Jun 2017 05:24:40: 7000000 INFO @ Wed, 28 Jun 2017 05:24:40: 7000000 INFO @ Wed, 28 Jun 2017 05:24:46: 8000000 INFO @ Wed, 28 Jun 2017 05:24:50: 8000000 INFO @ Wed, 28 Jun 2017 05:24:50: 8000000 INFO @ Wed, 28 Jun 2017 05:24:55: 9000000 INFO @ Wed, 28 Jun 2017 05:25:00: 9000000 INFO @ Wed, 28 Jun 2017 05:25:00: 9000000 INFO @ Wed, 28 Jun 2017 05:25:04: 10000000 INFO @ Wed, 28 Jun 2017 05:25:10: 10000000 INFO @ Wed, 28 Jun 2017 05:25:10: 10000000 INFO @ Wed, 28 Jun 2017 05:25:13: 11000000 INFO @ Wed, 28 Jun 2017 05:25:20: 11000000 INFO @ Wed, 28 Jun 2017 05:25:20: 11000000 INFO @ Wed, 28 Jun 2017 05:25:22: 12000000 INFO @ Wed, 28 Jun 2017 05:25:29: 12000000 INFO @ Wed, 28 Jun 2017 05:25:30: 12000000 INFO @ Wed, 28 Jun 2017 05:25:32: 13000000 INFO @ Wed, 28 Jun 2017 05:25:39: 13000000 INFO @ Wed, 28 Jun 2017 05:25:39: 13000000 INFO @ Wed, 28 Jun 2017 05:25:41: 14000000 INFO @ Wed, 28 Jun 2017 05:25:49: 14000000 INFO @ Wed, 28 Jun 2017 05:25:49: 14000000 INFO @ Wed, 28 Jun 2017 05:25:50: 15000000 INFO @ Wed, 28 Jun 2017 05:25:59: 15000000 INFO @ Wed, 28 Jun 2017 05:25:59: 15000000 INFO @ Wed, 28 Jun 2017 05:26:00: 16000000 INFO @ Wed, 28 Jun 2017 05:26:08: 17000000 INFO @ Wed, 28 Jun 2017 05:26:09: 16000000 INFO @ Wed, 28 Jun 2017 05:26:09: 16000000 INFO @ Wed, 28 Jun 2017 05:26:17: 18000000 INFO @ Wed, 28 Jun 2017 05:26:19: 17000000 INFO @ Wed, 28 Jun 2017 05:26:19: 17000000 INFO @ Wed, 28 Jun 2017 05:26:26: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:26:26: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:26:26: #1 total tags in treatment: 9297159 INFO @ Wed, 28 Jun 2017 05:26:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:26:26: #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 05:26:27: #1 tags after filtering in treatment: 6864477 INFO @ Wed, 28 Jun 2017 05:26:27: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 05:26:27: #1 finished! INFO @ Wed, 28 Jun 2017 05:26:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:26:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:26:27: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:26:27: 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 05:26:27: Process for pairing-model is terminated! cat: SRX1406632.05_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 `SRX1406632.05_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 `SRX1406632.05_*.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 `SRX1406632.05_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 INFO @ Wed, 28 Jun 2017 05:26:28: 18000000 INFO @ Wed, 28 Jun 2017 05:26:29: 18000000 INFO @ Wed, 28 Jun 2017 05:26:36: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:26:36: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:26:36: #1 total tags in treatment: 9297159 INFO @ Wed, 28 Jun 2017 05:26:36: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:26:36: #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 05:26:37: #1 tags after filtering in treatment: 6864477 INFO @ Wed, 28 Jun 2017 05:26:37: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 05:26:37: #1 finished! INFO @ Wed, 28 Jun 2017 05:26:37: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:26:37: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:26:37: 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 05:26:37: Process for pairing-model is terminated! cat: SRX1406632.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1406632.20_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 `SRX1406632.20_*.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 `SRX1406632.20_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 05:26:37: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:26:37: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:26:37: #1 total tags in treatment: 9297159 INFO @ Wed, 28 Jun 2017 05:26:37: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:26:37: #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 05:26:37: #1 tags after filtering in treatment: 6864477 INFO @ Wed, 28 Jun 2017 05:26:37: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 05:26:37: #1 finished! INFO @ Wed, 28 Jun 2017 05:26:37: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:26:38: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:26:38: 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 05:26:38: Process for pairing-model is terminated! cat: SRX1406632.10_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 `SRX1406632.10_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 `SRX1406632.10_*.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 `SRX1406632.10_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。