Job ID = 9162087 sra ファイルのダウンロード中... Completed: 2860926K bytes transferred in 24 seconds (973000K 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 103537543 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1625710/SRR3218445.sra Written 103537543 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: 00:22:41 103537543 reads; of these: 103537543 (100.00%) were paired; of these: 91200728 (88.08%) aligned concordantly 0 times 10758495 (10.39%) aligned concordantly exactly 1 time 1578320 (1.52%) aligned concordantly >1 times ---- 91200728 pairs aligned concordantly 0 times; of these: 2237083 (2.45%) aligned discordantly 1 time ---- 88963645 pairs aligned 0 times concordantly or discordantly; of these: 177927290 mates make up the pairs; of these: 175689932 (98.74%) aligned 0 times 603359 (0.34%) aligned exactly 1 time 1633999 (0.92%) aligned >1 times 15.16% overall alignment rate Time searching: 00:22:41 Overall time: 00:22:41 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] 3771214 / 14567228 = 0.2589 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 06:27:38: # Command line: callpeak -t SRX1625710.bam -f BAM -g 12100000 -n SRX1625710.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1625710.05 # format = BAM # ChIP-seq file = ['SRX1625710.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 06:27:38: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:27:38: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:27:38: # Command line: callpeak -t SRX1625710.bam -f BAM -g 12100000 -n SRX1625710.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1625710.20 # format = BAM # ChIP-seq file = ['SRX1625710.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 06:27:38: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:27:38: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:27:38: # Command line: callpeak -t SRX1625710.bam -f BAM -g 12100000 -n SRX1625710.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1625710.10 # format = BAM # ChIP-seq file = ['SRX1625710.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 06:27:38: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:27:38: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:27:43: 1000000 INFO @ Wed, 28 Jun 2017 06:27:43: 1000000 INFO @ Wed, 28 Jun 2017 06:27:43: 1000000 INFO @ Wed, 28 Jun 2017 06:27:47: 2000000 INFO @ Wed, 28 Jun 2017 06:27:48: 2000000 INFO @ Wed, 28 Jun 2017 06:27:48: 2000000 INFO @ Wed, 28 Jun 2017 06:27:52: 3000000 INFO @ Wed, 28 Jun 2017 06:27:53: 3000000 INFO @ Wed, 28 Jun 2017 06:27:54: 3000000 INFO @ Wed, 28 Jun 2017 06:27:57: 4000000 INFO @ Wed, 28 Jun 2017 06:27:58: 4000000 INFO @ Wed, 28 Jun 2017 06:27:59: 4000000 INFO @ Wed, 28 Jun 2017 06:28:02: 5000000 INFO @ Wed, 28 Jun 2017 06:28:03: 5000000 INFO @ Wed, 28 Jun 2017 06:28:04: 5000000 INFO @ Wed, 28 Jun 2017 06:28:07: 6000000 INFO @ Wed, 28 Jun 2017 06:28:09: 6000000 INFO @ Wed, 28 Jun 2017 06:28:10: 6000000 INFO @ Wed, 28 Jun 2017 06:28:12: 7000000 INFO @ Wed, 28 Jun 2017 06:28:14: 7000000 INFO @ Wed, 28 Jun 2017 06:28:15: 7000000 INFO @ Wed, 28 Jun 2017 06:28:17: 8000000 INFO @ Wed, 28 Jun 2017 06:28:19: 8000000 INFO @ Wed, 28 Jun 2017 06:28:20: 8000000 INFO @ Wed, 28 Jun 2017 06:28:22: 9000000 INFO @ Wed, 28 Jun 2017 06:28:24: 9000000 INFO @ Wed, 28 Jun 2017 06:28:25: 9000000 INFO @ Wed, 28 Jun 2017 06:28:27: 10000000 INFO @ Wed, 28 Jun 2017 06:28:30: 10000000 INFO @ Wed, 28 Jun 2017 06:28:31: 10000000 INFO @ Wed, 28 Jun 2017 06:28:32: 11000000 INFO @ Wed, 28 Jun 2017 06:28:35: 11000000 INFO @ Wed, 28 Jun 2017 06:28:36: 11000000 INFO @ Wed, 28 Jun 2017 06:28:37: 12000000 INFO @ Wed, 28 Jun 2017 06:28:40: 12000000 INFO @ Wed, 28 Jun 2017 06:28:41: 12000000 INFO @ Wed, 28 Jun 2017 06:28:42: 13000000 INFO @ Wed, 28 Jun 2017 06:28:46: 13000000 INFO @ Wed, 28 Jun 2017 06:28:46: 13000000 INFO @ Wed, 28 Jun 2017 06:28:47: 14000000 INFO @ Wed, 28 Jun 2017 06:28:51: 14000000 INFO @ Wed, 28 Jun 2017 06:28:52: 14000000 INFO @ Wed, 28 Jun 2017 06:28:52: 15000000 INFO @ Wed, 28 Jun 2017 06:28:56: 15000000 INFO @ Wed, 28 Jun 2017 06:28:56: 16000000 INFO @ Wed, 28 Jun 2017 06:28:57: 15000000 INFO @ Wed, 28 Jun 2017 06:29:01: 16000000 INFO @ Wed, 28 Jun 2017 06:29:01: 16000000 INFO @ Wed, 28 Jun 2017 06:29:01: 17000000 INFO @ Wed, 28 Jun 2017 06:29:06: 17000000 INFO @ Wed, 28 Jun 2017 06:29:06: 17000000 INFO @ Wed, 28 Jun 2017 06:29:06: 18000000 INFO @ Wed, 28 Jun 2017 06:29:11: 18000000 INFO @ Wed, 28 Jun 2017 06:29:11: 19000000 INFO @ Wed, 28 Jun 2017 06:29:12: 18000000 INFO @ Wed, 28 Jun 2017 06:29:16: 20000000 INFO @ Wed, 28 Jun 2017 06:29:16: 19000000 INFO @ Wed, 28 Jun 2017 06:29:17: 19000000 INFO @ Wed, 28 Jun 2017 06:29:21: 21000000 INFO @ Wed, 28 Jun 2017 06:29:21: 20000000 INFO @ Wed, 28 Jun 2017 06:29:22: 20000000 INFO @ Wed, 28 Jun 2017 06:29:26: 22000000 INFO @ Wed, 28 Jun 2017 06:29:27: 21000000 INFO @ Wed, 28 Jun 2017 06:29:27: 21000000 INFO @ Wed, 28 Jun 2017 06:29:31: 23000000 INFO @ Wed, 28 Jun 2017 06:29:32: 22000000 INFO @ Wed, 28 Jun 2017 06:29:33: 22000000 INFO @ Wed, 28 Jun 2017 06:29:35: #1 tag size is determined as 25 bps INFO @ Wed, 28 Jun 2017 06:29:35: #1 tag size = 25 INFO @ Wed, 28 Jun 2017 06:29:35: #1 total tags in treatment: 8796406 INFO @ Wed, 28 Jun 2017 06:29:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:29:35: #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 06:29:35: #1 tags after filtering in treatment: 4870851 INFO @ Wed, 28 Jun 2017 06:29:35: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 28 Jun 2017 06:29:35: #1 finished! INFO @ Wed, 28 Jun 2017 06:29:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:29:36: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:29:36: 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 06:29:36: Process for pairing-model is terminated! cat: SRX1625710.20_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 `SRX1625710.20_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 `SRX1625710.20_*.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 `SRX1625710.20_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 06:29:37: 23000000 INFO @ Wed, 28 Jun 2017 06:29:38: 23000000 INFO @ Wed, 28 Jun 2017 06:29:41: #1 tag size is determined as 25 bps INFO @ Wed, 28 Jun 2017 06:29:41: #1 tag size = 25 INFO @ Wed, 28 Jun 2017 06:29:41: #1 total tags in treatment: 8796406 INFO @ Wed, 28 Jun 2017 06:29:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:29:41: #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 06:29:42: #1 tags after filtering in treatment: 4870851 INFO @ Wed, 28 Jun 2017 06:29:42: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 28 Jun 2017 06:29:42: #1 finished! INFO @ Wed, 28 Jun 2017 06:29:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:29:42: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:29:42: 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 06:29:42: Process for pairing-model is terminated! cat: SRX1625710.05_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 `SRX1625710.05_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 `SRX1625710.05_*.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 `SRX1625710.05_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 06:29:42: #1 tag size is determined as 25 bps INFO @ Wed, 28 Jun 2017 06:29:42: #1 tag size = 25 INFO @ Wed, 28 Jun 2017 06:29:42: #1 total tags in treatment: 8796406 INFO @ Wed, 28 Jun 2017 06:29:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:29:42: #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 06:29:43: #1 tags after filtering in treatment: 4870851 INFO @ Wed, 28 Jun 2017 06:29:43: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 28 Jun 2017 06:29:43: #1 finished! INFO @ Wed, 28 Jun 2017 06:29:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:29:43: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:29:43: 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 06:29:43: Process for pairing-model is terminated! cat: SRX1625710.10_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 `SRX1625710.10_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 `SRX1625710.10_*.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 `SRX1625710.10_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。