Job ID = 10045039 sra ファイルのダウンロード中... Completed: 489254K bytes transferred in 24 seconds (164682K bits/sec), in 2 files, 3 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 9942029 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2704969/SRR5413016.sra Written 9942029 spots total Written 10375032 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2704969/SRR5413015.sra Written 10375032 spots total 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: 00:08:42 20317061 reads; of these: 20317061 (100.00%) were paired; of these: 4955339 (24.39%) aligned concordantly 0 times 13166101 (64.80%) aligned concordantly exactly 1 time 2195621 (10.81%) aligned concordantly >1 times ---- 4955339 pairs aligned concordantly 0 times; of these: 566419 (11.43%) aligned discordantly 1 time ---- 4388920 pairs aligned 0 times concordantly or discordantly; of these: 8777840 mates make up the pairs; of these: 7487583 (85.30%) aligned 0 times 941646 (10.73%) aligned exactly 1 time 348611 (3.97%) aligned >1 times 81.57% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 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] 7263853 / 15472844 = 0.4695 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 @ Mon, 02 Oct 2017 14:53:36: # Command line: callpeak -t SRX2704969.bam -f BAM -g 12100000 -n SRX2704969.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2704969.05 # format = BAM # ChIP-seq file = ['SRX2704969.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 @ Mon, 02 Oct 2017 14:53:36: #1 read tag files... INFO @ Mon, 02 Oct 2017 14:53:36: # Command line: callpeak -t SRX2704969.bam -f BAM -g 12100000 -n SRX2704969.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2704969.10 # format = BAM # ChIP-seq file = ['SRX2704969.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 @ Mon, 02 Oct 2017 14:53:36: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 14:53:36: #1 read tag files... INFO @ Mon, 02 Oct 2017 14:53:36: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 14:53:36: # Command line: callpeak -t SRX2704969.bam -f BAM -g 12100000 -n SRX2704969.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2704969.20 # format = BAM # ChIP-seq file = ['SRX2704969.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 @ Mon, 02 Oct 2017 14:53:36: #1 read tag files... INFO @ Mon, 02 Oct 2017 14:53:36: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 14:53:41: 1000000 INFO @ Mon, 02 Oct 2017 14:53:41: 1000000 INFO @ Mon, 02 Oct 2017 14:53:41: 1000000 INFO @ Mon, 02 Oct 2017 14:53:46: 2000000 INFO @ Mon, 02 Oct 2017 14:53:46: 2000000 INFO @ Mon, 02 Oct 2017 14:53:46: 2000000 INFO @ Mon, 02 Oct 2017 14:53:50: 3000000 INFO @ Mon, 02 Oct 2017 14:53:51: 3000000 INFO @ Mon, 02 Oct 2017 14:53:51: 3000000 INFO @ Mon, 02 Oct 2017 14:53:55: 4000000 INFO @ Mon, 02 Oct 2017 14:53:56: 4000000 INFO @ Mon, 02 Oct 2017 14:53:56: 4000000 INFO @ Mon, 02 Oct 2017 14:54:00: 5000000 INFO @ Mon, 02 Oct 2017 14:54:01: 5000000 INFO @ Mon, 02 Oct 2017 14:54:01: 5000000 INFO @ Mon, 02 Oct 2017 14:54:05: 6000000 INFO @ Mon, 02 Oct 2017 14:54:06: 6000000 INFO @ Mon, 02 Oct 2017 14:54:06: 6000000 INFO @ Mon, 02 Oct 2017 14:54:10: 7000000 INFO @ Mon, 02 Oct 2017 14:54:11: 7000000 INFO @ Mon, 02 Oct 2017 14:54:12: 7000000 INFO @ Mon, 02 Oct 2017 14:54:15: 8000000 INFO @ Mon, 02 Oct 2017 14:54:16: 8000000 INFO @ Mon, 02 Oct 2017 14:54:17: 8000000 INFO @ Mon, 02 Oct 2017 14:54:20: 9000000 INFO @ Mon, 02 Oct 2017 14:54:22: 9000000 INFO @ Mon, 02 Oct 2017 14:54:23: 9000000 INFO @ Mon, 02 Oct 2017 14:54:25: 10000000 INFO @ Mon, 02 Oct 2017 14:54:27: 10000000 INFO @ Mon, 02 Oct 2017 14:54:29: 10000000 INFO @ Mon, 02 Oct 2017 14:54:30: 11000000 INFO @ Mon, 02 Oct 2017 14:54:32: 11000000 INFO @ Mon, 02 Oct 2017 14:54:34: 12000000 INFO @ Mon, 02 Oct 2017 14:54:35: 11000000 INFO @ Mon, 02 Oct 2017 14:54:38: 12000000 INFO @ Mon, 02 Oct 2017 14:54:39: 13000000 INFO @ Mon, 02 Oct 2017 14:54:40: 12000000 INFO @ Mon, 02 Oct 2017 14:54:43: 13000000 INFO @ Mon, 02 Oct 2017 14:54:44: 14000000 INFO @ Mon, 02 Oct 2017 14:54:46: 13000000 INFO @ Mon, 02 Oct 2017 14:54:48: 14000000 INFO @ Mon, 02 Oct 2017 14:54:48: 15000000 INFO @ Mon, 02 Oct 2017 14:54:51: 14000000 INFO @ Mon, 02 Oct 2017 14:54:53: 16000000 INFO @ Mon, 02 Oct 2017 14:54:54: 15000000 INFO @ Mon, 02 Oct 2017 14:54:57: 15000000 INFO @ Mon, 02 Oct 2017 14:54:58: 17000000 INFO @ Mon, 02 Oct 2017 14:54:59: 16000000 INFO @ Mon, 02 Oct 2017 14:55:03: 18000000 INFO @ Mon, 02 Oct 2017 14:55:03: 16000000 INFO @ Mon, 02 Oct 2017 14:55:04: 17000000 INFO @ Mon, 02 Oct 2017 14:55:06: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 14:55:06: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 14:55:06: #1 total tags in treatment: 8098869 INFO @ Mon, 02 Oct 2017 14:55:06: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 14:55:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 14:55:06: #1 tags after filtering in treatment: 3070869 INFO @ Mon, 02 Oct 2017 14:55:06: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 02 Oct 2017 14:55:06: #1 finished! INFO @ Mon, 02 Oct 2017 14:55:06: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 14:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 14:55:06: #2 number of paired peaks: 31 WARNING @ Mon, 02 Oct 2017 14:55:06: Too few paired peaks (31) 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 @ Mon, 02 Oct 2017 14:55:06: Process for pairing-model is terminated! cat: SRX2704969.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2704969.05_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 `SRX2704969.05_*.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 `SRX2704969.05_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 @ Mon, 02 Oct 2017 14:55:09: 17000000 INFO @ Mon, 02 Oct 2017 14:55:10: 18000000 INFO @ Mon, 02 Oct 2017 14:55:13: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 14:55:13: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 14:55:13: #1 total tags in treatment: 8098869 INFO @ Mon, 02 Oct 2017 14:55:13: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 14:55:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 14:55:13: #1 tags after filtering in treatment: 3070869 INFO @ Mon, 02 Oct 2017 14:55:13: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 02 Oct 2017 14:55:13: #1 finished! INFO @ Mon, 02 Oct 2017 14:55:13: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 14:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 14:55:13: #2 number of paired peaks: 31 WARNING @ Mon, 02 Oct 2017 14:55:13: Too few paired peaks (31) 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 @ Mon, 02 Oct 2017 14:55:13: Process for pairing-model is terminated! cat: SRX2704969.20_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2704969.20_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 `SRX2704969.20_*.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 `SRX2704969.20_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 @ Mon, 02 Oct 2017 14:55:14: 18000000 INFO @ Mon, 02 Oct 2017 14:55:17: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 14:55:17: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 14:55:17: #1 total tags in treatment: 8098869 INFO @ Mon, 02 Oct 2017 14:55:17: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 14:55:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 14:55:17: #1 tags after filtering in treatment: 3070869 INFO @ Mon, 02 Oct 2017 14:55:17: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 02 Oct 2017 14:55:17: #1 finished! INFO @ Mon, 02 Oct 2017 14:55:17: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 14:55:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 14:55:18: #2 number of paired peaks: 31 WARNING @ Mon, 02 Oct 2017 14:55:18: Too few paired peaks (31) 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 @ Mon, 02 Oct 2017 14:55:18: Process for pairing-model is terminated! cat: SRX2704969.10_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2704969.10_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 `SRX2704969.10_*.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 `SRX2704969.10_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。