Job ID = 9161983 sra ファイルのダウンロード中... Completed: 962065K bytes transferred in 11 seconds (657873K 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 15234053 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423715/SRR2931004.sra Written 15234053 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: 00:11:13 15234053 reads; of these: 15234053 (100.00%) were paired; of these: 2411911 (15.83%) aligned concordantly 0 times 11611990 (76.22%) aligned concordantly exactly 1 time 1210152 (7.94%) aligned concordantly >1 times ---- 2411911 pairs aligned concordantly 0 times; of these: 53946 (2.24%) aligned discordantly 1 time ---- 2357965 pairs aligned 0 times concordantly or discordantly; of these: 4715930 mates make up the pairs; of these: 4608443 (97.72%) aligned 0 times 82609 (1.75%) aligned exactly 1 time 24878 (0.53%) aligned >1 times 84.87% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 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] 4790358 / 12853202 = 0.3727 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 05:28:06: # Command line: callpeak -t SRX1423715.bam -f BAM -g 12100000 -n SRX1423715.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423715.20 # format = BAM # ChIP-seq file = ['SRX1423715.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 05:28:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:28:06: # Command line: callpeak -t SRX1423715.bam -f BAM -g 12100000 -n SRX1423715.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423715.10 # format = BAM # ChIP-seq file = ['SRX1423715.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 05:28:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:28:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:28:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:28:06: # Command line: callpeak -t SRX1423715.bam -f BAM -g 12100000 -n SRX1423715.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423715.05 # format = BAM # ChIP-seq file = ['SRX1423715.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 05:28:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:28:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:28:13: 1000000 INFO @ Wed, 28 Jun 2017 05:28:13: 1000000 INFO @ Wed, 28 Jun 2017 05:28:13: 1000000 INFO @ Wed, 28 Jun 2017 05:28:20: 2000000 INFO @ Wed, 28 Jun 2017 05:28:20: 2000000 INFO @ Wed, 28 Jun 2017 05:28:20: 2000000 INFO @ Wed, 28 Jun 2017 05:28:26: 3000000 INFO @ Wed, 28 Jun 2017 05:28:26: 3000000 INFO @ Wed, 28 Jun 2017 05:28:26: 3000000 INFO @ Wed, 28 Jun 2017 05:28:33: 4000000 INFO @ Wed, 28 Jun 2017 05:28:33: 4000000 INFO @ Wed, 28 Jun 2017 05:28:33: 4000000 INFO @ Wed, 28 Jun 2017 05:28:39: 5000000 INFO @ Wed, 28 Jun 2017 05:28:39: 5000000 INFO @ Wed, 28 Jun 2017 05:28:39: 5000000 INFO @ Wed, 28 Jun 2017 05:28:46: 6000000 INFO @ Wed, 28 Jun 2017 05:28:46: 6000000 INFO @ Wed, 28 Jun 2017 05:28:46: 6000000 INFO @ Wed, 28 Jun 2017 05:28:53: 7000000 INFO @ Wed, 28 Jun 2017 05:28:53: 7000000 INFO @ Wed, 28 Jun 2017 05:28:53: 7000000 INFO @ Wed, 28 Jun 2017 05:28:59: 8000000 INFO @ Wed, 28 Jun 2017 05:28:59: 8000000 INFO @ Wed, 28 Jun 2017 05:28:59: 8000000 INFO @ Wed, 28 Jun 2017 05:29:06: 9000000 INFO @ Wed, 28 Jun 2017 05:29:06: 9000000 INFO @ Wed, 28 Jun 2017 05:29:06: 9000000 INFO @ Wed, 28 Jun 2017 05:29:12: 10000000 INFO @ Wed, 28 Jun 2017 05:29:12: 10000000 INFO @ Wed, 28 Jun 2017 05:29:12: 10000000 INFO @ Wed, 28 Jun 2017 05:29:18: 11000000 INFO @ Wed, 28 Jun 2017 05:29:19: 11000000 INFO @ Wed, 28 Jun 2017 05:29:19: 11000000 INFO @ Wed, 28 Jun 2017 05:29:25: 12000000 INFO @ Wed, 28 Jun 2017 05:29:25: 12000000 INFO @ Wed, 28 Jun 2017 05:29:25: 12000000 INFO @ Wed, 28 Jun 2017 05:29:31: 13000000 INFO @ Wed, 28 Jun 2017 05:29:31: 13000000 INFO @ Wed, 28 Jun 2017 05:29:32: 13000000 INFO @ Wed, 28 Jun 2017 05:29:38: 14000000 INFO @ Wed, 28 Jun 2017 05:29:38: 14000000 INFO @ Wed, 28 Jun 2017 05:29:38: 14000000 INFO @ Wed, 28 Jun 2017 05:29:44: 15000000 INFO @ Wed, 28 Jun 2017 05:29:44: 15000000 INFO @ Wed, 28 Jun 2017 05:29:45: 15000000 INFO @ Wed, 28 Jun 2017 05:29:51: 16000000 INFO @ Wed, 28 Jun 2017 05:29:51: 16000000 INFO @ Wed, 28 Jun 2017 05:29:52: 16000000 INFO @ Wed, 28 Jun 2017 05:29:53: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:29:53: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:29:53: #1 total tags in treatment: 8053795 INFO @ Wed, 28 Jun 2017 05:29:53: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:29:53: #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 05:29:53: #1 tags after filtering in treatment: 5748434 INFO @ Wed, 28 Jun 2017 05:29:53: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 05:29:53: #1 finished! INFO @ Wed, 28 Jun 2017 05:29:53: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:29:53: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:29:53: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:29:53: #1 total tags in treatment: 8053795 INFO @ Wed, 28 Jun 2017 05:29:53: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:29:53: #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 05:29:53: #1 tags after filtering in treatment: 5748434 INFO @ Wed, 28 Jun 2017 05:29:53: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 05:29:53: #1 finished! INFO @ Wed, 28 Jun 2017 05:29:53: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:29:54: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:29:54: 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 05:29:54: Process for pairing-model is terminated! cat: SRX1423715.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Wed, 28 Jun 2017 05:29:54: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:29:54: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:29:54: #1 total tags in treatment: 8053795 INFO @ Wed, 28 Jun 2017 05:29:54: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:29:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1423715.10_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 `SRX1423715.10_*.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 `SRX1423715.10_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 05:29:54: #1 tags after filtering in treatment: 5748434 INFO @ Wed, 28 Jun 2017 05:29:54: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 05:29:54: #1 finished! INFO @ Wed, 28 Jun 2017 05:29:54: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:29:54: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:29:54: 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 05:29:54: Process for pairing-model is terminated! cat: SRX1423715.20_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 `SRX1423715.20_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 `SRX1423715.20_*.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 `SRX1423715.20_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 05:29:54: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:29:54: 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 05:29:54: Process for pairing-model is terminated! cat: SRX1423715.05_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 `SRX1423715.05_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 `SRX1423715.05_*.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 `SRX1423715.05_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。