Job ID = 9163054 sra ファイルのダウンロード中... Completed: 1241607K bytes transferred in 13 seconds (736722K 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 4516197 spots for /home/okishinya/chipatlas/results/sacCer3/SRX475227/SRR1175176.sra Written 4516197 spots total Written 4570484 spots for /home/okishinya/chipatlas/results/sacCer3/SRX475227/SRR1175175.sra Written 4570484 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: 00:10:10 9086681 reads; of these: 9086681 (100.00%) were paired; of these: 4166652 (45.85%) aligned concordantly 0 times 3646646 (40.13%) aligned concordantly exactly 1 time 1273383 (14.01%) aligned concordantly >1 times ---- 4166652 pairs aligned concordantly 0 times; of these: 449304 (10.78%) aligned discordantly 1 time ---- 3717348 pairs aligned 0 times concordantly or discordantly; of these: 7434696 mates make up the pairs; of these: 7011126 (94.30%) aligned 0 times 75029 (1.01%) aligned exactly 1 time 348541 (4.69%) aligned >1 times 61.42% overall alignment rate Time searching: 00:10:10 Overall time: 00:10:10 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] 245742 / 5321178 = 0.0462 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 10:02:53: # Command line: callpeak -t SRX475227.bam -f BAM -g 12100000 -n SRX475227.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX475227.10 # format = BAM # ChIP-seq file = ['SRX475227.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 10:02:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:02:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:02:53: # Command line: callpeak -t SRX475227.bam -f BAM -g 12100000 -n SRX475227.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX475227.20 # format = BAM # ChIP-seq file = ['SRX475227.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 10:02:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:02:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:02:53: # Command line: callpeak -t SRX475227.bam -f BAM -g 12100000 -n SRX475227.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX475227.05 # format = BAM # ChIP-seq file = ['SRX475227.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 10:02:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:02:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:03:01: 1000000 INFO @ Wed, 28 Jun 2017 10:03:01: 1000000 INFO @ Wed, 28 Jun 2017 10:03:01: 1000000 INFO @ Wed, 28 Jun 2017 10:03:09: 2000000 INFO @ Wed, 28 Jun 2017 10:03:09: 2000000 INFO @ Wed, 28 Jun 2017 10:03:09: 2000000 INFO @ Wed, 28 Jun 2017 10:03:16: 3000000 INFO @ Wed, 28 Jun 2017 10:03:17: 3000000 INFO @ Wed, 28 Jun 2017 10:03:17: 3000000 INFO @ Wed, 28 Jun 2017 10:03:24: 4000000 INFO @ Wed, 28 Jun 2017 10:03:24: 4000000 INFO @ Wed, 28 Jun 2017 10:03:25: 4000000 INFO @ Wed, 28 Jun 2017 10:03:32: 5000000 INFO @ Wed, 28 Jun 2017 10:03:32: 5000000 INFO @ Wed, 28 Jun 2017 10:03:33: 5000000 INFO @ Wed, 28 Jun 2017 10:03:39: 6000000 INFO @ Wed, 28 Jun 2017 10:03:40: 6000000 INFO @ Wed, 28 Jun 2017 10:03:41: 6000000 INFO @ Wed, 28 Jun 2017 10:03:46: 7000000 INFO @ Wed, 28 Jun 2017 10:03:47: 7000000 INFO @ Wed, 28 Jun 2017 10:03:48: 7000000 INFO @ Wed, 28 Jun 2017 10:03:54: 8000000 INFO @ Wed, 28 Jun 2017 10:03:55: 8000000 INFO @ Wed, 28 Jun 2017 10:03:56: 8000000 INFO @ Wed, 28 Jun 2017 10:04:02: 9000000 INFO @ Wed, 28 Jun 2017 10:04:03: 9000000 INFO @ Wed, 28 Jun 2017 10:04:04: 9000000 INFO @ Wed, 28 Jun 2017 10:04:10: 10000000 INFO @ Wed, 28 Jun 2017 10:04:10: 10000000 INFO @ Wed, 28 Jun 2017 10:04:13: 10000000 INFO @ Wed, 28 Jun 2017 10:04:15: #1 tag size is determined as 126 bps INFO @ Wed, 28 Jun 2017 10:04:15: #1 tag size = 126 INFO @ Wed, 28 Jun 2017 10:04:15: #1 total tags in treatment: 4684601 INFO @ Wed, 28 Jun 2017 10:04:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:04:15: #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 10:04:15: #1 tags after filtering in treatment: 3469707 INFO @ Wed, 28 Jun 2017 10:04:15: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 10:04:15: #1 finished! INFO @ Wed, 28 Jun 2017 10:04:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:04:15: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 10:04:15: Too few paired peaks (29) 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 10:04:15: Process for pairing-model is terminated! cat: SRX475227.05_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 `SRX475227.05_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 `SRX475227.05_*.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 `SRX475227.05_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 10:04:16: #1 tag size is determined as 126 bps INFO @ Wed, 28 Jun 2017 10:04:16: #1 tag size = 126 INFO @ Wed, 28 Jun 2017 10:04:16: #1 total tags in treatment: 4684601 INFO @ Wed, 28 Jun 2017 10:04:16: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:04:16: #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 10:04:16: #1 tags after filtering in treatment: 3469707 INFO @ Wed, 28 Jun 2017 10:04:16: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 10:04:16: #1 finished! INFO @ Wed, 28 Jun 2017 10:04:16: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:04:17: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 10:04:17: Too few paired peaks (29) 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 10:04:17: Process for pairing-model is terminated! cat: SRX475227.10_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 `SRX475227.10_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 `SRX475227.10_*.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 `SRX475227.10_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 10:04:19: #1 tag size is determined as 126 bps INFO @ Wed, 28 Jun 2017 10:04:19: #1 tag size = 126 INFO @ Wed, 28 Jun 2017 10:04:19: #1 total tags in treatment: 4684601 INFO @ Wed, 28 Jun 2017 10:04:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:04:19: #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 10:04:19: #1 tags after filtering in treatment: 3469707 INFO @ Wed, 28 Jun 2017 10:04:19: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 10:04:19: #1 finished! INFO @ Wed, 28 Jun 2017 10:04:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:04:19: #2 number of paired peaks: 29 WARNING @ Wed, 28 Jun 2017 10:04:19: Too few paired peaks (29) 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 10:04:19: Process for pairing-model is terminated! cat: SRX475227.20_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 `SRX475227.20_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 `SRX475227.20_*.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 `SRX475227.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。