Job ID = 11192883 sra ファイルのダウンロード中... Completed: 626928K bytes transferred in 38 seconds (131975K bits/sec), in 1 file. 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... Read 11185790 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771761/SRR5488916.sra Written 11185790 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771761/SRR5488916.sra rm: cannot remove `[DSE]RX*': 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 `[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: 00:08:00 11185790 reads; of these: 11185790 (100.00%) were paired; of these: 4137836 (36.99%) aligned concordantly 0 times 5961718 (53.30%) aligned concordantly exactly 1 time 1086236 (9.71%) aligned concordantly >1 times ---- 4137836 pairs aligned concordantly 0 times; of these: 339377 (8.20%) aligned discordantly 1 time ---- 3798459 pairs aligned 0 times concordantly or discordantly; of these: 7596918 mates make up the pairs; of these: 7242490 (95.33%) aligned 0 times 222667 (2.93%) aligned exactly 1 time 131761 (1.73%) aligned >1 times 67.63% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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 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] 1095748 / 7369156 = 0.1487 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 @ Sat, 15 Sep 2018 10:28:43: # Command line: callpeak -t SRX2771761.bam -f BAM -g 12100000 -n SRX2771761.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2771761.20 # format = BAM # ChIP-seq file = ['SRX2771761.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 @ Sat, 15 Sep 2018 10:28:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:28:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:28:43: # Command line: callpeak -t SRX2771761.bam -f BAM -g 12100000 -n SRX2771761.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2771761.05 # format = BAM # ChIP-seq file = ['SRX2771761.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 @ Sat, 15 Sep 2018 10:28:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:28:43: # Command line: callpeak -t SRX2771761.bam -f BAM -g 12100000 -n SRX2771761.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2771761.10 # format = BAM # ChIP-seq file = ['SRX2771761.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 @ Sat, 15 Sep 2018 10:28:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:28:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:28:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:28:50: 1000000 INFO @ Sat, 15 Sep 2018 10:28:51: 1000000 INFO @ Sat, 15 Sep 2018 10:28:51: 1000000 INFO @ Sat, 15 Sep 2018 10:28:57: 2000000 INFO @ Sat, 15 Sep 2018 10:28:58: 2000000 INFO @ Sat, 15 Sep 2018 10:28:58: 2000000 INFO @ Sat, 15 Sep 2018 10:29:04: 3000000 INFO @ Sat, 15 Sep 2018 10:29:06: 3000000 INFO @ Sat, 15 Sep 2018 10:29:06: 3000000 INFO @ Sat, 15 Sep 2018 10:29:11: 4000000 INFO @ Sat, 15 Sep 2018 10:29:13: 4000000 INFO @ Sat, 15 Sep 2018 10:29:13: 4000000 INFO @ Sat, 15 Sep 2018 10:29:17: 5000000 INFO @ Sat, 15 Sep 2018 10:29:20: 5000000 INFO @ Sat, 15 Sep 2018 10:29:20: 5000000 INFO @ Sat, 15 Sep 2018 10:29:24: 6000000 INFO @ Sat, 15 Sep 2018 10:29:27: 6000000 INFO @ Sat, 15 Sep 2018 10:29:27: 6000000 INFO @ Sat, 15 Sep 2018 10:29:31: 7000000 INFO @ Sat, 15 Sep 2018 10:29:35: 7000000 INFO @ Sat, 15 Sep 2018 10:29:35: 7000000 INFO @ Sat, 15 Sep 2018 10:29:38: 8000000 INFO @ Sat, 15 Sep 2018 10:29:42: 8000000 INFO @ Sat, 15 Sep 2018 10:29:42: 8000000 INFO @ Sat, 15 Sep 2018 10:29:44: 9000000 INFO @ Sat, 15 Sep 2018 10:29:49: 9000000 INFO @ Sat, 15 Sep 2018 10:29:49: 9000000 INFO @ Sat, 15 Sep 2018 10:29:52: 10000000 INFO @ Sat, 15 Sep 2018 10:29:56: 10000000 INFO @ Sat, 15 Sep 2018 10:29:57: 10000000 INFO @ Sat, 15 Sep 2018 10:29:59: 11000000 INFO @ Sat, 15 Sep 2018 10:30:02: 11000000 INFO @ Sat, 15 Sep 2018 10:30:04: 11000000 INFO @ Sat, 15 Sep 2018 10:30:07: 12000000 INFO @ Sat, 15 Sep 2018 10:30:09: 12000000 INFO @ Sat, 15 Sep 2018 10:30:12: 12000000 INFO @ Sat, 15 Sep 2018 10:30:13: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:30:13: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:30:13: #1 total tags in treatment: 5970818 INFO @ Sat, 15 Sep 2018 10:30:13: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:30:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:30:14: #1 tags after filtering in treatment: 4589077 INFO @ Sat, 15 Sep 2018 10:30:14: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Sep 2018 10:30:14: #1 finished! INFO @ Sat, 15 Sep 2018 10:30:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:30:14: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 10:30:14: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 10:30:14: Process for pairing-model is terminated! cat: SRX2771761.20_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 `SRX2771761.20_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 `SRX2771761.20_*.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 `SRX2771761.20_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 @ Sat, 15 Sep 2018 10:30:15: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:30:15: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:30:15: #1 total tags in treatment: 5970818 INFO @ Sat, 15 Sep 2018 10:30:15: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:30:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:30:15: #1 tags after filtering in treatment: 4589077 INFO @ Sat, 15 Sep 2018 10:30:15: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Sep 2018 10:30:15: #1 finished! INFO @ Sat, 15 Sep 2018 10:30:15: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:30:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:30:16: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 10:30:16: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 10:30:16: Process for pairing-model is terminated! cat: SRX2771761.10_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 `SRX2771761.10_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 `SRX2771761.10_*.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 `SRX2771761.10_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 @ Sat, 15 Sep 2018 10:30:18: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:30:18: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:30:18: #1 total tags in treatment: 5970818 INFO @ Sat, 15 Sep 2018 10:30:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:30:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:30:18: #1 tags after filtering in treatment: 4589077 INFO @ Sat, 15 Sep 2018 10:30:18: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Sep 2018 10:30:18: #1 finished! INFO @ Sat, 15 Sep 2018 10:30:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:30:19: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 10:30:19: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 10:30:19: Process for pairing-model is terminated! cat: SRX2771761.05_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 `SRX2771761.05_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 `SRX2771761.05_*.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 `SRX2771761.05_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。