Job ID = 10536456 sra ファイルのダウンロード中... Completed: 1552231K bytes transferred in 31 seconds (400977K 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... Written 36278419 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671170/SRR6696922.sra Written 36278419 spots total 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: 00:18:01 36278419 reads; of these: 36278419 (100.00%) were paired; of these: 14786674 (40.76%) aligned concordantly 0 times 18694843 (51.53%) aligned concordantly exactly 1 time 2796902 (7.71%) aligned concordantly >1 times ---- 14786674 pairs aligned concordantly 0 times; of these: 52838 (0.36%) aligned discordantly 1 time ---- 14733836 pairs aligned 0 times concordantly or discordantly; of these: 29467672 mates make up the pairs; of these: 29050711 (98.59%) aligned 0 times 341333 (1.16%) aligned exactly 1 time 75628 (0.26%) aligned >1 times 59.96% overall alignment rate Time searching: 00:18:01 Overall time: 00:18:01 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 20 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] 10022602 / 21512071 = 0.4659 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 @ Thu, 05 Apr 2018 10:12:27: # Command line: callpeak -t SRX3671170.bam -f BAM -g 12100000 -n SRX3671170.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671170.20 # format = BAM # ChIP-seq file = ['SRX3671170.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 @ Thu, 05 Apr 2018 10:12:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:12:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:12:27: # Command line: callpeak -t SRX3671170.bam -f BAM -g 12100000 -n SRX3671170.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671170.05 # format = BAM # ChIP-seq file = ['SRX3671170.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 @ Thu, 05 Apr 2018 10:12:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:12:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:12:27: # Command line: callpeak -t SRX3671170.bam -f BAM -g 12100000 -n SRX3671170.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671170.10 # format = BAM # ChIP-seq file = ['SRX3671170.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 @ Thu, 05 Apr 2018 10:12:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:12:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:12:33: 1000000 INFO @ Thu, 05 Apr 2018 10:12:33: 1000000 INFO @ Thu, 05 Apr 2018 10:12:33: 1000000 INFO @ Thu, 05 Apr 2018 10:12:39: 2000000 INFO @ Thu, 05 Apr 2018 10:12:39: 2000000 INFO @ Thu, 05 Apr 2018 10:12:39: 2000000 INFO @ Thu, 05 Apr 2018 10:12:45: 3000000 INFO @ Thu, 05 Apr 2018 10:12:46: 3000000 INFO @ Thu, 05 Apr 2018 10:12:46: 3000000 INFO @ Thu, 05 Apr 2018 10:12:52: 4000000 INFO @ Thu, 05 Apr 2018 10:12:52: 4000000 INFO @ Thu, 05 Apr 2018 10:12:52: 4000000 INFO @ Thu, 05 Apr 2018 10:12:58: 5000000 INFO @ Thu, 05 Apr 2018 10:12:58: 5000000 INFO @ Thu, 05 Apr 2018 10:12:59: 5000000 INFO @ Thu, 05 Apr 2018 10:13:04: 6000000 INFO @ Thu, 05 Apr 2018 10:13:05: 6000000 INFO @ Thu, 05 Apr 2018 10:13:05: 6000000 INFO @ Thu, 05 Apr 2018 10:13:11: 7000000 INFO @ Thu, 05 Apr 2018 10:13:12: 7000000 INFO @ Thu, 05 Apr 2018 10:13:12: 7000000 INFO @ Thu, 05 Apr 2018 10:13:18: 8000000 INFO @ Thu, 05 Apr 2018 10:13:18: 8000000 INFO @ Thu, 05 Apr 2018 10:13:19: 8000000 INFO @ Thu, 05 Apr 2018 10:13:24: 9000000 INFO @ Thu, 05 Apr 2018 10:13:25: 9000000 INFO @ Thu, 05 Apr 2018 10:13:26: 9000000 INFO @ Thu, 05 Apr 2018 10:13:31: 10000000 INFO @ Thu, 05 Apr 2018 10:13:32: 10000000 INFO @ Thu, 05 Apr 2018 10:13:33: 10000000 INFO @ Thu, 05 Apr 2018 10:13:38: 11000000 INFO @ Thu, 05 Apr 2018 10:13:39: 11000000 INFO @ Thu, 05 Apr 2018 10:13:40: 11000000 INFO @ Thu, 05 Apr 2018 10:13:45: 12000000 INFO @ Thu, 05 Apr 2018 10:13:46: 12000000 INFO @ Thu, 05 Apr 2018 10:13:47: 12000000 INFO @ Thu, 05 Apr 2018 10:13:52: 13000000 INFO @ Thu, 05 Apr 2018 10:13:53: 13000000 INFO @ Thu, 05 Apr 2018 10:13:54: 13000000 INFO @ Thu, 05 Apr 2018 10:13:58: 14000000 INFO @ Thu, 05 Apr 2018 10:14:00: 14000000 INFO @ Thu, 05 Apr 2018 10:14:01: 14000000 INFO @ Thu, 05 Apr 2018 10:14:05: 15000000 INFO @ Thu, 05 Apr 2018 10:14:07: 15000000 INFO @ Thu, 05 Apr 2018 10:14:08: 15000000 INFO @ Thu, 05 Apr 2018 10:14:12: 16000000 INFO @ Thu, 05 Apr 2018 10:14:15: 16000000 INFO @ Thu, 05 Apr 2018 10:14:16: 16000000 INFO @ Thu, 05 Apr 2018 10:14:19: 17000000 INFO @ Thu, 05 Apr 2018 10:14:22: 17000000 INFO @ Thu, 05 Apr 2018 10:14:23: 17000000 INFO @ Thu, 05 Apr 2018 10:14:26: 18000000 INFO @ Thu, 05 Apr 2018 10:14:29: 18000000 INFO @ Thu, 05 Apr 2018 10:14:30: 18000000 INFO @ Thu, 05 Apr 2018 10:14:33: 19000000 INFO @ Thu, 05 Apr 2018 10:14:36: 19000000 INFO @ Thu, 05 Apr 2018 10:14:37: 19000000 INFO @ Thu, 05 Apr 2018 10:14:39: 20000000 INFO @ Thu, 05 Apr 2018 10:14:43: 20000000 INFO @ Thu, 05 Apr 2018 10:14:44: 20000000 INFO @ Thu, 05 Apr 2018 10:14:46: 21000000 INFO @ Thu, 05 Apr 2018 10:14:50: 21000000 INFO @ Thu, 05 Apr 2018 10:14:52: 21000000 INFO @ Thu, 05 Apr 2018 10:14:53: 22000000 INFO @ Thu, 05 Apr 2018 10:14:57: 22000000 INFO @ Thu, 05 Apr 2018 10:14:59: 22000000 INFO @ Thu, 05 Apr 2018 10:15:00: 23000000 INFO @ Thu, 05 Apr 2018 10:15:03: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:15:03: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:15:03: #1 total tags in treatment: 11479846 INFO @ Thu, 05 Apr 2018 10:15:03: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:15:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:15:03: #1 tags after filtering in treatment: 8257976 INFO @ Thu, 05 Apr 2018 10:15:03: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 05 Apr 2018 10:15:03: #1 finished! INFO @ Thu, 05 Apr 2018 10:15:03: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:15:04: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:15:04: 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 @ Thu, 05 Apr 2018 10:15:04: Process for pairing-model is terminated! cat: SRX3671170.05_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 `SRX3671170.05_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 `SRX3671170.05_*.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 `SRX3671170.05_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 @ Thu, 05 Apr 2018 10:15:04: 23000000 INFO @ Thu, 05 Apr 2018 10:15:06: 23000000 INFO @ Thu, 05 Apr 2018 10:15:07: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:15:07: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:15:07: #1 total tags in treatment: 11479846 INFO @ Thu, 05 Apr 2018 10:15:07: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:15:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:15:08: #1 tags after filtering in treatment: 8257976 INFO @ Thu, 05 Apr 2018 10:15:08: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 05 Apr 2018 10:15:08: #1 finished! INFO @ Thu, 05 Apr 2018 10:15:08: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:15:08: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:15:08: 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 @ Thu, 05 Apr 2018 10:15:08: Process for pairing-model is terminated! cat: SRX3671170.20_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 `SRX3671170.20_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 `SRX3671170.20_*.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 `SRX3671170.20_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 @ Thu, 05 Apr 2018 10:15:08: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:15:08: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:15:08: #1 total tags in treatment: 11479846 INFO @ Thu, 05 Apr 2018 10:15:08: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:15:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:15:09: #1 tags after filtering in treatment: 8257976 INFO @ Thu, 05 Apr 2018 10:15:09: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 05 Apr 2018 10:15:09: #1 finished! INFO @ Thu, 05 Apr 2018 10:15:09: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:15:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:15:09: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:15:09: 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 @ Thu, 05 Apr 2018 10:15:09: Process for pairing-model is terminated! cat: SRX3671170.10_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 `SRX3671170.10_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 `SRX3671170.10_*.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 `SRX3671170.10_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。