Job ID = 10937433 sra ファイルのダウンロード中... Completed: 571093K bytes transferred in 7 seconds (598499K 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 10525253 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198728/SRR4304458.sra Written 10525253 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198728/SRR4304458.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: 00:07:34 10525253 reads; of these: 10525253 (100.00%) were paired; of these: 599028 (5.69%) aligned concordantly 0 times 8542455 (81.16%) aligned concordantly exactly 1 time 1383770 (13.15%) aligned concordantly >1 times ---- 599028 pairs aligned concordantly 0 times; of these: 250359 (41.79%) aligned discordantly 1 time ---- 348669 pairs aligned 0 times concordantly or discordantly; of these: 697338 mates make up the pairs; of these: 422144 (60.54%) aligned 0 times 158837 (22.78%) aligned exactly 1 time 116357 (16.69%) aligned >1 times 97.99% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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] 268781 / 10065937 = 0.0267 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 @ Fri, 10 Aug 2018 02:18:14: # Command line: callpeak -t SRX2198728.bam -f BAM -g 12100000 -n SRX2198728.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198728.10 # format = BAM # ChIP-seq file = ['SRX2198728.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 @ Fri, 10 Aug 2018 02:18:14: # Command line: callpeak -t SRX2198728.bam -f BAM -g 12100000 -n SRX2198728.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198728.05 # format = BAM # ChIP-seq file = ['SRX2198728.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 @ Fri, 10 Aug 2018 02:18:14: # Command line: callpeak -t SRX2198728.bam -f BAM -g 12100000 -n SRX2198728.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198728.20 # format = BAM # ChIP-seq file = ['SRX2198728.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 @ Fri, 10 Aug 2018 02:18:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:18:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:18:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:18:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:18:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:18:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:18:20: 1000000 INFO @ Fri, 10 Aug 2018 02:18:20: 1000000 INFO @ Fri, 10 Aug 2018 02:18:21: 1000000 INFO @ Fri, 10 Aug 2018 02:18:27: 2000000 INFO @ Fri, 10 Aug 2018 02:18:27: 2000000 INFO @ Fri, 10 Aug 2018 02:18:28: 2000000 INFO @ Fri, 10 Aug 2018 02:18:33: 3000000 INFO @ Fri, 10 Aug 2018 02:18:34: 3000000 INFO @ Fri, 10 Aug 2018 02:18:34: 3000000 INFO @ Fri, 10 Aug 2018 02:18:40: 4000000 INFO @ Fri, 10 Aug 2018 02:18:41: 4000000 INFO @ Fri, 10 Aug 2018 02:18:41: 4000000 INFO @ Fri, 10 Aug 2018 02:18:47: 5000000 INFO @ Fri, 10 Aug 2018 02:18:47: 5000000 INFO @ Fri, 10 Aug 2018 02:18:48: 5000000 INFO @ Fri, 10 Aug 2018 02:18:53: 6000000 INFO @ Fri, 10 Aug 2018 02:18:54: 6000000 INFO @ Fri, 10 Aug 2018 02:18:54: 6000000 INFO @ Fri, 10 Aug 2018 02:18:59: 7000000 INFO @ Fri, 10 Aug 2018 02:19:01: 7000000 INFO @ Fri, 10 Aug 2018 02:19:01: 7000000 INFO @ Fri, 10 Aug 2018 02:19:06: 8000000 INFO @ Fri, 10 Aug 2018 02:19:07: 8000000 INFO @ Fri, 10 Aug 2018 02:19:08: 8000000 INFO @ Fri, 10 Aug 2018 02:19:13: 9000000 INFO @ Fri, 10 Aug 2018 02:19:14: 9000000 INFO @ Fri, 10 Aug 2018 02:19:15: 9000000 INFO @ Fri, 10 Aug 2018 02:19:20: 10000000 INFO @ Fri, 10 Aug 2018 02:19:20: 10000000 INFO @ Fri, 10 Aug 2018 02:19:22: 10000000 INFO @ Fri, 10 Aug 2018 02:19:26: 11000000 INFO @ Fri, 10 Aug 2018 02:19:27: 11000000 INFO @ Fri, 10 Aug 2018 02:19:29: 11000000 INFO @ Fri, 10 Aug 2018 02:19:33: 12000000 INFO @ Fri, 10 Aug 2018 02:19:33: 12000000 INFO @ Fri, 10 Aug 2018 02:19:36: 12000000 INFO @ Fri, 10 Aug 2018 02:19:39: 13000000 INFO @ Fri, 10 Aug 2018 02:19:40: 13000000 INFO @ Fri, 10 Aug 2018 02:19:43: 13000000 INFO @ Fri, 10 Aug 2018 02:19:46: 14000000 INFO @ Fri, 10 Aug 2018 02:19:46: 14000000 INFO @ Fri, 10 Aug 2018 02:19:49: 14000000 INFO @ Fri, 10 Aug 2018 02:19:52: 15000000 INFO @ Fri, 10 Aug 2018 02:19:53: 15000000 INFO @ Fri, 10 Aug 2018 02:19:55: 15000000 INFO @ Fri, 10 Aug 2018 02:19:58: 16000000 INFO @ Fri, 10 Aug 2018 02:20:00: 16000000 INFO @ Fri, 10 Aug 2018 02:20:01: 16000000 INFO @ Fri, 10 Aug 2018 02:20:04: 17000000 INFO @ Fri, 10 Aug 2018 02:20:07: 17000000 INFO @ Fri, 10 Aug 2018 02:20:08: 17000000 INFO @ Fri, 10 Aug 2018 02:20:11: 18000000 INFO @ Fri, 10 Aug 2018 02:20:13: 18000000 INFO @ Fri, 10 Aug 2018 02:20:15: 18000000 INFO @ Fri, 10 Aug 2018 02:20:18: 19000000 INFO @ Fri, 10 Aug 2018 02:20:19: 19000000 INFO @ Fri, 10 Aug 2018 02:20:23: 19000000 INFO @ Fri, 10 Aug 2018 02:20:24: 20000000 INFO @ Fri, 10 Aug 2018 02:20:25: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:20:25: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:20:25: #1 total tags in treatment: 9658202 INFO @ Fri, 10 Aug 2018 02:20:25: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:20:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:20:25: #1 tags after filtering in treatment: 5535503 INFO @ Fri, 10 Aug 2018 02:20:25: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Aug 2018 02:20:25: #1 finished! INFO @ Fri, 10 Aug 2018 02:20:25: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:20:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:20:25: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:20:25: 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 @ Fri, 10 Aug 2018 02:20:25: Process for pairing-model is terminated! cat: SRX2198728.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198728.05_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 `SRX2198728.05_*.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 `SRX2198728.05_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 @ Fri, 10 Aug 2018 02:20:26: 20000000 INFO @ Fri, 10 Aug 2018 02:20:26: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:20:26: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:20:26: #1 total tags in treatment: 9658202 INFO @ Fri, 10 Aug 2018 02:20:26: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:20:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:20:26: #1 tags after filtering in treatment: 5535503 INFO @ Fri, 10 Aug 2018 02:20:26: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Aug 2018 02:20:26: #1 finished! INFO @ Fri, 10 Aug 2018 02:20:26: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:20:27: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:20:27: 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 @ Fri, 10 Aug 2018 02:20:27: Process for pairing-model is terminated! cat: SRX2198728.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198728.10_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 `SRX2198728.10_*.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 `SRX2198728.10_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 @ Fri, 10 Aug 2018 02:20:29: 20000000 INFO @ Fri, 10 Aug 2018 02:20:30: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:20:30: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:20:30: #1 total tags in treatment: 9658202 INFO @ Fri, 10 Aug 2018 02:20:30: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:20:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:20:30: #1 tags after filtering in treatment: 5535503 INFO @ Fri, 10 Aug 2018 02:20:30: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Aug 2018 02:20:30: #1 finished! INFO @ Fri, 10 Aug 2018 02:20:30: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:20:30: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:20:30: 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 @ Fri, 10 Aug 2018 02:20:30: Process for pairing-model is terminated! cat: SRX2198728.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198728.20_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 `SRX2198728.20_*.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 `SRX2198728.20_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。