Job ID = 11245213 sra ファイルのダウンロード中... Completed: 411570K bytes transferred in 7 seconds (462542K bits/sec), in 1 file. Completed: 414827K bytes transferred in 7 seconds (463781K bits/sec), in 1 file. Completed: 419361K bytes transferred in 6 seconds (491377K bits/sec), in 1 file. Completed: 230369K bytes transferred in 5 seconds (344310K 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 2214864 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669664/SRR7818304.sra Written 2214864 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669664/SRR7818304.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669664/SRR7818303.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669664/SRR7818303.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669664/SRR7818301.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669664/SRR7818301.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669664/SRR7818302.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669664/SRR7818302.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 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: 00:13:20 14214864 reads; of these: 14214864 (100.00%) were paired; of these: 2179269 (15.33%) aligned concordantly 0 times 10541332 (74.16%) aligned concordantly exactly 1 time 1494263 (10.51%) aligned concordantly >1 times ---- 2179269 pairs aligned concordantly 0 times; of these: 181599 (8.33%) aligned discordantly 1 time ---- 1997670 pairs aligned 0 times concordantly or discordantly; of these: 3995340 mates make up the pairs; of these: 3409402 (85.33%) aligned 0 times 430263 (10.77%) aligned exactly 1 time 155675 (3.90%) aligned >1 times 88.01% overall alignment rate Time searching: 00:13:20 Overall time: 00:13:20 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] 245311 / 12177409 = 0.0201 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, 10 Oct 2018 00:14:18: # Command line: callpeak -t SRX4669664.bam -f BAM -g 12100000 -n SRX4669664.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669664.05 # format = BAM # ChIP-seq file = ['SRX4669664.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, 10 Oct 2018 00:14:18: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:14:18: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:14:18: # Command line: callpeak -t SRX4669664.bam -f BAM -g 12100000 -n SRX4669664.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669664.20 # format = BAM # ChIP-seq file = ['SRX4669664.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, 10 Oct 2018 00:14:18: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:14:18: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:14:18: # Command line: callpeak -t SRX4669664.bam -f BAM -g 12100000 -n SRX4669664.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669664.10 # format = BAM # ChIP-seq file = ['SRX4669664.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, 10 Oct 2018 00:14:18: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:14:18: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:14:26: 1000000 INFO @ Wed, 10 Oct 2018 00:14:27: 1000000 INFO @ Wed, 10 Oct 2018 00:14:27: 1000000 INFO @ Wed, 10 Oct 2018 00:14:34: 2000000 INFO @ Wed, 10 Oct 2018 00:14:35: 2000000 INFO @ Wed, 10 Oct 2018 00:14:35: 2000000 INFO @ Wed, 10 Oct 2018 00:14:42: 3000000 INFO @ Wed, 10 Oct 2018 00:14:44: 3000000 INFO @ Wed, 10 Oct 2018 00:14:44: 3000000 INFO @ Wed, 10 Oct 2018 00:14:50: 4000000 INFO @ Wed, 10 Oct 2018 00:14:53: 4000000 INFO @ Wed, 10 Oct 2018 00:14:53: 4000000 INFO @ Wed, 10 Oct 2018 00:14:58: 5000000 INFO @ Wed, 10 Oct 2018 00:15:02: 5000000 INFO @ Wed, 10 Oct 2018 00:15:02: 5000000 INFO @ Wed, 10 Oct 2018 00:15:06: 6000000 INFO @ Wed, 10 Oct 2018 00:15:11: 6000000 INFO @ Wed, 10 Oct 2018 00:15:11: 6000000 INFO @ Wed, 10 Oct 2018 00:15:13: 7000000 INFO @ Wed, 10 Oct 2018 00:15:20: 7000000 INFO @ Wed, 10 Oct 2018 00:15:20: 7000000 INFO @ Wed, 10 Oct 2018 00:15:21: 8000000 INFO @ Wed, 10 Oct 2018 00:15:28: 8000000 INFO @ Wed, 10 Oct 2018 00:15:28: 8000000 INFO @ Wed, 10 Oct 2018 00:15:29: 9000000 INFO @ Wed, 10 Oct 2018 00:15:37: 10000000 INFO @ Wed, 10 Oct 2018 00:15:37: 9000000 INFO @ Wed, 10 Oct 2018 00:15:37: 9000000 INFO @ Wed, 10 Oct 2018 00:15:44: 11000000 INFO @ Wed, 10 Oct 2018 00:15:46: 10000000 INFO @ Wed, 10 Oct 2018 00:15:46: 10000000 INFO @ Wed, 10 Oct 2018 00:15:52: 12000000 INFO @ Wed, 10 Oct 2018 00:15:54: 11000000 INFO @ Wed, 10 Oct 2018 00:15:54: 11000000 INFO @ Wed, 10 Oct 2018 00:16:00: 13000000 INFO @ Wed, 10 Oct 2018 00:16:03: 12000000 INFO @ Wed, 10 Oct 2018 00:16:03: 12000000 INFO @ Wed, 10 Oct 2018 00:16:08: 14000000 INFO @ Wed, 10 Oct 2018 00:16:12: 13000000 INFO @ Wed, 10 Oct 2018 00:16:12: 13000000 INFO @ Wed, 10 Oct 2018 00:16:15: 15000000 INFO @ Wed, 10 Oct 2018 00:16:20: 14000000 INFO @ Wed, 10 Oct 2018 00:16:20: 14000000 INFO @ Wed, 10 Oct 2018 00:16:23: 16000000 INFO @ Wed, 10 Oct 2018 00:16:29: 15000000 INFO @ Wed, 10 Oct 2018 00:16:29: 15000000 INFO @ Wed, 10 Oct 2018 00:16:31: 17000000 INFO @ Wed, 10 Oct 2018 00:16:38: 16000000 INFO @ Wed, 10 Oct 2018 00:16:38: 16000000 INFO @ Wed, 10 Oct 2018 00:16:38: 18000000 INFO @ Wed, 10 Oct 2018 00:16:46: 19000000 INFO @ Wed, 10 Oct 2018 00:16:46: 17000000 INFO @ Wed, 10 Oct 2018 00:16:46: 17000000 INFO @ Wed, 10 Oct 2018 00:16:53: 20000000 INFO @ Wed, 10 Oct 2018 00:16:55: 18000000 INFO @ Wed, 10 Oct 2018 00:16:55: 18000000 INFO @ Wed, 10 Oct 2018 00:17:01: 21000000 INFO @ Wed, 10 Oct 2018 00:17:03: 19000000 INFO @ Wed, 10 Oct 2018 00:17:03: 19000000 INFO @ Wed, 10 Oct 2018 00:17:09: 22000000 INFO @ Wed, 10 Oct 2018 00:17:12: 20000000 INFO @ Wed, 10 Oct 2018 00:17:12: 20000000 INFO @ Wed, 10 Oct 2018 00:17:16: 23000000 INFO @ Wed, 10 Oct 2018 00:17:21: 21000000 INFO @ Wed, 10 Oct 2018 00:17:21: 21000000 INFO @ Wed, 10 Oct 2018 00:17:24: 24000000 INFO @ Wed, 10 Oct 2018 00:17:28: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:17:28: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:17:28: #1 total tags in treatment: 11791757 INFO @ Wed, 10 Oct 2018 00:17:28: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:17:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:17:28: #1 tags after filtering in treatment: 8594493 INFO @ Wed, 10 Oct 2018 00:17:28: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 10 Oct 2018 00:17:28: #1 finished! INFO @ Wed, 10 Oct 2018 00:17:28: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:17:29: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:17:29: 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, 10 Oct 2018 00:17:29: Process for pairing-model is terminated! cat: SRX4669664.10_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 `SRX4669664.10_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 `SRX4669664.10_*.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 `SRX4669664.10_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, 10 Oct 2018 00:17:29: 22000000 INFO @ Wed, 10 Oct 2018 00:17:29: 22000000 INFO @ Wed, 10 Oct 2018 00:17:38: 23000000 INFO @ Wed, 10 Oct 2018 00:17:38: 23000000 INFO @ Wed, 10 Oct 2018 00:17:47: 24000000 INFO @ Wed, 10 Oct 2018 00:17:47: 24000000 INFO @ Wed, 10 Oct 2018 00:17:52: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:17:52: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:17:52: #1 total tags in treatment: 11791757 INFO @ Wed, 10 Oct 2018 00:17:52: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:17:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:17:52: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:17:52: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:17:52: #1 total tags in treatment: 11791757 INFO @ Wed, 10 Oct 2018 00:17:52: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:17:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:17:52: #1 tags after filtering in treatment: 8594493 INFO @ Wed, 10 Oct 2018 00:17:52: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 10 Oct 2018 00:17:52: #1 finished! INFO @ Wed, 10 Oct 2018 00:17:52: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:17:52: #1 tags after filtering in treatment: 8594493 INFO @ Wed, 10 Oct 2018 00:17:52: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 10 Oct 2018 00:17:52: #1 finished! INFO @ Wed, 10 Oct 2018 00:17:52: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:17:52: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:17:52: 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, 10 Oct 2018 00:17:52: Process for pairing-model is terminated! cat: SRX4669664.05_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 `SRX4669664.05_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 `SRX4669664.05_*.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 `SRX4669664.05_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, 10 Oct 2018 00:17:53: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:17:53: 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, 10 Oct 2018 00:17:53: Process for pairing-model is terminated! cat: SRX4669664.20_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 `SRX4669664.20_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 `SRX4669664.20_*.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 `SRX4669664.20_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。