Job ID = 11245200 sra ファイルのダウンロード中... Completed: 409893K bytes transferred in 7 seconds (462000K bits/sec), in 1 file. Completed: 414703K bytes transferred in 6 seconds (505461K bits/sec), in 1 file. Completed: 199057K bytes transferred in 5 seconds (320768K 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 1926353 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669654/SRR7818276.sra Written 1926353 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669654/SRR7818276.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669654/SRR7818275.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669654/SRR7818275.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669654/SRR7818274.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669654/SRR7818274.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: 00:08:45 9926353 reads; of these: 9926353 (100.00%) were paired; of these: 1540335 (15.52%) aligned concordantly 0 times 7698933 (77.56%) aligned concordantly exactly 1 time 687085 (6.92%) aligned concordantly >1 times ---- 1540335 pairs aligned concordantly 0 times; of these: 116400 (7.56%) aligned discordantly 1 time ---- 1423935 pairs aligned 0 times concordantly or discordantly; of these: 2847870 mates make up the pairs; of these: 2549187 (89.51%) aligned 0 times 219823 (7.72%) aligned exactly 1 time 78860 (2.77%) aligned >1 times 87.16% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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] 90556 / 8480291 = 0.0107 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 00:04:01: # Command line: callpeak -t SRX4669654.bam -f BAM -g 12100000 -n SRX4669654.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669654.20 # format = BAM # ChIP-seq file = ['SRX4669654.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 00:04:01: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:01: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:01: # Command line: callpeak -t SRX4669654.bam -f BAM -g 12100000 -n SRX4669654.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669654.05 # format = BAM # ChIP-seq file = ['SRX4669654.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 00:04:01: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:01: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:01: # Command line: callpeak -t SRX4669654.bam -f BAM -g 12100000 -n SRX4669654.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669654.10 # format = BAM # ChIP-seq file = ['SRX4669654.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 00:04:01: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:01: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:07: 1000000 INFO @ Wed, 10 Oct 2018 00:04:07: 1000000 INFO @ Wed, 10 Oct 2018 00:04:07: 1000000 INFO @ Wed, 10 Oct 2018 00:04:13: 2000000 INFO @ Wed, 10 Oct 2018 00:04:14: 2000000 INFO @ Wed, 10 Oct 2018 00:04:14: 2000000 INFO @ Wed, 10 Oct 2018 00:04:20: 3000000 INFO @ Wed, 10 Oct 2018 00:04:20: 3000000 INFO @ Wed, 10 Oct 2018 00:04:21: 3000000 INFO @ Wed, 10 Oct 2018 00:04:27: 4000000 INFO @ Wed, 10 Oct 2018 00:04:27: 4000000 INFO @ Wed, 10 Oct 2018 00:04:28: 4000000 INFO @ Wed, 10 Oct 2018 00:04:33: 5000000 INFO @ Wed, 10 Oct 2018 00:04:34: 5000000 INFO @ Wed, 10 Oct 2018 00:04:35: 5000000 INFO @ Wed, 10 Oct 2018 00:04:40: 6000000 INFO @ Wed, 10 Oct 2018 00:04:41: 6000000 INFO @ Wed, 10 Oct 2018 00:04:42: 6000000 INFO @ Wed, 10 Oct 2018 00:04:47: 7000000 INFO @ Wed, 10 Oct 2018 00:04:48: 7000000 INFO @ Wed, 10 Oct 2018 00:04:49: 7000000 INFO @ Wed, 10 Oct 2018 00:04:54: 8000000 INFO @ Wed, 10 Oct 2018 00:04:55: 8000000 INFO @ Wed, 10 Oct 2018 00:04:57: 8000000 INFO @ Wed, 10 Oct 2018 00:05:01: 9000000 INFO @ Wed, 10 Oct 2018 00:05:02: 9000000 INFO @ Wed, 10 Oct 2018 00:05:04: 9000000 INFO @ Wed, 10 Oct 2018 00:05:08: 10000000 INFO @ Wed, 10 Oct 2018 00:05:09: 10000000 INFO @ Wed, 10 Oct 2018 00:05:11: 10000000 INFO @ Wed, 10 Oct 2018 00:05:15: 11000000 INFO @ Wed, 10 Oct 2018 00:05:16: 11000000 INFO @ Wed, 10 Oct 2018 00:05:18: 11000000 INFO @ Wed, 10 Oct 2018 00:05:21: 12000000 INFO @ Wed, 10 Oct 2018 00:05:22: 12000000 INFO @ Wed, 10 Oct 2018 00:05:24: 12000000 INFO @ Wed, 10 Oct 2018 00:05:27: 13000000 INFO @ Wed, 10 Oct 2018 00:05:28: 13000000 INFO @ Wed, 10 Oct 2018 00:05:30: 13000000 INFO @ Wed, 10 Oct 2018 00:05:34: 14000000 INFO @ Wed, 10 Oct 2018 00:05:34: 14000000 INFO @ Wed, 10 Oct 2018 00:05:37: 14000000 INFO @ Wed, 10 Oct 2018 00:05:40: 15000000 INFO @ Wed, 10 Oct 2018 00:05:41: 15000000 INFO @ Wed, 10 Oct 2018 00:05:43: 15000000 INFO @ Wed, 10 Oct 2018 00:05:46: 16000000 INFO @ Wed, 10 Oct 2018 00:05:47: 16000000 INFO @ Wed, 10 Oct 2018 00:05:49: 16000000 INFO @ Wed, 10 Oct 2018 00:05:52: 17000000 INFO @ Wed, 10 Oct 2018 00:05:53: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:05:53: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:05:53: #1 total tags in treatment: 8296121 INFO @ Wed, 10 Oct 2018 00:05:53: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:05:53: #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 00:05:53: #1 tags after filtering in treatment: 6412413 INFO @ Wed, 10 Oct 2018 00:05:53: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 10 Oct 2018 00:05:53: #1 finished! INFO @ Wed, 10 Oct 2018 00:05:53: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:05:53: 17000000 INFO @ Wed, 10 Oct 2018 00:05:54: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:05:54: 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 00:05:54: Process for pairing-model is terminated! cat: SRX4669654.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669654.20_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 `SRX4669654.20_*.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 `SRX4669654.20_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 @ Wed, 10 Oct 2018 00:05:54: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:05:54: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:05:54: #1 total tags in treatment: 8296121 INFO @ Wed, 10 Oct 2018 00:05:54: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:05:54: #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 00:05:54: #1 tags after filtering in treatment: 6412413 INFO @ Wed, 10 Oct 2018 00:05:54: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 10 Oct 2018 00:05:54: #1 finished! INFO @ Wed, 10 Oct 2018 00:05:54: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:05:55: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:05:55: 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 00:05:55: Process for pairing-model is terminated! cat: SRX4669654.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669654.10_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 `SRX4669654.10_*.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 `SRX4669654.10_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 00:05:55: 17000000 INFO @ Wed, 10 Oct 2018 00:05:56: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:05:56: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:05:56: #1 total tags in treatment: 8296121 INFO @ Wed, 10 Oct 2018 00:05:56: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:05:56: #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 00:05:56: #1 tags after filtering in treatment: 6412413 INFO @ Wed, 10 Oct 2018 00:05:56: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 10 Oct 2018 00:05:56: #1 finished! INFO @ Wed, 10 Oct 2018 00:05:56: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:05:56: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:05:56: 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 00:05:56: Process for pairing-model is terminated! cat: SRX4669654.05_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 `SRX4669654.05_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 `SRX4669654.05_*.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 `SRX4669654.05_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。