Job ID = 11245065 sra ファイルのダウンロード中... Completed: 361279K bytes transferred in 11 seconds (250419K 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 12642829 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554777/SRR7696449.sra Written 12642829 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554777/SRR7696449.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: 00:06:30 12642829 reads; of these: 12642829 (100.00%) were paired; of these: 5890782 (46.59%) aligned concordantly 0 times 6524412 (51.61%) aligned concordantly exactly 1 time 227635 (1.80%) aligned concordantly >1 times ---- 5890782 pairs aligned concordantly 0 times; of these: 118142 (2.01%) aligned discordantly 1 time ---- 5772640 pairs aligned 0 times concordantly or discordantly; of these: 11545280 mates make up the pairs; of these: 6319132 (54.73%) aligned 0 times 4997160 (43.28%) aligned exactly 1 time 228988 (1.98%) aligned >1 times 75.01% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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] 407576 / 6869003 = 0.0593 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 @ Tue, 09 Oct 2018 23:29:24: # Command line: callpeak -t SRX4554777.bam -f BAM -g 12100000 -n SRX4554777.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554777.05 # format = BAM # ChIP-seq file = ['SRX4554777.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 @ Tue, 09 Oct 2018 23:29:24: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:29:24: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:29:24: # Command line: callpeak -t SRX4554777.bam -f BAM -g 12100000 -n SRX4554777.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554777.10 # format = BAM # ChIP-seq file = ['SRX4554777.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 @ Tue, 09 Oct 2018 23:29:24: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:29:24: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:29:24: # Command line: callpeak -t SRX4554777.bam -f BAM -g 12100000 -n SRX4554777.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554777.20 # format = BAM # ChIP-seq file = ['SRX4554777.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 @ Tue, 09 Oct 2018 23:29:24: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:29:24: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:29:29: 1000000 INFO @ Tue, 09 Oct 2018 23:29:29: 1000000 INFO @ Tue, 09 Oct 2018 23:29:29: 1000000 INFO @ Tue, 09 Oct 2018 23:29:33: 2000000 INFO @ Tue, 09 Oct 2018 23:29:33: 2000000 INFO @ Tue, 09 Oct 2018 23:29:34: 2000000 INFO @ Tue, 09 Oct 2018 23:29:38: 3000000 INFO @ Tue, 09 Oct 2018 23:29:38: 3000000 INFO @ Tue, 09 Oct 2018 23:29:38: 3000000 INFO @ Tue, 09 Oct 2018 23:29:43: 4000000 INFO @ Tue, 09 Oct 2018 23:29:43: 4000000 INFO @ Tue, 09 Oct 2018 23:29:43: 4000000 INFO @ Tue, 09 Oct 2018 23:29:47: 5000000 INFO @ Tue, 09 Oct 2018 23:29:48: 5000000 INFO @ Tue, 09 Oct 2018 23:29:48: 5000000 INFO @ Tue, 09 Oct 2018 23:29:52: 6000000 INFO @ Tue, 09 Oct 2018 23:29:53: 6000000 INFO @ Tue, 09 Oct 2018 23:29:53: 6000000 INFO @ Tue, 09 Oct 2018 23:29:57: 7000000 INFO @ Tue, 09 Oct 2018 23:29:58: 7000000 INFO @ Tue, 09 Oct 2018 23:29:58: 7000000 INFO @ Tue, 09 Oct 2018 23:30:01: 8000000 INFO @ Tue, 09 Oct 2018 23:30:02: 8000000 INFO @ Tue, 09 Oct 2018 23:30:03: 8000000 INFO @ Tue, 09 Oct 2018 23:30:06: 9000000 INFO @ Tue, 09 Oct 2018 23:30:07: 9000000 INFO @ Tue, 09 Oct 2018 23:30:08: 9000000 INFO @ Tue, 09 Oct 2018 23:30:11: 10000000 INFO @ Tue, 09 Oct 2018 23:30:12: 10000000 INFO @ Tue, 09 Oct 2018 23:30:12: 10000000 INFO @ Tue, 09 Oct 2018 23:30:16: 11000000 INFO @ Tue, 09 Oct 2018 23:30:17: 11000000 INFO @ Tue, 09 Oct 2018 23:30:17: 11000000 INFO @ Tue, 09 Oct 2018 23:30:20: 12000000 INFO @ Tue, 09 Oct 2018 23:30:21: 12000000 INFO @ Tue, 09 Oct 2018 23:30:22: 12000000 INFO @ Tue, 09 Oct 2018 23:30:25: 13000000 INFO @ Tue, 09 Oct 2018 23:30:26: 13000000 INFO @ Tue, 09 Oct 2018 23:30:27: 13000000 INFO @ Tue, 09 Oct 2018 23:30:29: 14000000 INFO @ Tue, 09 Oct 2018 23:30:31: 14000000 INFO @ Tue, 09 Oct 2018 23:30:32: 14000000 INFO @ Tue, 09 Oct 2018 23:30:34: 15000000 INFO @ Tue, 09 Oct 2018 23:30:36: 15000000 INFO @ Tue, 09 Oct 2018 23:30:37: 15000000 INFO @ Tue, 09 Oct 2018 23:30:39: 16000000 INFO @ Tue, 09 Oct 2018 23:30:40: 16000000 INFO @ Tue, 09 Oct 2018 23:30:42: 16000000 INFO @ Tue, 09 Oct 2018 23:30:43: 17000000 INFO @ Tue, 09 Oct 2018 23:30:45: 17000000 INFO @ Tue, 09 Oct 2018 23:30:47: 17000000 INFO @ Tue, 09 Oct 2018 23:30:48: 18000000 INFO @ Tue, 09 Oct 2018 23:30:49: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:30:49: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:30:49: #1 total tags in treatment: 6345441 INFO @ Tue, 09 Oct 2018 23:30:49: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:30:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:30:49: #1 tags after filtering in treatment: 3356530 INFO @ Tue, 09 Oct 2018 23:30:49: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:30:49: #1 finished! INFO @ Tue, 09 Oct 2018 23:30:49: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:30:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:30:49: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:30:49: 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 @ Tue, 09 Oct 2018 23:30:49: Process for pairing-model is terminated! cat: SRX4554777.20_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 `SRX4554777.20_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 `SRX4554777.20_*.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 `SRX4554777.20_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 @ Tue, 09 Oct 2018 23:30:50: 18000000 INFO @ Tue, 09 Oct 2018 23:30:50: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:30:50: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:30:50: #1 total tags in treatment: 6345441 INFO @ Tue, 09 Oct 2018 23:30:50: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:30:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:30:51: #1 tags after filtering in treatment: 3356530 INFO @ Tue, 09 Oct 2018 23:30:51: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:30:51: #1 finished! INFO @ Tue, 09 Oct 2018 23:30:51: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:30:51: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:30:51: 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 @ Tue, 09 Oct 2018 23:30:51: Process for pairing-model is terminated! cat: SRX4554777.05_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 `SRX4554777.05_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 `SRX4554777.05_*.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 `SRX4554777.05_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 @ Tue, 09 Oct 2018 23:30:52: 18000000 INFO @ Tue, 09 Oct 2018 23:30:52: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:30:52: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:30:52: #1 total tags in treatment: 6345441 INFO @ Tue, 09 Oct 2018 23:30:52: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:30:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:30:53: #1 tags after filtering in treatment: 3356530 INFO @ Tue, 09 Oct 2018 23:30:53: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:30:53: #1 finished! INFO @ Tue, 09 Oct 2018 23:30:53: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:30:53: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:30:53: 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 @ Tue, 09 Oct 2018 23:30:53: Process for pairing-model is terminated! cat: SRX4554777.10_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 `SRX4554777.10_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 `SRX4554777.10_*.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 `SRX4554777.10_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。