Job ID = 11244943 sra ファイルのダウンロード中... Completed: 474086K bytes transferred in 8 seconds (463253K 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 14564427 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554675/SRR7696348.sra Written 14564427 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554675/SRR7696348.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: 00:08:12 14564427 reads; of these: 14564427 (100.00%) were paired; of these: 2987134 (20.51%) aligned concordantly 0 times 8990301 (61.73%) aligned concordantly exactly 1 time 2586992 (17.76%) aligned concordantly >1 times ---- 2987134 pairs aligned concordantly 0 times; of these: 284973 (9.54%) aligned discordantly 1 time ---- 2702161 pairs aligned 0 times concordantly or discordantly; of these: 5404322 mates make up the pairs; of these: 4846692 (89.68%) aligned 0 times 290090 (5.37%) aligned exactly 1 time 267540 (4.95%) aligned >1 times 83.36% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 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] 935191 / 11803110 = 0.0792 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 23:09:37: # Command line: callpeak -t SRX4554675.bam -f BAM -g 12100000 -n SRX4554675.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554675.10 # format = BAM # ChIP-seq file = ['SRX4554675.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 23:09:37: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:09:37: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:09:37: # Command line: callpeak -t SRX4554675.bam -f BAM -g 12100000 -n SRX4554675.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554675.20 # format = BAM # ChIP-seq file = ['SRX4554675.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 23:09:37: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:09:37: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:09:37: # Command line: callpeak -t SRX4554675.bam -f BAM -g 12100000 -n SRX4554675.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554675.05 # format = BAM # ChIP-seq file = ['SRX4554675.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 23:09:37: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:09:37: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:09:43: 1000000 INFO @ Tue, 09 Oct 2018 23:09:43: 1000000 INFO @ Tue, 09 Oct 2018 23:09:43: 1000000 INFO @ Tue, 09 Oct 2018 23:09:48: 2000000 INFO @ Tue, 09 Oct 2018 23:09:48: 2000000 INFO @ Tue, 09 Oct 2018 23:09:48: 2000000 INFO @ Tue, 09 Oct 2018 23:09:53: 3000000 INFO @ Tue, 09 Oct 2018 23:09:53: 3000000 INFO @ Tue, 09 Oct 2018 23:09:53: 3000000 INFO @ Tue, 09 Oct 2018 23:09:58: 4000000 INFO @ Tue, 09 Oct 2018 23:09:58: 4000000 INFO @ Tue, 09 Oct 2018 23:09:59: 4000000 INFO @ Tue, 09 Oct 2018 23:10:03: 5000000 INFO @ Tue, 09 Oct 2018 23:10:03: 5000000 INFO @ Tue, 09 Oct 2018 23:10:04: 5000000 INFO @ Tue, 09 Oct 2018 23:10:08: 6000000 INFO @ Tue, 09 Oct 2018 23:10:08: 6000000 INFO @ Tue, 09 Oct 2018 23:10:09: 6000000 INFO @ Tue, 09 Oct 2018 23:10:13: 7000000 INFO @ Tue, 09 Oct 2018 23:10:13: 7000000 INFO @ Tue, 09 Oct 2018 23:10:14: 7000000 INFO @ Tue, 09 Oct 2018 23:10:18: 8000000 INFO @ Tue, 09 Oct 2018 23:10:18: 8000000 INFO @ Tue, 09 Oct 2018 23:10:19: 8000000 INFO @ Tue, 09 Oct 2018 23:10:23: 9000000 INFO @ Tue, 09 Oct 2018 23:10:23: 9000000 INFO @ Tue, 09 Oct 2018 23:10:24: 9000000 INFO @ Tue, 09 Oct 2018 23:10:28: 10000000 INFO @ Tue, 09 Oct 2018 23:10:28: 10000000 INFO @ Tue, 09 Oct 2018 23:10:30: 10000000 INFO @ Tue, 09 Oct 2018 23:10:33: 11000000 INFO @ Tue, 09 Oct 2018 23:10:33: 11000000 INFO @ Tue, 09 Oct 2018 23:10:35: 11000000 INFO @ Tue, 09 Oct 2018 23:10:38: 12000000 INFO @ Tue, 09 Oct 2018 23:10:38: 12000000 INFO @ Tue, 09 Oct 2018 23:10:40: 12000000 INFO @ Tue, 09 Oct 2018 23:10:43: 13000000 INFO @ Tue, 09 Oct 2018 23:10:44: 13000000 INFO @ Tue, 09 Oct 2018 23:10:45: 13000000 INFO @ Tue, 09 Oct 2018 23:10:49: 14000000 INFO @ Tue, 09 Oct 2018 23:10:49: 14000000 INFO @ Tue, 09 Oct 2018 23:10:51: 14000000 INFO @ Tue, 09 Oct 2018 23:10:54: 15000000 INFO @ Tue, 09 Oct 2018 23:10:54: 15000000 INFO @ Tue, 09 Oct 2018 23:10:56: 15000000 INFO @ Tue, 09 Oct 2018 23:10:59: 16000000 INFO @ Tue, 09 Oct 2018 23:10:59: 16000000 INFO @ Tue, 09 Oct 2018 23:11:01: 16000000 INFO @ Tue, 09 Oct 2018 23:11:04: 17000000 INFO @ Tue, 09 Oct 2018 23:11:04: 17000000 INFO @ Tue, 09 Oct 2018 23:11:06: 17000000 INFO @ Tue, 09 Oct 2018 23:11:09: 18000000 INFO @ Tue, 09 Oct 2018 23:11:09: 18000000 INFO @ Tue, 09 Oct 2018 23:11:11: 18000000 INFO @ Tue, 09 Oct 2018 23:11:14: 19000000 INFO @ Tue, 09 Oct 2018 23:11:14: 19000000 INFO @ Tue, 09 Oct 2018 23:11:16: 19000000 INFO @ Tue, 09 Oct 2018 23:11:19: 20000000 INFO @ Tue, 09 Oct 2018 23:11:19: 20000000 INFO @ Tue, 09 Oct 2018 23:11:21: 20000000 INFO @ Tue, 09 Oct 2018 23:11:24: 21000000 INFO @ Tue, 09 Oct 2018 23:11:24: 21000000 INFO @ Tue, 09 Oct 2018 23:11:27: 21000000 INFO @ Tue, 09 Oct 2018 23:11:29: 22000000 INFO @ Tue, 09 Oct 2018 23:11:30: 22000000 INFO @ Tue, 09 Oct 2018 23:11:31: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:31: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:31: #1 total tags in treatment: 10654413 INFO @ Tue, 09 Oct 2018 23:11:31: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:31: #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 23:11:32: #1 tags after filtering in treatment: 6329814 INFO @ Tue, 09 Oct 2018 23:11:32: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:11:32: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:32: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:32: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:32: #1 total tags in treatment: 10654413 INFO @ Tue, 09 Oct 2018 23:11:32: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:32: #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 23:11:32: 22000000 INFO @ Tue, 09 Oct 2018 23:11:32: #1 tags after filtering in treatment: 6329814 INFO @ Tue, 09 Oct 2018 23:11:32: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:11:32: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:32: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:11:32: 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 23:11:32: Process for pairing-model is terminated! cat: SRX4554675.05_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 `SRX4554675.05_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 `SRX4554675.05_*.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 `SRX4554675.05_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 23:11:32: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:11:32: 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 23:11:32: Process for pairing-model is terminated! cat: SRX4554675.20_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 `SRX4554675.20_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 `SRX4554675.20_*.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 `SRX4554675.20_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 23:11:34: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:34: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:34: #1 total tags in treatment: 10654413 INFO @ Tue, 09 Oct 2018 23:11:34: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:34: #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 23:11:34: #1 tags after filtering in treatment: 6329814 INFO @ Tue, 09 Oct 2018 23:11:34: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:11:34: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:34: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:35: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:11:35: 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 23:11:35: Process for pairing-model is terminated! cat: SRX4554675.10_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 `SRX4554675.10_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 `SRX4554675.10_*.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 `SRX4554675.10_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。