Job ID = 11245128 sra ファイルのダウンロード中... Completed: 343105K bytes transferred in 6 seconds (411580K 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 7011466 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669582/SRR7818156.sra Written 7011466 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669582/SRR7818156.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: 00:04:40 7011466 reads; of these: 7011466 (100.00%) were paired; of these: 830904 (11.85%) aligned concordantly 0 times 5617395 (80.12%) aligned concordantly exactly 1 time 563167 (8.03%) aligned concordantly >1 times ---- 830904 pairs aligned concordantly 0 times; of these: 28988 (3.49%) aligned discordantly 1 time ---- 801916 pairs aligned 0 times concordantly or discordantly; of these: 1603832 mates make up the pairs; of these: 1435517 (89.51%) aligned 0 times 115462 (7.20%) aligned exactly 1 time 52853 (3.30%) aligned >1 times 89.76% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 62032 / 6188871 = 0.0100 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 23:37:53: # Command line: callpeak -t SRX4669582.bam -f BAM -g 12100000 -n SRX4669582.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669582.20 # format = BAM # ChIP-seq file = ['SRX4669582.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 23:37:53: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:53: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:53: # Command line: callpeak -t SRX4669582.bam -f BAM -g 12100000 -n SRX4669582.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669582.05 # format = BAM # ChIP-seq file = ['SRX4669582.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 23:37:53: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:53: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:53: # Command line: callpeak -t SRX4669582.bam -f BAM -g 12100000 -n SRX4669582.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669582.10 # format = BAM # ChIP-seq file = ['SRX4669582.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 23:37:53: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:53: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:59: 1000000 INFO @ Tue, 09 Oct 2018 23:37:59: 1000000 INFO @ Tue, 09 Oct 2018 23:38:00: 1000000 INFO @ Tue, 09 Oct 2018 23:38:06: 2000000 INFO @ Tue, 09 Oct 2018 23:38:06: 2000000 INFO @ Tue, 09 Oct 2018 23:38:07: 2000000 INFO @ Tue, 09 Oct 2018 23:38:13: 3000000 INFO @ Tue, 09 Oct 2018 23:38:13: 3000000 INFO @ Tue, 09 Oct 2018 23:38:15: 3000000 INFO @ Tue, 09 Oct 2018 23:38:20: 4000000 INFO @ Tue, 09 Oct 2018 23:38:20: 4000000 INFO @ Tue, 09 Oct 2018 23:38:22: 4000000 INFO @ Tue, 09 Oct 2018 23:38:26: 5000000 INFO @ Tue, 09 Oct 2018 23:38:26: 5000000 INFO @ Tue, 09 Oct 2018 23:38:29: 5000000 INFO @ Tue, 09 Oct 2018 23:38:33: 6000000 INFO @ Tue, 09 Oct 2018 23:38:33: 6000000 INFO @ Tue, 09 Oct 2018 23:38:36: 6000000 INFO @ Tue, 09 Oct 2018 23:38:40: 7000000 INFO @ Tue, 09 Oct 2018 23:38:40: 7000000 INFO @ Tue, 09 Oct 2018 23:38:44: 7000000 INFO @ Tue, 09 Oct 2018 23:38:47: 8000000 INFO @ Tue, 09 Oct 2018 23:38:47: 8000000 INFO @ Tue, 09 Oct 2018 23:38:51: 8000000 INFO @ Tue, 09 Oct 2018 23:38:53: 9000000 INFO @ Tue, 09 Oct 2018 23:38:53: 9000000 INFO @ Tue, 09 Oct 2018 23:38:58: 9000000 INFO @ Tue, 09 Oct 2018 23:39:00: 10000000 INFO @ Tue, 09 Oct 2018 23:39:00: 10000000 INFO @ Tue, 09 Oct 2018 23:39:06: 10000000 INFO @ Tue, 09 Oct 2018 23:39:06: 11000000 INFO @ Tue, 09 Oct 2018 23:39:06: 11000000 INFO @ Tue, 09 Oct 2018 23:39:13: 12000000 INFO @ Tue, 09 Oct 2018 23:39:13: 12000000 INFO @ Tue, 09 Oct 2018 23:39:13: 11000000 INFO @ Tue, 09 Oct 2018 23:39:16: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:39:16: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:39:16: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:39:16: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:39:16: #1 total tags in treatment: 6118627 INFO @ Tue, 09 Oct 2018 23:39:16: #1 total tags in treatment: 6118627 INFO @ Tue, 09 Oct 2018 23:39:16: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:39:16: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:39:16: #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 23:39:16: #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 23:39:16: #1 tags after filtering in treatment: 4835825 INFO @ Tue, 09 Oct 2018 23:39:16: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:39:16: #1 tags after filtering in treatment: 4835825 INFO @ Tue, 09 Oct 2018 23:39:16: #1 finished! INFO @ Tue, 09 Oct 2018 23:39:16: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:39:16: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:39:16: #1 finished! INFO @ Tue, 09 Oct 2018 23:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:39:16: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:39:16: #2 number of paired peaks: 12 WARNING @ Tue, 09 Oct 2018 23:39:16: Too few paired peaks (12) 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 23:39:16: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:39:16: #2 number of paired peaks: 12 WARNING @ Tue, 09 Oct 2018 23:39:16: Too few paired peaks (12) 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 23:39:16: Process for pairing-model is terminated! cat: SRX4669582.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4669582.20_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) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669582.05_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 `SRX4669582.05_*.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 `SRX4669582.20_model.r'rm: cannot remove `SRX4669582.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません : 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 `SRX4669582.20_*.xls': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling rm: cannot remove `SRX4669582.20_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 23:39:21: 12000000 INFO @ Tue, 09 Oct 2018 23:39:24: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:39:24: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:39:24: #1 total tags in treatment: 6118627 INFO @ Tue, 09 Oct 2018 23:39:24: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:39:24: #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 23:39:24: #1 tags after filtering in treatment: 4835825 INFO @ Tue, 09 Oct 2018 23:39:24: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:39:24: #1 finished! INFO @ Tue, 09 Oct 2018 23:39:24: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:39:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:39:24: #2 number of paired peaks: 12 WARNING @ Tue, 09 Oct 2018 23:39:24: Too few paired peaks (12) 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 23:39:24: Process for pairing-model is terminated! cat: SRX4669582.10_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 `SRX4669582.10_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 `SRX4669582.10_*.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 `SRX4669582.10_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。