Job ID = 11245118 sra ファイルのダウンロード中... Completed: 370479K bytes transferred in 7 seconds (415578K 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 7621727 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669574/SRR7818148.sra Written 7621727 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669574/SRR7818148.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: 00:05:28 7621727 reads; of these: 7621727 (100.00%) were paired; of these: 437975 (5.75%) aligned concordantly 0 times 6647205 (87.21%) aligned concordantly exactly 1 time 536547 (7.04%) aligned concordantly >1 times ---- 437975 pairs aligned concordantly 0 times; of these: 31058 (7.09%) aligned discordantly 1 time ---- 406917 pairs aligned 0 times concordantly or discordantly; of these: 813834 mates make up the pairs; of these: 645647 (79.33%) aligned 0 times 116937 (14.37%) aligned exactly 1 time 51250 (6.30%) aligned >1 times 95.76% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 70218 / 7192087 = 0.0098 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 23:38:16: # Command line: callpeak -t SRX4669574.bam -f BAM -g 12100000 -n SRX4669574.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669574.05 # format = BAM # ChIP-seq file = ['SRX4669574.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 23:38:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:38:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:38:16: # Command line: callpeak -t SRX4669574.bam -f BAM -g 12100000 -n SRX4669574.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669574.10 # format = BAM # ChIP-seq file = ['SRX4669574.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 23:38:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:38:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:38:16: # Command line: callpeak -t SRX4669574.bam -f BAM -g 12100000 -n SRX4669574.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669574.20 # format = BAM # ChIP-seq file = ['SRX4669574.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 23:38:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:38:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:38:23: 1000000 INFO @ Tue, 09 Oct 2018 23:38:24: 1000000 INFO @ Tue, 09 Oct 2018 23:38:24: 1000000 INFO @ Tue, 09 Oct 2018 23:38:29: 2000000 INFO @ Tue, 09 Oct 2018 23:38:32: 2000000 INFO @ Tue, 09 Oct 2018 23:38:32: 2000000 INFO @ Tue, 09 Oct 2018 23:38:36: 3000000 INFO @ Tue, 09 Oct 2018 23:38:39: 3000000 INFO @ Tue, 09 Oct 2018 23:38:39: 3000000 INFO @ Tue, 09 Oct 2018 23:38:42: 4000000 INFO @ Tue, 09 Oct 2018 23:38:47: 4000000 INFO @ Tue, 09 Oct 2018 23:38:47: 4000000 INFO @ Tue, 09 Oct 2018 23:38:48: 5000000 INFO @ Tue, 09 Oct 2018 23:38:54: 5000000 INFO @ Tue, 09 Oct 2018 23:38:54: 5000000 INFO @ Tue, 09 Oct 2018 23:38:55: 6000000 INFO @ Tue, 09 Oct 2018 23:39:01: 7000000 INFO @ Tue, 09 Oct 2018 23:39:02: 6000000 INFO @ Tue, 09 Oct 2018 23:39:02: 6000000 INFO @ Tue, 09 Oct 2018 23:39:07: 8000000 INFO @ Tue, 09 Oct 2018 23:39:10: 7000000 INFO @ Tue, 09 Oct 2018 23:39:10: 7000000 INFO @ Tue, 09 Oct 2018 23:39:14: 9000000 INFO @ Tue, 09 Oct 2018 23:39:17: 8000000 INFO @ Tue, 09 Oct 2018 23:39:17: 8000000 INFO @ Tue, 09 Oct 2018 23:39:20: 10000000 INFO @ Tue, 09 Oct 2018 23:39:25: 9000000 INFO @ Tue, 09 Oct 2018 23:39:25: 9000000 INFO @ Tue, 09 Oct 2018 23:39:26: 11000000 INFO @ Tue, 09 Oct 2018 23:39:32: 10000000 INFO @ Tue, 09 Oct 2018 23:39:32: 10000000 INFO @ Tue, 09 Oct 2018 23:39:33: 12000000 INFO @ Tue, 09 Oct 2018 23:39:39: 13000000 INFO @ Tue, 09 Oct 2018 23:39:40: 11000000 INFO @ Tue, 09 Oct 2018 23:39:40: 11000000 INFO @ Tue, 09 Oct 2018 23:39:45: 14000000 INFO @ Tue, 09 Oct 2018 23:39:47: 12000000 INFO @ Tue, 09 Oct 2018 23:39:47: 12000000 INFO @ Tue, 09 Oct 2018 23:39:48: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:39:48: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:39:48: #1 total tags in treatment: 7113608 INFO @ Tue, 09 Oct 2018 23:39:48: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:39:48: #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 23:39:48: #1 tags after filtering in treatment: 5469239 INFO @ Tue, 09 Oct 2018 23:39:48: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 09 Oct 2018 23:39:48: #1 finished! INFO @ Tue, 09 Oct 2018 23:39:48: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:39:49: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:39:49: 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 23:39:49: Process for pairing-model is terminated! cat: SRX4669574.05_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 `SRX4669574.05_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 `SRX4669574.05_*.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 `SRX4669574.05_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 23:39:55: 13000000 INFO @ Tue, 09 Oct 2018 23:39:55: 13000000 INFO @ Tue, 09 Oct 2018 23:40:03: 14000000 INFO @ Tue, 09 Oct 2018 23:40:03: 14000000 INFO @ Tue, 09 Oct 2018 23:40:06: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:40:06: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:40:06: #1 total tags in treatment: 7113608 INFO @ Tue, 09 Oct 2018 23:40:06: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:40:06: #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 23:40:06: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:40:06: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:40:06: #1 total tags in treatment: 7113608 INFO @ Tue, 09 Oct 2018 23:40:06: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:40:06: #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 23:40:06: #1 tags after filtering in treatment: 5469239 INFO @ Tue, 09 Oct 2018 23:40:06: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 09 Oct 2018 23:40:06: #1 finished! INFO @ Tue, 09 Oct 2018 23:40:06: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:40:06: #1 tags after filtering in treatment: 5469239 INFO @ Tue, 09 Oct 2018 23:40:06: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 09 Oct 2018 23:40:06: #1 finished! INFO @ Tue, 09 Oct 2018 23:40:06: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:40:06: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:40:06: 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 23:40:06: Process for pairing-model is terminated! cat: SRX4669574.10_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 `SRX4669574.10_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 `SRX4669574.10_*.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 `SRX4669574.10_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 @ Tue, 09 Oct 2018 23:40:06: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:40:06: 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 23:40:06: Process for pairing-model is terminated! cat: SRX4669574.20_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 `SRX4669574.20_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 `SRX4669574.20_*.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 `SRX4669574.20_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。