Job ID = 11245075 sra ファイルのダウンロード中... Completed: 621852K bytes transferred in 12 seconds (423660K 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 18439765 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554785/SRR7696457.sra Written 18439765 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554785/SRR7696457.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: 00:10:21 18439765 reads; of these: 18439765 (100.00%) were paired; of these: 8945250 (48.51%) aligned concordantly 0 times 8530542 (46.26%) aligned concordantly exactly 1 time 963973 (5.23%) aligned concordantly >1 times ---- 8945250 pairs aligned concordantly 0 times; of these: 15265 (0.17%) aligned discordantly 1 time ---- 8929985 pairs aligned 0 times concordantly or discordantly; of these: 17859970 mates make up the pairs; of these: 10783195 (60.38%) aligned 0 times 6368181 (35.66%) aligned exactly 1 time 708594 (3.97%) aligned >1 times 70.76% overall alignment rate Time searching: 00:10:21 Overall time: 00:10:21 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] 961519 / 9508445 = 0.1011 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 23:39:13: # Command line: callpeak -t SRX4554785.bam -f BAM -g 12100000 -n SRX4554785.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554785.05 # format = BAM # ChIP-seq file = ['SRX4554785.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 23:39:13: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:39:13: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:39:13: # Command line: callpeak -t SRX4554785.bam -f BAM -g 12100000 -n SRX4554785.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554785.10 # format = BAM # ChIP-seq file = ['SRX4554785.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 23:39:13: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:39:13: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:39:13: # Command line: callpeak -t SRX4554785.bam -f BAM -g 12100000 -n SRX4554785.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554785.20 # format = BAM # ChIP-seq file = ['SRX4554785.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 23:39:13: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:39:13: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:39:19: 1000000 INFO @ Tue, 09 Oct 2018 23:39:20: 1000000 INFO @ Tue, 09 Oct 2018 23:39:20: 1000000 INFO @ Tue, 09 Oct 2018 23:39:25: 2000000 INFO @ Tue, 09 Oct 2018 23:39:26: 2000000 INFO @ Tue, 09 Oct 2018 23:39:26: 2000000 INFO @ Tue, 09 Oct 2018 23:39:30: 3000000 INFO @ Tue, 09 Oct 2018 23:39:32: 3000000 INFO @ Tue, 09 Oct 2018 23:39:32: 3000000 INFO @ Tue, 09 Oct 2018 23:39:36: 4000000 INFO @ Tue, 09 Oct 2018 23:39:39: 4000000 INFO @ Tue, 09 Oct 2018 23:39:39: 4000000 INFO @ Tue, 09 Oct 2018 23:39:42: 5000000 INFO @ Tue, 09 Oct 2018 23:39:45: 5000000 INFO @ Tue, 09 Oct 2018 23:39:45: 5000000 INFO @ Tue, 09 Oct 2018 23:39:47: 6000000 INFO @ Tue, 09 Oct 2018 23:39:52: 6000000 INFO @ Tue, 09 Oct 2018 23:39:52: 6000000 INFO @ Tue, 09 Oct 2018 23:39:53: 7000000 INFO @ Tue, 09 Oct 2018 23:39:58: 7000000 INFO @ Tue, 09 Oct 2018 23:39:58: 7000000 INFO @ Tue, 09 Oct 2018 23:39:59: 8000000 INFO @ Tue, 09 Oct 2018 23:40:05: 9000000 INFO @ Tue, 09 Oct 2018 23:40:05: 8000000 INFO @ Tue, 09 Oct 2018 23:40:05: 8000000 INFO @ Tue, 09 Oct 2018 23:40:11: 10000000 INFO @ Tue, 09 Oct 2018 23:40:12: 9000000 INFO @ Tue, 09 Oct 2018 23:40:12: 9000000 INFO @ Tue, 09 Oct 2018 23:40:16: 11000000 INFO @ Tue, 09 Oct 2018 23:40:19: 10000000 INFO @ Tue, 09 Oct 2018 23:40:19: 10000000 INFO @ Tue, 09 Oct 2018 23:40:22: 12000000 INFO @ Tue, 09 Oct 2018 23:40:26: 11000000 INFO @ Tue, 09 Oct 2018 23:40:26: 11000000 INFO @ Tue, 09 Oct 2018 23:40:28: 13000000 INFO @ Tue, 09 Oct 2018 23:40:32: 12000000 INFO @ Tue, 09 Oct 2018 23:40:32: 12000000 INFO @ Tue, 09 Oct 2018 23:40:34: 14000000 INFO @ Tue, 09 Oct 2018 23:40:39: 13000000 INFO @ Tue, 09 Oct 2018 23:40:39: 13000000 INFO @ Tue, 09 Oct 2018 23:40:39: 15000000 INFO @ Tue, 09 Oct 2018 23:40:45: 16000000 INFO @ Tue, 09 Oct 2018 23:40:46: 14000000 INFO @ Tue, 09 Oct 2018 23:40:46: 14000000 INFO @ Tue, 09 Oct 2018 23:40:51: 17000000 INFO @ Tue, 09 Oct 2018 23:40:53: 15000000 INFO @ Tue, 09 Oct 2018 23:40:53: 15000000 INFO @ Tue, 09 Oct 2018 23:40:56: 18000000 INFO @ Tue, 09 Oct 2018 23:40:59: 16000000 INFO @ Tue, 09 Oct 2018 23:40:59: 16000000 INFO @ Tue, 09 Oct 2018 23:41:02: 19000000 INFO @ Tue, 09 Oct 2018 23:41:06: 17000000 INFO @ Tue, 09 Oct 2018 23:41:06: 17000000 INFO @ Tue, 09 Oct 2018 23:41:08: 20000000 INFO @ Tue, 09 Oct 2018 23:41:13: 18000000 INFO @ Tue, 09 Oct 2018 23:41:13: 18000000 INFO @ Tue, 09 Oct 2018 23:41:14: 21000000 INFO @ Tue, 09 Oct 2018 23:41:19: 19000000 INFO @ Tue, 09 Oct 2018 23:41:19: 19000000 INFO @ Tue, 09 Oct 2018 23:41:19: 22000000 INFO @ Tue, 09 Oct 2018 23:41:25: 23000000 INFO @ Tue, 09 Oct 2018 23:41:26: 20000000 INFO @ Tue, 09 Oct 2018 23:41:26: 20000000 INFO @ Tue, 09 Oct 2018 23:41:31: 24000000 INFO @ Tue, 09 Oct 2018 23:41:32: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:41:32: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:41:32: #1 total tags in treatment: 8533050 INFO @ Tue, 09 Oct 2018 23:41:32: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:41:32: #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 23:41:32: #1 tags after filtering in treatment: 4086049 INFO @ Tue, 09 Oct 2018 23:41:32: #1 Redundant rate of treatment: 0.52 INFO @ Tue, 09 Oct 2018 23:41:32: #1 finished! INFO @ Tue, 09 Oct 2018 23:41:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:41:32: #2 number of paired peaks: 2 WARNING @ Tue, 09 Oct 2018 23:41:32: Too few paired peaks (2) 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 23:41:32: Process for pairing-model is terminated! cat: SRX4554785.10_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 `SRX4554785.10_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 `SRX4554785.10_*.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 `SRX4554785.10_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 23:41:33: 21000000 INFO @ Tue, 09 Oct 2018 23:41:33: 21000000 INFO @ Tue, 09 Oct 2018 23:41:40: 22000000 INFO @ Tue, 09 Oct 2018 23:41:40: 22000000 INFO @ Tue, 09 Oct 2018 23:41:47: 23000000 INFO @ Tue, 09 Oct 2018 23:41:47: 23000000 INFO @ Tue, 09 Oct 2018 23:41:54: 24000000 INFO @ Tue, 09 Oct 2018 23:41:54: 24000000 INFO @ Tue, 09 Oct 2018 23:41:55: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:41:55: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:41:55: #1 total tags in treatment: 8533050 INFO @ Tue, 09 Oct 2018 23:41:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:41:55: #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 23:41:55: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:41:55: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:41:55: #1 total tags in treatment: 8533050 INFO @ Tue, 09 Oct 2018 23:41:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:41:55: #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 23:41:55: #1 tags after filtering in treatment: 4086049 INFO @ Tue, 09 Oct 2018 23:41:55: #1 Redundant rate of treatment: 0.52 INFO @ Tue, 09 Oct 2018 23:41:55: #1 finished! INFO @ Tue, 09 Oct 2018 23:41:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:41:55: #1 tags after filtering in treatment: 4086049 INFO @ Tue, 09 Oct 2018 23:41:55: #1 Redundant rate of treatment: 0.52 INFO @ Tue, 09 Oct 2018 23:41:55: #1 finished! INFO @ Tue, 09 Oct 2018 23:41:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:41:55: #2 number of paired peaks: 2 WARNING @ Tue, 09 Oct 2018 23:41:55: Too few paired peaks (2) 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 23:41:55: Process for pairing-model is terminated! cat: SRX4554785.05_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 `SRX4554785.05_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 `SRX4554785.05_*.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 `SRX4554785.05_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 23:41:55: #2 number of paired peaks: 2 WARNING @ Tue, 09 Oct 2018 23:41:55: Too few paired peaks (2) 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 23:41:55: Process for pairing-model is terminated! cat: SRX4554785.20_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 `SRX4554785.20_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 `SRX4554785.20_*.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 `SRX4554785.20_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。