Job ID = 11245015 sra ファイルのダウンロード中... Completed: 281532K bytes transferred in 7 seconds (318460K 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 5665123 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554729/SRR7696401.sra Written 5665123 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554729/SRR7696401.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: 00:04:02 5665123 reads; of these: 5665123 (100.00%) were paired; of these: 399848 (7.06%) aligned concordantly 0 times 5025202 (88.70%) aligned concordantly exactly 1 time 240073 (4.24%) aligned concordantly >1 times ---- 399848 pairs aligned concordantly 0 times; of these: 178460 (44.63%) aligned discordantly 1 time ---- 221388 pairs aligned 0 times concordantly or discordantly; of these: 442776 mates make up the pairs; of these: 339961 (76.78%) aligned 0 times 76141 (17.20%) aligned exactly 1 time 26674 (6.02%) aligned >1 times 97.00% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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] 258295 / 5432926 = 0.0475 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 23:15:03: # Command line: callpeak -t SRX4554729.bam -f BAM -g 12100000 -n SRX4554729.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554729.10 # format = BAM # ChIP-seq file = ['SRX4554729.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 23:15:03: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:15:03: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:15:03: # Command line: callpeak -t SRX4554729.bam -f BAM -g 12100000 -n SRX4554729.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554729.20 # format = BAM # ChIP-seq file = ['SRX4554729.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 23:15:03: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:15:03: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:15:03: # Command line: callpeak -t SRX4554729.bam -f BAM -g 12100000 -n SRX4554729.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554729.05 # format = BAM # ChIP-seq file = ['SRX4554729.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 23:15:03: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:15:03: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:15:10: 1000000 INFO @ Tue, 09 Oct 2018 23:15:10: 1000000 INFO @ Tue, 09 Oct 2018 23:15:10: 1000000 INFO @ Tue, 09 Oct 2018 23:15:16: 2000000 INFO @ Tue, 09 Oct 2018 23:15:16: 2000000 INFO @ Tue, 09 Oct 2018 23:15:16: 2000000 INFO @ Tue, 09 Oct 2018 23:15:22: 3000000 INFO @ Tue, 09 Oct 2018 23:15:23: 3000000 INFO @ Tue, 09 Oct 2018 23:15:23: 3000000 INFO @ Tue, 09 Oct 2018 23:15:28: 4000000 INFO @ Tue, 09 Oct 2018 23:15:29: 4000000 INFO @ Tue, 09 Oct 2018 23:15:30: 4000000 INFO @ Tue, 09 Oct 2018 23:15:34: 5000000 INFO @ Tue, 09 Oct 2018 23:15:36: 5000000 INFO @ Tue, 09 Oct 2018 23:15:36: 5000000 INFO @ Tue, 09 Oct 2018 23:15:40: 6000000 INFO @ Tue, 09 Oct 2018 23:15:42: 6000000 INFO @ Tue, 09 Oct 2018 23:15:43: 6000000 INFO @ Tue, 09 Oct 2018 23:15:46: 7000000 INFO @ Tue, 09 Oct 2018 23:15:49: 7000000 INFO @ Tue, 09 Oct 2018 23:15:50: 7000000 INFO @ Tue, 09 Oct 2018 23:15:53: 8000000 INFO @ Tue, 09 Oct 2018 23:15:56: 8000000 INFO @ Tue, 09 Oct 2018 23:15:57: 8000000 INFO @ Tue, 09 Oct 2018 23:15:59: 9000000 INFO @ Tue, 09 Oct 2018 23:16:02: 9000000 INFO @ Tue, 09 Oct 2018 23:16:03: 9000000 INFO @ Tue, 09 Oct 2018 23:16:05: 10000000 INFO @ Tue, 09 Oct 2018 23:16:08: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:16:08: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:16:08: #1 total tags in treatment: 5009746 INFO @ Tue, 09 Oct 2018 23:16:08: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:16:08: #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 23:16:08: #1 tags after filtering in treatment: 3289445 INFO @ Tue, 09 Oct 2018 23:16:08: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:16:08: #1 finished! INFO @ Tue, 09 Oct 2018 23:16:08: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:16:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:16:08: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:16:08: 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 23:16:08: Process for pairing-model is terminated! cat: SRX4554729.10_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 `SRX4554729.10_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 `SRX4554729.10_*.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 `SRX4554729.10_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 23:16:09: 10000000 INFO @ Tue, 09 Oct 2018 23:16:10: 10000000 INFO @ Tue, 09 Oct 2018 23:16:12: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:16:12: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:16:12: #1 total tags in treatment: 5009746 INFO @ Tue, 09 Oct 2018 23:16:12: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:16:12: #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 23:16:12: #1 tags after filtering in treatment: 3289445 INFO @ Tue, 09 Oct 2018 23:16:12: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:16:12: #1 finished! INFO @ Tue, 09 Oct 2018 23:16:12: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:16:12: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:16:12: 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 23:16:12: Process for pairing-model is terminated! cat: SRX4554729.20_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 `SRX4554729.20_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 `SRX4554729.20_*.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 `SRX4554729.20_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 23:16:13: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:16:13: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:16:13: #1 total tags in treatment: 5009746 INFO @ Tue, 09 Oct 2018 23:16:13: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:16:13: #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 23:16:13: #1 tags after filtering in treatment: 3289445 INFO @ Tue, 09 Oct 2018 23:16:13: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:16:13: #1 finished! INFO @ Tue, 09 Oct 2018 23:16:13: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:16:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:16:14: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:16:14: 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 23:16:14: Process for pairing-model is terminated! cat: SRX4554729.05_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 `SRX4554729.05_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 `SRX4554729.05_*.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 `SRX4554729.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。