Job ID = 10937455 sra ファイルのダウンロード中... Completed: 608967K bytes transferred in 8 seconds (611199K 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 11265343 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198735/SRR4304465.sra Written 11265343 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198735/SRR4304465.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: 00:07:42 11265343 reads; of these: 11265343 (100.00%) were paired; of these: 574624 (5.10%) aligned concordantly 0 times 9422685 (83.64%) aligned concordantly exactly 1 time 1268034 (11.26%) aligned concordantly >1 times ---- 574624 pairs aligned concordantly 0 times; of these: 161578 (28.12%) aligned discordantly 1 time ---- 413046 pairs aligned 0 times concordantly or discordantly; of these: 826092 mates make up the pairs; of these: 609460 (73.78%) aligned 0 times 139795 (16.92%) aligned exactly 1 time 76837 (9.30%) aligned >1 times 97.29% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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] 319039 / 10738780 = 0.0297 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 @ Fri, 10 Aug 2018 02:27:48: # Command line: callpeak -t SRX2198735.bam -f BAM -g 12100000 -n SRX2198735.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198735.05 # format = BAM # ChIP-seq file = ['SRX2198735.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 @ Fri, 10 Aug 2018 02:27:48: # Command line: callpeak -t SRX2198735.bam -f BAM -g 12100000 -n SRX2198735.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198735.10 # format = BAM # ChIP-seq file = ['SRX2198735.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 @ Fri, 10 Aug 2018 02:27:48: # Command line: callpeak -t SRX2198735.bam -f BAM -g 12100000 -n SRX2198735.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198735.20 # format = BAM # ChIP-seq file = ['SRX2198735.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 @ Fri, 10 Aug 2018 02:27:48: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:27:48: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:27:48: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:27:48: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:27:48: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:27:48: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:27:54: 1000000 INFO @ Fri, 10 Aug 2018 02:27:54: 1000000 INFO @ Fri, 10 Aug 2018 02:27:54: 1000000 INFO @ Fri, 10 Aug 2018 02:28:00: 2000000 INFO @ Fri, 10 Aug 2018 02:28:00: 2000000 INFO @ Fri, 10 Aug 2018 02:28:00: 2000000 INFO @ Fri, 10 Aug 2018 02:28:06: 3000000 INFO @ Fri, 10 Aug 2018 02:28:06: 3000000 INFO @ Fri, 10 Aug 2018 02:28:06: 3000000 INFO @ Fri, 10 Aug 2018 02:28:13: 4000000 INFO @ Fri, 10 Aug 2018 02:28:13: 4000000 INFO @ Fri, 10 Aug 2018 02:28:13: 4000000 INFO @ Fri, 10 Aug 2018 02:28:21: 5000000 INFO @ Fri, 10 Aug 2018 02:28:21: 5000000 INFO @ Fri, 10 Aug 2018 02:28:21: 5000000 INFO @ Fri, 10 Aug 2018 02:28:28: 6000000 INFO @ Fri, 10 Aug 2018 02:28:28: 6000000 INFO @ Fri, 10 Aug 2018 02:28:28: 6000000 INFO @ Fri, 10 Aug 2018 02:28:35: 7000000 INFO @ Fri, 10 Aug 2018 02:28:35: 7000000 INFO @ Fri, 10 Aug 2018 02:28:35: 7000000 INFO @ Fri, 10 Aug 2018 02:28:42: 8000000 INFO @ Fri, 10 Aug 2018 02:28:42: 8000000 INFO @ Fri, 10 Aug 2018 02:28:42: 8000000 INFO @ Fri, 10 Aug 2018 02:28:49: 9000000 INFO @ Fri, 10 Aug 2018 02:28:49: 9000000 INFO @ Fri, 10 Aug 2018 02:28:49: 9000000 INFO @ Fri, 10 Aug 2018 02:28:56: 10000000 INFO @ Fri, 10 Aug 2018 02:28:56: 10000000 INFO @ Fri, 10 Aug 2018 02:28:56: 10000000 INFO @ Fri, 10 Aug 2018 02:29:03: 11000000 INFO @ Fri, 10 Aug 2018 02:29:03: 11000000 INFO @ Fri, 10 Aug 2018 02:29:03: 11000000 INFO @ Fri, 10 Aug 2018 02:29:09: 12000000 INFO @ Fri, 10 Aug 2018 02:29:10: 12000000 INFO @ Fri, 10 Aug 2018 02:29:10: 12000000 INFO @ Fri, 10 Aug 2018 02:29:16: 13000000 INFO @ Fri, 10 Aug 2018 02:29:16: 13000000 INFO @ Fri, 10 Aug 2018 02:29:17: 13000000 INFO @ Fri, 10 Aug 2018 02:29:22: 14000000 INFO @ Fri, 10 Aug 2018 02:29:23: 14000000 INFO @ Fri, 10 Aug 2018 02:29:24: 14000000 INFO @ Fri, 10 Aug 2018 02:29:29: 15000000 INFO @ Fri, 10 Aug 2018 02:29:30: 15000000 INFO @ Fri, 10 Aug 2018 02:29:30: 15000000 INFO @ Fri, 10 Aug 2018 02:29:35: 16000000 INFO @ Fri, 10 Aug 2018 02:29:37: 16000000 INFO @ Fri, 10 Aug 2018 02:29:37: 16000000 INFO @ Fri, 10 Aug 2018 02:29:42: 17000000 INFO @ Fri, 10 Aug 2018 02:29:44: 17000000 INFO @ Fri, 10 Aug 2018 02:29:44: 17000000 INFO @ Fri, 10 Aug 2018 02:29:49: 18000000 INFO @ Fri, 10 Aug 2018 02:29:51: 18000000 INFO @ Fri, 10 Aug 2018 02:29:51: 18000000 INFO @ Fri, 10 Aug 2018 02:29:55: 19000000 INFO @ Fri, 10 Aug 2018 02:29:58: 19000000 INFO @ Fri, 10 Aug 2018 02:29:58: 19000000 INFO @ Fri, 10 Aug 2018 02:30:02: 20000000 INFO @ Fri, 10 Aug 2018 02:30:05: 20000000 INFO @ Fri, 10 Aug 2018 02:30:05: 20000000 INFO @ Fri, 10 Aug 2018 02:30:08: 21000000 INFO @ Fri, 10 Aug 2018 02:30:10: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:30:10: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:30:10: #1 total tags in treatment: 10372008 INFO @ Fri, 10 Aug 2018 02:30:10: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:30:10: #1 tags after filtering in treatment: 5868629 INFO @ Fri, 10 Aug 2018 02:30:10: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Aug 2018 02:30:10: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:10: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:11: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:30:11: 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 @ Fri, 10 Aug 2018 02:30:11: Process for pairing-model is terminated! cat: SRX2198735.20_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 `SRX2198735.20_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 `SRX2198735.20_*.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 `SRX2198735.20_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 @ Fri, 10 Aug 2018 02:30:12: 21000000 INFO @ Fri, 10 Aug 2018 02:30:12: 21000000 INFO @ Fri, 10 Aug 2018 02:30:13: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:30:13: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:30:13: #1 total tags in treatment: 10372008 INFO @ Fri, 10 Aug 2018 02:30:13: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:30:14: #1 tags after filtering in treatment: 5868629 INFO @ Fri, 10 Aug 2018 02:30:14: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Aug 2018 02:30:14: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:14: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:14: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:30:14: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:30:14: #1 total tags in treatment: 10372008 INFO @ Fri, 10 Aug 2018 02:30:14: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:30:14: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:30:14: 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 @ Fri, 10 Aug 2018 02:30:14: Process for pairing-model is terminated! cat: SRX2198735.10_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 `SRX2198735.10_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 `SRX2198735.10_*.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 `SRX2198735.10_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 @ Fri, 10 Aug 2018 02:30:14: #1 tags after filtering in treatment: 5868629 INFO @ Fri, 10 Aug 2018 02:30:14: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Aug 2018 02:30:14: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:14: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:14: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:30:14: 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 @ Fri, 10 Aug 2018 02:30:14: Process for pairing-model is terminated! cat: SRX2198735.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198735.05_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 `SRX2198735.05_*.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 `SRX2198735.05_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。