Job ID = 11192889 sra ファイルのダウンロード中... Completed: 1272992K bytes transferred in 57 seconds (180255K 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 17772980 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771767/SRR5488922.sra Written 17772980 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771767/SRR5488922.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: 00:16:35 17772980 reads; of these: 17772980 (100.00%) were paired; of these: 1850445 (10.41%) aligned concordantly 0 times 13752486 (77.38%) aligned concordantly exactly 1 time 2170049 (12.21%) aligned concordantly >1 times ---- 1850445 pairs aligned concordantly 0 times; of these: 45995 (2.49%) aligned discordantly 1 time ---- 1804450 pairs aligned 0 times concordantly or discordantly; of these: 3608900 mates make up the pairs; of these: 3242066 (89.84%) aligned 0 times 290151 (8.04%) aligned exactly 1 time 76683 (2.12%) aligned >1 times 90.88% overall alignment rate Time searching: 00:16:35 Overall time: 00:16:35 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 16 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] 650397 / 15953860 = 0.0408 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 @ Sat, 15 Sep 2018 10:49:24: # Command line: callpeak -t SRX2771767.bam -f BAM -g 12100000 -n SRX2771767.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2771767.05 # format = BAM # ChIP-seq file = ['SRX2771767.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 @ Sat, 15 Sep 2018 10:49:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:49:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:49:24: # Command line: callpeak -t SRX2771767.bam -f BAM -g 12100000 -n SRX2771767.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2771767.20 # format = BAM # ChIP-seq file = ['SRX2771767.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 @ Sat, 15 Sep 2018 10:49:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:49:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:49:24: # Command line: callpeak -t SRX2771767.bam -f BAM -g 12100000 -n SRX2771767.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2771767.10 # format = BAM # ChIP-seq file = ['SRX2771767.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 @ Sat, 15 Sep 2018 10:49:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:49:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:49:31: 1000000 INFO @ Sat, 15 Sep 2018 10:49:31: 1000000 INFO @ Sat, 15 Sep 2018 10:49:31: 1000000 INFO @ Sat, 15 Sep 2018 10:49:38: 2000000 INFO @ Sat, 15 Sep 2018 10:49:39: 2000000 INFO @ Sat, 15 Sep 2018 10:49:39: 2000000 INFO @ Sat, 15 Sep 2018 10:49:46: 3000000 INFO @ Sat, 15 Sep 2018 10:49:46: 3000000 INFO @ Sat, 15 Sep 2018 10:49:46: 3000000 INFO @ Sat, 15 Sep 2018 10:49:53: 4000000 INFO @ Sat, 15 Sep 2018 10:49:53: 4000000 INFO @ Sat, 15 Sep 2018 10:49:53: 4000000 INFO @ Sat, 15 Sep 2018 10:50:00: 5000000 INFO @ Sat, 15 Sep 2018 10:50:01: 5000000 INFO @ Sat, 15 Sep 2018 10:50:01: 5000000 INFO @ Sat, 15 Sep 2018 10:50:07: 6000000 INFO @ Sat, 15 Sep 2018 10:50:08: 6000000 INFO @ Sat, 15 Sep 2018 10:50:08: 6000000 INFO @ Sat, 15 Sep 2018 10:50:14: 7000000 INFO @ Sat, 15 Sep 2018 10:50:16: 7000000 INFO @ Sat, 15 Sep 2018 10:50:16: 7000000 INFO @ Sat, 15 Sep 2018 10:50:21: 8000000 INFO @ Sat, 15 Sep 2018 10:50:23: 8000000 INFO @ Sat, 15 Sep 2018 10:50:23: 8000000 INFO @ Sat, 15 Sep 2018 10:50:28: 9000000 INFO @ Sat, 15 Sep 2018 10:50:30: 9000000 INFO @ Sat, 15 Sep 2018 10:50:31: 9000000 INFO @ Sat, 15 Sep 2018 10:50:34: 10000000 INFO @ Sat, 15 Sep 2018 10:50:38: 10000000 INFO @ Sat, 15 Sep 2018 10:50:38: 10000000 INFO @ Sat, 15 Sep 2018 10:50:41: 11000000 INFO @ Sat, 15 Sep 2018 10:50:45: 11000000 INFO @ Sat, 15 Sep 2018 10:50:46: 11000000 INFO @ Sat, 15 Sep 2018 10:50:48: 12000000 INFO @ Sat, 15 Sep 2018 10:50:53: 12000000 INFO @ Sat, 15 Sep 2018 10:50:53: 12000000 INFO @ Sat, 15 Sep 2018 10:50:55: 13000000 INFO @ Sat, 15 Sep 2018 10:51:00: 13000000 INFO @ Sat, 15 Sep 2018 10:51:01: 13000000 INFO @ Sat, 15 Sep 2018 10:51:02: 14000000 INFO @ Sat, 15 Sep 2018 10:51:08: 14000000 INFO @ Sat, 15 Sep 2018 10:51:09: 14000000 INFO @ Sat, 15 Sep 2018 10:51:09: 15000000 INFO @ Sat, 15 Sep 2018 10:51:15: 15000000 INFO @ Sat, 15 Sep 2018 10:51:16: 16000000 INFO @ Sat, 15 Sep 2018 10:51:16: 15000000 INFO @ Sat, 15 Sep 2018 10:51:23: 16000000 INFO @ Sat, 15 Sep 2018 10:51:23: 17000000 INFO @ Sat, 15 Sep 2018 10:51:24: 16000000 INFO @ Sat, 15 Sep 2018 10:51:30: 17000000 INFO @ Sat, 15 Sep 2018 10:51:30: 18000000 INFO @ Sat, 15 Sep 2018 10:51:32: 17000000 INFO @ Sat, 15 Sep 2018 10:51:37: 19000000 INFO @ Sat, 15 Sep 2018 10:51:38: 18000000 INFO @ Sat, 15 Sep 2018 10:51:40: 18000000 INFO @ Sat, 15 Sep 2018 10:51:44: 20000000 INFO @ Sat, 15 Sep 2018 10:51:45: 19000000 INFO @ Sat, 15 Sep 2018 10:51:47: 19000000 INFO @ Sat, 15 Sep 2018 10:51:51: 21000000 INFO @ Sat, 15 Sep 2018 10:51:52: 20000000 INFO @ Sat, 15 Sep 2018 10:51:55: 20000000 INFO @ Sat, 15 Sep 2018 10:51:58: 22000000 INFO @ Sat, 15 Sep 2018 10:52:00: 21000000 INFO @ Sat, 15 Sep 2018 10:52:03: 21000000 INFO @ Sat, 15 Sep 2018 10:52:05: 23000000 INFO @ Sat, 15 Sep 2018 10:52:07: 22000000 INFO @ Sat, 15 Sep 2018 10:52:10: 22000000 INFO @ Sat, 15 Sep 2018 10:52:12: 24000000 INFO @ Sat, 15 Sep 2018 10:52:15: 23000000 INFO @ Sat, 15 Sep 2018 10:52:18: 23000000 INFO @ Sat, 15 Sep 2018 10:52:19: 25000000 INFO @ Sat, 15 Sep 2018 10:52:22: 24000000 INFO @ Sat, 15 Sep 2018 10:52:26: 24000000 INFO @ Sat, 15 Sep 2018 10:52:26: 26000000 INFO @ Sat, 15 Sep 2018 10:52:30: 25000000 INFO @ Sat, 15 Sep 2018 10:52:33: 27000000 INFO @ Sat, 15 Sep 2018 10:52:33: 25000000 INFO @ Sat, 15 Sep 2018 10:52:37: 26000000 INFO @ Sat, 15 Sep 2018 10:52:40: 28000000 INFO @ Sat, 15 Sep 2018 10:52:41: 26000000 INFO @ Sat, 15 Sep 2018 10:52:45: 27000000 INFO @ Sat, 15 Sep 2018 10:52:47: 29000000 INFO @ Sat, 15 Sep 2018 10:52:49: 27000000 INFO @ Sat, 15 Sep 2018 10:52:52: 28000000 INFO @ Sat, 15 Sep 2018 10:52:54: 30000000 INFO @ Sat, 15 Sep 2018 10:52:56: 28000000 INFO @ Sat, 15 Sep 2018 10:53:00: 29000000 INFO @ Sat, 15 Sep 2018 10:53:01: 31000000 INFO @ Sat, 15 Sep 2018 10:53:01: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:53:01: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:53:01: #1 total tags in treatment: 15272808 INFO @ Sat, 15 Sep 2018 10:53:01: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:53:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:53:01: #1 tags after filtering in treatment: 9843096 INFO @ Sat, 15 Sep 2018 10:53:01: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Sep 2018 10:53:01: #1 finished! INFO @ Sat, 15 Sep 2018 10:53:01: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:53:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:53:02: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:53:02: 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 @ Sat, 15 Sep 2018 10:53:02: Process for pairing-model is terminated! cat: SRX2771767.10_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 `SRX2771767.10_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 `SRX2771767.10_*.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 `SRX2771767.10_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 @ Sat, 15 Sep 2018 10:53:04: 29000000 INFO @ Sat, 15 Sep 2018 10:53:07: 30000000 INFO @ Sat, 15 Sep 2018 10:53:11: 30000000 INFO @ Sat, 15 Sep 2018 10:53:14: 31000000 INFO @ Sat, 15 Sep 2018 10:53:15: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:53:15: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:53:15: #1 total tags in treatment: 15272808 INFO @ Sat, 15 Sep 2018 10:53:15: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:53:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:53:15: #1 tags after filtering in treatment: 9843096 INFO @ Sat, 15 Sep 2018 10:53:15: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Sep 2018 10:53:15: #1 finished! INFO @ Sat, 15 Sep 2018 10:53:15: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:53:16: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:53:16: 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 @ Sat, 15 Sep 2018 10:53:16: Process for pairing-model is terminated! cat: SRX2771767.05_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 `SRX2771767.05_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 `SRX2771767.05_*.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 `SRX2771767.05_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 @ Sat, 15 Sep 2018 10:53:18: 31000000 INFO @ Sat, 15 Sep 2018 10:53:18: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:53:18: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:53:18: #1 total tags in treatment: 15272808 INFO @ Sat, 15 Sep 2018 10:53:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:53:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:53:19: #1 tags after filtering in treatment: 9843096 INFO @ Sat, 15 Sep 2018 10:53:19: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Sep 2018 10:53:19: #1 finished! INFO @ Sat, 15 Sep 2018 10:53:19: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:53:19: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:53:19: 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 @ Sat, 15 Sep 2018 10:53:19: Process for pairing-model is terminated! cat: SRX2771767.20_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 `SRX2771767.20_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 `SRX2771767.20_*.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 `SRX2771767.20_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。