Job ID = 10721729 sra ファイルのダウンロード中... Completed: 494537K bytes transferred in 8 seconds (495764K bits/sec), in 1 file. Completed: 500430K bytes transferred in 9 seconds (447535K 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 14675635 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4141422/SRR7235056.sra Written 14675635 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4141422/SRR7235056.sra Read 14778115 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4141422/SRR7235057.sra Written 14778115 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4141422/SRR7235057.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 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: 00:15:35 29453750 reads; of these: 29453750 (100.00%) were paired; of these: 2402295 (8.16%) aligned concordantly 0 times 21771140 (73.92%) aligned concordantly exactly 1 time 5280315 (17.93%) aligned concordantly >1 times ---- 2402295 pairs aligned concordantly 0 times; of these: 185490 (7.72%) aligned discordantly 1 time ---- 2216805 pairs aligned 0 times concordantly or discordantly; of these: 4433610 mates make up the pairs; of these: 3820461 (86.17%) aligned 0 times 410556 (9.26%) aligned exactly 1 time 202593 (4.57%) aligned >1 times 93.51% overall alignment rate Time searching: 00:15:35 Overall time: 00:15:35 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] 11352765 / 27167342 = 0.4179 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 @ Mon, 04 Jun 2018 04:18:09: # Command line: callpeak -t SRX4141422.bam -f BAM -g 12100000 -n SRX4141422.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4141422.20 # format = BAM # ChIP-seq file = ['SRX4141422.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 @ Mon, 04 Jun 2018 04:18:09: #1 read tag files... INFO @ Mon, 04 Jun 2018 04:18:09: #1 read treatment tags... INFO @ Mon, 04 Jun 2018 04:18:09: # Command line: callpeak -t SRX4141422.bam -f BAM -g 12100000 -n SRX4141422.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4141422.10 # format = BAM # ChIP-seq file = ['SRX4141422.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 @ Mon, 04 Jun 2018 04:18:09: #1 read tag files... INFO @ Mon, 04 Jun 2018 04:18:09: #1 read treatment tags... INFO @ Mon, 04 Jun 2018 04:18:09: # Command line: callpeak -t SRX4141422.bam -f BAM -g 12100000 -n SRX4141422.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4141422.05 # format = BAM # ChIP-seq file = ['SRX4141422.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 @ Mon, 04 Jun 2018 04:18:09: #1 read tag files... INFO @ Mon, 04 Jun 2018 04:18:09: #1 read treatment tags... INFO @ Mon, 04 Jun 2018 04:18:14: 1000000 INFO @ Mon, 04 Jun 2018 04:18:14: 1000000 INFO @ Mon, 04 Jun 2018 04:18:14: 1000000 INFO @ Mon, 04 Jun 2018 04:18:19: 2000000 INFO @ Mon, 04 Jun 2018 04:18:19: 2000000 INFO @ Mon, 04 Jun 2018 04:18:19: 2000000 INFO @ Mon, 04 Jun 2018 04:18:24: 3000000 INFO @ Mon, 04 Jun 2018 04:18:24: 3000000 INFO @ Mon, 04 Jun 2018 04:18:24: 3000000 INFO @ Mon, 04 Jun 2018 04:18:28: 4000000 INFO @ Mon, 04 Jun 2018 04:18:28: 4000000 INFO @ Mon, 04 Jun 2018 04:18:29: 4000000 INFO @ Mon, 04 Jun 2018 04:18:33: 5000000 INFO @ Mon, 04 Jun 2018 04:18:33: 5000000 INFO @ Mon, 04 Jun 2018 04:18:34: 5000000 INFO @ Mon, 04 Jun 2018 04:18:38: 6000000 INFO @ Mon, 04 Jun 2018 04:18:38: 6000000 INFO @ Mon, 04 Jun 2018 04:18:39: 6000000 INFO @ Mon, 04 Jun 2018 04:18:42: 7000000 INFO @ Mon, 04 Jun 2018 04:18:43: 7000000 INFO @ Mon, 04 Jun 2018 04:18:45: 7000000 INFO @ Mon, 04 Jun 2018 04:18:47: 8000000 INFO @ Mon, 04 Jun 2018 04:18:48: 8000000 INFO @ Mon, 04 Jun 2018 04:18:51: 8000000 INFO @ Mon, 04 Jun 2018 04:18:52: 9000000 INFO @ Mon, 04 Jun 2018 04:18:53: 9000000 INFO @ Mon, 04 Jun 2018 04:18:56: 10000000 INFO @ Mon, 04 Jun 2018 04:18:57: 9000000 INFO @ Mon, 04 Jun 2018 04:18:58: 10000000 INFO @ Mon, 04 Jun 2018 04:19:01: 11000000 INFO @ Mon, 04 Jun 2018 04:19:03: 10000000 INFO @ Mon, 04 Jun 2018 04:19:04: 11000000 INFO @ Mon, 04 Jun 2018 04:19:05: 12000000 INFO @ Mon, 04 Jun 2018 04:19:09: 12000000 INFO @ Mon, 04 Jun 2018 04:19:09: 11000000 INFO @ Mon, 04 Jun 2018 04:19:10: 13000000 INFO @ Mon, 04 Jun 2018 04:19:14: 13000000 INFO @ Mon, 04 Jun 2018 04:19:15: 14000000 INFO @ Mon, 04 Jun 2018 04:19:15: 12000000 INFO @ Mon, 04 Jun 2018 04:19:19: 14000000 INFO @ Mon, 04 Jun 2018 04:19:19: 15000000 INFO @ Mon, 04 Jun 2018 04:19:22: 13000000 INFO @ Mon, 04 Jun 2018 04:19:24: 16000000 INFO @ Mon, 04 Jun 2018 04:19:24: 15000000 INFO @ Mon, 04 Jun 2018 04:19:27: 14000000 INFO @ Mon, 04 Jun 2018 04:19:29: 17000000 INFO @ Mon, 04 Jun 2018 04:19:29: 16000000 INFO @ Mon, 04 Jun 2018 04:19:33: 18000000 INFO @ Mon, 04 Jun 2018 04:19:34: 15000000 INFO @ Mon, 04 Jun 2018 04:19:35: 17000000 INFO @ Mon, 04 Jun 2018 04:19:38: 19000000 INFO @ Mon, 04 Jun 2018 04:19:40: 18000000 INFO @ Mon, 04 Jun 2018 04:19:40: 16000000 INFO @ Mon, 04 Jun 2018 04:19:42: 20000000 INFO @ Mon, 04 Jun 2018 04:19:45: 19000000 INFO @ Mon, 04 Jun 2018 04:19:47: 17000000 INFO @ Mon, 04 Jun 2018 04:19:47: 21000000 INFO @ Mon, 04 Jun 2018 04:19:50: 20000000 INFO @ Mon, 04 Jun 2018 04:19:52: 22000000 INFO @ Mon, 04 Jun 2018 04:19:53: 18000000 INFO @ Mon, 04 Jun 2018 04:19:55: 21000000 INFO @ Mon, 04 Jun 2018 04:19:56: 23000000 INFO @ Mon, 04 Jun 2018 04:20:00: 19000000 INFO @ Mon, 04 Jun 2018 04:20:00: 22000000 INFO @ Mon, 04 Jun 2018 04:20:01: 24000000 INFO @ Mon, 04 Jun 2018 04:20:05: 23000000 INFO @ Mon, 04 Jun 2018 04:20:05: 25000000 INFO @ Mon, 04 Jun 2018 04:20:06: 20000000 INFO @ Mon, 04 Jun 2018 04:20:10: 26000000 INFO @ Mon, 04 Jun 2018 04:20:10: 24000000 INFO @ Mon, 04 Jun 2018 04:20:13: 21000000 INFO @ Mon, 04 Jun 2018 04:20:15: 27000000 INFO @ Mon, 04 Jun 2018 04:20:15: 25000000 INFO @ Mon, 04 Jun 2018 04:20:18: 22000000 INFO @ Mon, 04 Jun 2018 04:20:20: 28000000 INFO @ Mon, 04 Jun 2018 04:20:20: 26000000 INFO @ Mon, 04 Jun 2018 04:20:23: 23000000 INFO @ Mon, 04 Jun 2018 04:20:25: 29000000 INFO @ Mon, 04 Jun 2018 04:20:25: 27000000 INFO @ Mon, 04 Jun 2018 04:20:27: 24000000 INFO @ Mon, 04 Jun 2018 04:20:30: 28000000 INFO @ Mon, 04 Jun 2018 04:20:30: 30000000 INFO @ Mon, 04 Jun 2018 04:20:32: 25000000 INFO @ Mon, 04 Jun 2018 04:20:34: 29000000 INFO @ Mon, 04 Jun 2018 04:20:35: 31000000 INFO @ Mon, 04 Jun 2018 04:20:37: 26000000 INFO @ Mon, 04 Jun 2018 04:20:39: 30000000 INFO @ Mon, 04 Jun 2018 04:20:40: 32000000 INFO @ Mon, 04 Jun 2018 04:20:42: #1 tag size is determined as 24 bps INFO @ Mon, 04 Jun 2018 04:20:42: #1 tag size = 24 INFO @ Mon, 04 Jun 2018 04:20:42: #1 total tags in treatment: 15718792 INFO @ Mon, 04 Jun 2018 04:20:42: #1 user defined the maximum tags... INFO @ Mon, 04 Jun 2018 04:20:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Jun 2018 04:20:42: #1 tags after filtering in treatment: 6553254 INFO @ Mon, 04 Jun 2018 04:20:42: #1 Redundant rate of treatment: 0.58 INFO @ Mon, 04 Jun 2018 04:20:42: #1 finished! INFO @ Mon, 04 Jun 2018 04:20:42: #2 Build Peak Model... INFO @ Mon, 04 Jun 2018 04:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Jun 2018 04:20:42: 27000000 INFO @ Mon, 04 Jun 2018 04:20:42: #2 number of paired peaks: 0 WARNING @ Mon, 04 Jun 2018 04:20:42: 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 @ Mon, 04 Jun 2018 04:20:42: Process for pairing-model is terminated! cat: SRX4141422.05_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 `SRX4141422.05_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 `SRX4141422.05_*.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 `SRX4141422.05_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 @ Mon, 04 Jun 2018 04:20:44: 31000000 INFO @ Mon, 04 Jun 2018 04:20:47: 28000000 INFO @ Mon, 04 Jun 2018 04:20:49: 32000000 INFO @ Mon, 04 Jun 2018 04:20:51: #1 tag size is determined as 24 bps INFO @ Mon, 04 Jun 2018 04:20:51: #1 tag size = 24 INFO @ Mon, 04 Jun 2018 04:20:51: #1 total tags in treatment: 15718792 INFO @ Mon, 04 Jun 2018 04:20:51: #1 user defined the maximum tags... INFO @ Mon, 04 Jun 2018 04:20:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Jun 2018 04:20:51: #1 tags after filtering in treatment: 6553254 INFO @ Mon, 04 Jun 2018 04:20:51: #1 Redundant rate of treatment: 0.58 INFO @ Mon, 04 Jun 2018 04:20:51: #1 finished! INFO @ Mon, 04 Jun 2018 04:20:51: #2 Build Peak Model... INFO @ Mon, 04 Jun 2018 04:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Jun 2018 04:20:51: 29000000 INFO @ Mon, 04 Jun 2018 04:20:51: #2 number of paired peaks: 0 WARNING @ Mon, 04 Jun 2018 04:20:51: 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 @ Mon, 04 Jun 2018 04:20:51: Process for pairing-model is terminated! cat: SRX4141422.10_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 `SRX4141422.10_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 `SRX4141422.10_*.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 `SRX4141422.10_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 @ Mon, 04 Jun 2018 04:20:56: 30000000 INFO @ Mon, 04 Jun 2018 04:21:01: 31000000 INFO @ Mon, 04 Jun 2018 04:21:05: 32000000 INFO @ Mon, 04 Jun 2018 04:21:07: #1 tag size is determined as 24 bps INFO @ Mon, 04 Jun 2018 04:21:07: #1 tag size = 24 INFO @ Mon, 04 Jun 2018 04:21:07: #1 total tags in treatment: 15718792 INFO @ Mon, 04 Jun 2018 04:21:07: #1 user defined the maximum tags... INFO @ Mon, 04 Jun 2018 04:21:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Jun 2018 04:21:08: #1 tags after filtering in treatment: 6553254 INFO @ Mon, 04 Jun 2018 04:21:08: #1 Redundant rate of treatment: 0.58 INFO @ Mon, 04 Jun 2018 04:21:08: #1 finished! INFO @ Mon, 04 Jun 2018 04:21:08: #2 Build Peak Model... INFO @ Mon, 04 Jun 2018 04:21:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Jun 2018 04:21:08: #2 number of paired peaks: 0 WARNING @ Mon, 04 Jun 2018 04:21:08: 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 @ Mon, 04 Jun 2018 04:21:08: Process for pairing-model is terminated! cat: SRX4141422.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4141422.20_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 `SRX4141422.20_*.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 `SRX4141422.20_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。