Job ID = 11388937 sra ファイルのダウンロード中... Completed: 611799K bytes transferred in 15 seconds (323118K 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 11093095 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017456/SRR8198079.sra Written 11093095 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017456/SRR8198079.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: 00:21:21 11093095 reads; of these: 11093095 (100.00%) were paired; of these: 647986 (5.84%) aligned concordantly 0 times 9395422 (84.70%) aligned concordantly exactly 1 time 1049687 (9.46%) aligned concordantly >1 times ---- 647986 pairs aligned concordantly 0 times; of these: 125485 (19.37%) aligned discordantly 1 time ---- 522501 pairs aligned 0 times concordantly or discordantly; of these: 1045002 mates make up the pairs; of these: 895349 (85.68%) aligned 0 times 95440 (9.13%) aligned exactly 1 time 54213 (5.19%) aligned >1 times 95.96% overall alignment rate Time searching: 00:21:21 Overall time: 00:21:21 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 12 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] 1173429 / 10509686 = 0.1117 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 @ Thu, 13 Dec 2018 00:48:15: # Command line: callpeak -t SRX5017456.bam -f BAM -g 12100000 -n SRX5017456.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017456.10 # format = BAM # ChIP-seq file = ['SRX5017456.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 @ Thu, 13 Dec 2018 00:48:15: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:48:15: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:48:15: # Command line: callpeak -t SRX5017456.bam -f BAM -g 12100000 -n SRX5017456.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017456.20 # format = BAM # ChIP-seq file = ['SRX5017456.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 @ Thu, 13 Dec 2018 00:48:15: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:48:15: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:48:15: # Command line: callpeak -t SRX5017456.bam -f BAM -g 12100000 -n SRX5017456.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017456.05 # format = BAM # ChIP-seq file = ['SRX5017456.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 @ Thu, 13 Dec 2018 00:48:15: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:48:15: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:48:28: 1000000 INFO @ Thu, 13 Dec 2018 00:48:31: 1000000 INFO @ Thu, 13 Dec 2018 00:48:32: 1000000 INFO @ Thu, 13 Dec 2018 00:48:42: 2000000 INFO @ Thu, 13 Dec 2018 00:48:46: 2000000 INFO @ Thu, 13 Dec 2018 00:48:49: 2000000 INFO @ Thu, 13 Dec 2018 00:48:55: 3000000 INFO @ Thu, 13 Dec 2018 00:48:59: 3000000 INFO @ Thu, 13 Dec 2018 00:49:07: 3000000 INFO @ Thu, 13 Dec 2018 00:49:08: 4000000 INFO @ Thu, 13 Dec 2018 00:49:11: 4000000 INFO @ Thu, 13 Dec 2018 00:49:19: 5000000 INFO @ Thu, 13 Dec 2018 00:49:22: 5000000 INFO @ Thu, 13 Dec 2018 00:49:27: 4000000 INFO @ Thu, 13 Dec 2018 00:49:31: 6000000 INFO @ Thu, 13 Dec 2018 00:49:32: 6000000 INFO @ Thu, 13 Dec 2018 00:49:42: 7000000 INFO @ Thu, 13 Dec 2018 00:49:43: 7000000 INFO @ Thu, 13 Dec 2018 00:49:47: 5000000 INFO @ Thu, 13 Dec 2018 00:49:54: 8000000 INFO @ Thu, 13 Dec 2018 00:50:01: 8000000 INFO @ Thu, 13 Dec 2018 00:50:06: 9000000 INFO @ Thu, 13 Dec 2018 00:50:07: 6000000 INFO @ Thu, 13 Dec 2018 00:50:17: 10000000 INFO @ Thu, 13 Dec 2018 00:50:21: 9000000 INFO @ Thu, 13 Dec 2018 00:50:27: 7000000 INFO @ Thu, 13 Dec 2018 00:50:30: 11000000 INFO @ Thu, 13 Dec 2018 00:50:36: 10000000 INFO @ Thu, 13 Dec 2018 00:50:42: 8000000 INFO @ Thu, 13 Dec 2018 00:50:43: 12000000 INFO @ Thu, 13 Dec 2018 00:50:48: 11000000 INFO @ Thu, 13 Dec 2018 00:50:57: 13000000 INFO @ Thu, 13 Dec 2018 00:50:59: 9000000 INFO @ Thu, 13 Dec 2018 00:50:59: 12000000 INFO @ Thu, 13 Dec 2018 00:51:12: 14000000 INFO @ Thu, 13 Dec 2018 00:51:15: 13000000 INFO @ Thu, 13 Dec 2018 00:51:17: 10000000 INFO @ Thu, 13 Dec 2018 00:51:28: 15000000 INFO @ Thu, 13 Dec 2018 00:51:29: 14000000 INFO @ Thu, 13 Dec 2018 00:51:35: 11000000 INFO @ Thu, 13 Dec 2018 00:51:42: 15000000 INFO @ Thu, 13 Dec 2018 00:51:44: 16000000 INFO @ Thu, 13 Dec 2018 00:51:53: 16000000 INFO @ Thu, 13 Dec 2018 00:51:54: 12000000 INFO @ Thu, 13 Dec 2018 00:52:02: 17000000 INFO @ Thu, 13 Dec 2018 00:52:08: 17000000 INFO @ Thu, 13 Dec 2018 00:52:12: 13000000 INFO @ Thu, 13 Dec 2018 00:52:22: 18000000 INFO @ Thu, 13 Dec 2018 00:52:25: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 00:52:30: 14000000 INFO @ Thu, 13 Dec 2018 00:52:39: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:52:39: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:52:39: #1 total tags in treatment: 9276224 INFO @ Thu, 13 Dec 2018 00:52:39: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:52:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:52:40: #1 tags after filtering in treatment: 6885415 INFO @ Thu, 13 Dec 2018 00:52:40: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 13 Dec 2018 00:52:40: #1 finished! INFO @ Thu, 13 Dec 2018 00:52:40: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:52:40: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:52:40: 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 @ Thu, 13 Dec 2018 00:52:40: Process for pairing-model is terminated! cat: SRX5017456.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017456.05_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 `SRX5017456.05_*.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 `SRX5017456.05_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 @ Thu, 13 Dec 2018 00:52:41: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:52:41: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:52:41: #1 total tags in treatment: 9276224 INFO @ Thu, 13 Dec 2018 00:52:41: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:52:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:52:41: #1 tags after filtering in treatment: 6885415 INFO @ Thu, 13 Dec 2018 00:52:41: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 13 Dec 2018 00:52:41: #1 finished! INFO @ Thu, 13 Dec 2018 00:52:41: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:52:42: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:52:42: 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 @ Thu, 13 Dec 2018 00:52:42: Process for pairing-model is terminated! cat: SRX5017456.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017456.20_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 `SRX5017456.20_*.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 `SRX5017456.20_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 @ Thu, 13 Dec 2018 00:52:43: 15000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 00:52:58: 16000000 INFO @ Thu, 13 Dec 2018 00:53:14: 17000000 INFO @ Thu, 13 Dec 2018 00:53:32: 18000000 INFO @ Thu, 13 Dec 2018 00:53:48: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:53:48: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:53:48: #1 total tags in treatment: 9276224 INFO @ Thu, 13 Dec 2018 00:53:48: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:53:48: #1 tags after filtering in treatment: 6885415 INFO @ Thu, 13 Dec 2018 00:53:48: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 13 Dec 2018 00:53:48: #1 finished! INFO @ Thu, 13 Dec 2018 00:53:48: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:53:49: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:53:49: 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 @ Thu, 13 Dec 2018 00:53:49: Process for pairing-model is terminated! cat: SRX5017456.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017456.10_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 `SRX5017456.10_*.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 `SRX5017456.10_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