Job ID = 11388929 sra ファイルのダウンロード中... Completed: 776033K bytes transferred in 16 seconds (391509K 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 13723176 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017448/SRR8198071.sra Written 13723176 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017448/SRR8198071.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: 00:28:06 13723176 reads; of these: 13723176 (100.00%) were paired; of these: 1017778 (7.42%) aligned concordantly 0 times 11304583 (82.38%) aligned concordantly exactly 1 time 1400815 (10.21%) aligned concordantly >1 times ---- 1017778 pairs aligned concordantly 0 times; of these: 138857 (13.64%) aligned discordantly 1 time ---- 878921 pairs aligned 0 times concordantly or discordantly; of these: 1757842 mates make up the pairs; of these: 1547246 (88.02%) aligned 0 times 138979 (7.91%) aligned exactly 1 time 71617 (4.07%) aligned >1 times 94.36% overall alignment rate Time searching: 00:28:06 Overall time: 00:28:06 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] 1306590 / 12751954 = 0.1025 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 00:54:16: # Command line: callpeak -t SRX5017448.bam -f BAM -g 12100000 -n SRX5017448.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017448.20 # format = BAM # ChIP-seq file = ['SRX5017448.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 00:54:16: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:54:16: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:54:16: # Command line: callpeak -t SRX5017448.bam -f BAM -g 12100000 -n SRX5017448.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017448.10 # format = BAM # ChIP-seq file = ['SRX5017448.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 00:54:16: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:54:16: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:54:16: # Command line: callpeak -t SRX5017448.bam -f BAM -g 12100000 -n SRX5017448.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017448.05 # format = BAM # ChIP-seq file = ['SRX5017448.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 00:54:16: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:54:16: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:54:25: 1000000 INFO @ Thu, 13 Dec 2018 00:54:25: 1000000 INFO @ Thu, 13 Dec 2018 00:54:26: 1000000 INFO @ Thu, 13 Dec 2018 00:54:33: 2000000 INFO @ Thu, 13 Dec 2018 00:54:34: 2000000 INFO @ Thu, 13 Dec 2018 00:54:35: 2000000 INFO @ Thu, 13 Dec 2018 00:54:41: 3000000 INFO @ Thu, 13 Dec 2018 00:54:43: 3000000 INFO @ Thu, 13 Dec 2018 00:54:44: 3000000 INFO @ Thu, 13 Dec 2018 00:54:49: 4000000 INFO @ Thu, 13 Dec 2018 00:54:55: 4000000 INFO @ Thu, 13 Dec 2018 00:54:55: 4000000 INFO @ Thu, 13 Dec 2018 00:54:58: 5000000 INFO @ Thu, 13 Dec 2018 00:55:05: 5000000 INFO @ Thu, 13 Dec 2018 00:55:05: 5000000 INFO @ Thu, 13 Dec 2018 00:55:08: 6000000 INFO @ Thu, 13 Dec 2018 00:55:14: 6000000 INFO @ Thu, 13 Dec 2018 00:55:16: 6000000 INFO @ Thu, 13 Dec 2018 00:55:19: 7000000 INFO @ Thu, 13 Dec 2018 00:55:23: 7000000 INFO @ Thu, 13 Dec 2018 00:55:26: 7000000 INFO @ Thu, 13 Dec 2018 00:55:28: 8000000 INFO @ Thu, 13 Dec 2018 00:55:32: 8000000 INFO @ Thu, 13 Dec 2018 00:55:36: 8000000 INFO @ Thu, 13 Dec 2018 00:55:38: 9000000 INFO @ Thu, 13 Dec 2018 00:55:40: 9000000 INFO @ Thu, 13 Dec 2018 00:55:46: 9000000 INFO @ Thu, 13 Dec 2018 00:55:48: 10000000 INFO @ Thu, 13 Dec 2018 00:55:48: 10000000 INFO @ Thu, 13 Dec 2018 00:55:57: 11000000 INFO @ Thu, 13 Dec 2018 00:55:58: 10000000 INFO @ Thu, 13 Dec 2018 00:55:58: 11000000 INFO @ Thu, 13 Dec 2018 00:56:04: 12000000 INFO @ Thu, 13 Dec 2018 00:56:09: 11000000 INFO @ Thu, 13 Dec 2018 00:56:12: 13000000 INFO @ Thu, 13 Dec 2018 00:56:13: 12000000 INFO @ Thu, 13 Dec 2018 00:56:21: 14000000 INFO @ Thu, 13 Dec 2018 00:56:24: 12000000 INFO @ Thu, 13 Dec 2018 00:56:28: 13000000 INFO @ Thu, 13 Dec 2018 00:56:31: 15000000 INFO @ Thu, 13 Dec 2018 00:56:39: 13000000 INFO @ Thu, 13 Dec 2018 00:56:40: 14000000 INFO @ Thu, 13 Dec 2018 00:56:41: 16000000 INFO @ Thu, 13 Dec 2018 00:56:50: 15000000 INFO @ Thu, 13 Dec 2018 00:56:53: 14000000 INFO @ Thu, 13 Dec 2018 00:56:54: 17000000 INFO @ Thu, 13 Dec 2018 00:57:02: 16000000 INFO @ Thu, 13 Dec 2018 00:57:07: 18000000 INFO @ Thu, 13 Dec 2018 00:57:08: 15000000 INFO @ Thu, 13 Dec 2018 00:57:13: 17000000 INFO @ Thu, 13 Dec 2018 00:57:21: 19000000 INFO @ Thu, 13 Dec 2018 00:57:24: 16000000 INFO @ Thu, 13 Dec 2018 00:57:25: 18000000 INFO @ Thu, 13 Dec 2018 00:57:33: 20000000 INFO @ Thu, 13 Dec 2018 00:57:38: 19000000 INFO @ Thu, 13 Dec 2018 00:57:40: 17000000 INFO @ Thu, 13 Dec 2018 00:57:45: 21000000 INFO @ Thu, 13 Dec 2018 00:57:47: 20000000 INFO @ Thu, 13 Dec 2018 00:57:53: 18000000 INFO @ Thu, 13 Dec 2018 00:57:55: 21000000 INFO @ Thu, 13 Dec 2018 00:57:58: 22000000 INFO @ Thu, 13 Dec 2018 00:58:05: 22000000 INFO @ Thu, 13 Dec 2018 00:58:07: 19000000 INFO @ Thu, 13 Dec 2018 00:58:11: 23000000 INFO @ Thu, 13 Dec 2018 00:58:14: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:58:14: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:58:14: #1 total tags in treatment: 11402023 INFO @ Thu, 13 Dec 2018 00:58:14: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:58:14: #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 00:58:15: #1 tags after filtering in treatment: 8196319 INFO @ Thu, 13 Dec 2018 00:58:15: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 13 Dec 2018 00:58:15: #1 finished! INFO @ Thu, 13 Dec 2018 00:58:15: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:58:16: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:58:16: 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 @ Thu, 13 Dec 2018 00:58:16: Process for pairing-model is terminated! cat: SRX5017448.10_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017448.10_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 `SRX5017448.10_*.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 `SRX5017448.10_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 @ Thu, 13 Dec 2018 00:58:20: 20000000 INFO @ Thu, 13 Dec 2018 00:58:21: 23000000 INFO @ Thu, 13 Dec 2018 00:58:25: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:58:25: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:58:25: #1 total tags in treatment: 11402023 INFO @ Thu, 13 Dec 2018 00:58:25: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:58:25: #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 00:58:26: #1 tags after filtering in treatment: 8196319 INFO @ Thu, 13 Dec 2018 00:58:26: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 13 Dec 2018 00:58:26: #1 finished! INFO @ Thu, 13 Dec 2018 00:58:26: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:58:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:58:26: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:58:26: 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 00:58:26: Process for pairing-model is terminated! cat: SRX5017448.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017448.05_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 `SRX5017448.05_*.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 `SRX5017448.05_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 00:58:32: 21000000 INFO @ Thu, 13 Dec 2018 00:58:44: 22000000 INFO @ Thu, 13 Dec 2018 00:58:56: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 00:59:00: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:59:00: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:59:00: #1 total tags in treatment: 11402023 INFO @ Thu, 13 Dec 2018 00:59:00: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:59:00: #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 00:59:00: #1 tags after filtering in treatment: 8196319 INFO @ Thu, 13 Dec 2018 00:59:00: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 13 Dec 2018 00:59:00: #1 finished! INFO @ Thu, 13 Dec 2018 00:59:00: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:59:01: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:59:01: 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 00:59:01: Process for pairing-model is terminated! cat: SRX5017448.20_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017448.20_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 `SRX5017448.20_*.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 `SRX5017448.20_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 BigWig に変換しました。