Job ID = 11192639 sra ファイルのダウンロード中... Completed: 966433K bytes transferred in 11 seconds (712868K 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 29440994 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1743200/SRR3476614.sra Written 29440994 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1743200/SRR3476614.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: 00:19:29 29440994 reads; of these: 29440994 (100.00%) were paired; of these: 10464266 (35.54%) aligned concordantly 0 times 16840195 (57.20%) aligned concordantly exactly 1 time 2136533 (7.26%) aligned concordantly >1 times ---- 10464266 pairs aligned concordantly 0 times; of these: 264392 (2.53%) aligned discordantly 1 time ---- 10199874 pairs aligned 0 times concordantly or discordantly; of these: 20399748 mates make up the pairs; of these: 12415073 (60.86%) aligned 0 times 6983148 (34.23%) aligned exactly 1 time 1001527 (4.91%) aligned >1 times 78.92% overall alignment rate Time searching: 00:19:29 Overall time: 00:19:29 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] 6463948 / 19110849 = 0.3382 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 10:12:49: # Command line: callpeak -t SRX1743200.bam -f BAM -g 12100000 -n SRX1743200.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1743200.20 # format = BAM # ChIP-seq file = ['SRX1743200.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 10:12:49: # Command line: callpeak -t SRX1743200.bam -f BAM -g 12100000 -n SRX1743200.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1743200.10 # format = BAM # ChIP-seq file = ['SRX1743200.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 10:12:49: # Command line: callpeak -t SRX1743200.bam -f BAM -g 12100000 -n SRX1743200.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1743200.05 # format = BAM # ChIP-seq file = ['SRX1743200.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 10:12:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:12:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:12:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:12:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:12:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:12:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:12:54: 1000000 INFO @ Sat, 15 Sep 2018 10:12:56: 1000000 INFO @ Sat, 15 Sep 2018 10:12:56: 1000000 INFO @ Sat, 15 Sep 2018 10:13:01: 2000000 INFO @ Sat, 15 Sep 2018 10:13:03: 2000000 INFO @ Sat, 15 Sep 2018 10:13:03: 2000000 INFO @ Sat, 15 Sep 2018 10:13:07: 3000000 INFO @ Sat, 15 Sep 2018 10:13:09: 3000000 INFO @ Sat, 15 Sep 2018 10:13:09: 3000000 INFO @ Sat, 15 Sep 2018 10:13:14: 4000000 INFO @ Sat, 15 Sep 2018 10:13:16: 4000000 INFO @ Sat, 15 Sep 2018 10:13:16: 4000000 INFO @ Sat, 15 Sep 2018 10:13:19: 5000000 INFO @ Sat, 15 Sep 2018 10:13:23: 5000000 INFO @ Sat, 15 Sep 2018 10:13:23: 5000000 INFO @ Sat, 15 Sep 2018 10:13:26: 6000000 INFO @ Sat, 15 Sep 2018 10:13:29: 6000000 INFO @ Sat, 15 Sep 2018 10:13:29: 6000000 INFO @ Sat, 15 Sep 2018 10:13:32: 7000000 INFO @ Sat, 15 Sep 2018 10:13:36: 7000000 INFO @ Sat, 15 Sep 2018 10:13:36: 7000000 INFO @ Sat, 15 Sep 2018 10:13:38: 8000000 INFO @ Sat, 15 Sep 2018 10:13:42: 8000000 INFO @ Sat, 15 Sep 2018 10:13:42: 8000000 INFO @ Sat, 15 Sep 2018 10:13:44: 9000000 INFO @ Sat, 15 Sep 2018 10:13:48: 9000000 INFO @ Sat, 15 Sep 2018 10:13:48: 9000000 INFO @ Sat, 15 Sep 2018 10:13:51: 10000000 INFO @ Sat, 15 Sep 2018 10:13:54: 10000000 INFO @ Sat, 15 Sep 2018 10:13:54: 10000000 INFO @ Sat, 15 Sep 2018 10:13:57: 11000000 INFO @ Sat, 15 Sep 2018 10:14:00: 11000000 INFO @ Sat, 15 Sep 2018 10:14:00: 11000000 INFO @ Sat, 15 Sep 2018 10:14:04: 12000000 INFO @ Sat, 15 Sep 2018 10:14:07: 12000000 INFO @ Sat, 15 Sep 2018 10:14:07: 12000000 INFO @ Sat, 15 Sep 2018 10:14:09: 13000000 INFO @ Sat, 15 Sep 2018 10:14:14: 13000000 INFO @ Sat, 15 Sep 2018 10:14:14: 13000000 INFO @ Sat, 15 Sep 2018 10:14:15: 14000000 INFO @ Sat, 15 Sep 2018 10:14:21: 14000000 INFO @ Sat, 15 Sep 2018 10:14:21: 14000000 INFO @ Sat, 15 Sep 2018 10:14:21: 15000000 INFO @ Sat, 15 Sep 2018 10:14:27: 16000000 INFO @ Sat, 15 Sep 2018 10:14:28: 15000000 INFO @ Sat, 15 Sep 2018 10:14:28: 15000000 INFO @ Sat, 15 Sep 2018 10:14:33: 17000000 INFO @ Sat, 15 Sep 2018 10:14:34: 16000000 INFO @ Sat, 15 Sep 2018 10:14:34: 16000000 INFO @ Sat, 15 Sep 2018 10:14:39: 18000000 INFO @ Sat, 15 Sep 2018 10:14:41: 17000000 INFO @ Sat, 15 Sep 2018 10:14:41: 17000000 INFO @ Sat, 15 Sep 2018 10:14:45: 19000000 INFO @ Sat, 15 Sep 2018 10:14:48: 18000000 INFO @ Sat, 15 Sep 2018 10:14:48: 18000000 INFO @ Sat, 15 Sep 2018 10:14:51: 20000000 INFO @ Sat, 15 Sep 2018 10:14:55: 19000000 INFO @ Sat, 15 Sep 2018 10:14:55: 19000000 INFO @ Sat, 15 Sep 2018 10:14:57: 21000000 INFO @ Sat, 15 Sep 2018 10:15:02: 20000000 INFO @ Sat, 15 Sep 2018 10:15:02: 20000000 INFO @ Sat, 15 Sep 2018 10:15:04: 22000000 INFO @ Sat, 15 Sep 2018 10:15:09: 21000000 INFO @ Sat, 15 Sep 2018 10:15:09: 21000000 INFO @ Sat, 15 Sep 2018 10:15:10: 23000000 INFO @ Sat, 15 Sep 2018 10:15:15: 22000000 INFO @ Sat, 15 Sep 2018 10:15:15: 22000000 INFO @ Sat, 15 Sep 2018 10:15:16: 24000000 INFO @ Sat, 15 Sep 2018 10:15:22: 25000000 INFO @ Sat, 15 Sep 2018 10:15:22: 23000000 INFO @ Sat, 15 Sep 2018 10:15:22: 23000000 INFO @ Sat, 15 Sep 2018 10:15:28: 26000000 INFO @ Sat, 15 Sep 2018 10:15:29: 24000000 INFO @ Sat, 15 Sep 2018 10:15:29: 24000000 INFO @ Sat, 15 Sep 2018 10:15:34: 27000000 INFO @ Sat, 15 Sep 2018 10:15:35: 25000000 INFO @ Sat, 15 Sep 2018 10:15:35: 25000000 INFO @ Sat, 15 Sep 2018 10:15:40: 28000000 INFO @ Sat, 15 Sep 2018 10:15:42: 26000000 INFO @ Sat, 15 Sep 2018 10:15:42: 26000000 INFO @ Sat, 15 Sep 2018 10:15:46: 29000000 INFO @ Sat, 15 Sep 2018 10:15:49: 27000000 INFO @ Sat, 15 Sep 2018 10:15:49: 27000000 INFO @ Sat, 15 Sep 2018 10:15:52: 30000000 INFO @ Sat, 15 Sep 2018 10:15:55: 28000000 INFO @ Sat, 15 Sep 2018 10:15:55: 28000000 INFO @ Sat, 15 Sep 2018 10:15:58: 31000000 INFO @ Sat, 15 Sep 2018 10:16:02: 29000000 INFO @ Sat, 15 Sep 2018 10:16:02: 29000000 INFO @ Sat, 15 Sep 2018 10:16:04: 32000000 INFO @ Sat, 15 Sep 2018 10:16:09: 30000000 INFO @ Sat, 15 Sep 2018 10:16:09: 30000000 INFO @ Sat, 15 Sep 2018 10:16:10: 33000000 INFO @ Sat, 15 Sep 2018 10:16:13: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:16:13: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:16:13: #1 total tags in treatment: 12540433 INFO @ Sat, 15 Sep 2018 10:16:13: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:16:13: #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 10:16:13: #1 tags after filtering in treatment: 8549566 INFO @ Sat, 15 Sep 2018 10:16:13: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Sep 2018 10:16:13: #1 finished! INFO @ Sat, 15 Sep 2018 10:16:13: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:16:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:16:14: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:16:14: 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 @ Sat, 15 Sep 2018 10:16:14: Process for pairing-model is terminated! cat: SRX1743200.05_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 `SRX1743200.05_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 `SRX1743200.05_*.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 `SRX1743200.05_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 10:16:16: 31000000 INFO @ Sat, 15 Sep 2018 10:16:16: 31000000 INFO @ Sat, 15 Sep 2018 10:16:22: 32000000 INFO @ Sat, 15 Sep 2018 10:16:22: 32000000 INFO @ Sat, 15 Sep 2018 10:16:28: 33000000 INFO @ Sat, 15 Sep 2018 10:16:28: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Sep 2018 10:16:32: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:16:32: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:16:32: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:16:32: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:16:32: #1 total tags in treatment: 12540433 INFO @ Sat, 15 Sep 2018 10:16:32: #1 total tags in treatment: 12540433 INFO @ Sat, 15 Sep 2018 10:16:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:16:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:16:32: #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 10:16:32: #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 10:16:32: #1 tags after filtering in treatment: 8549566 INFO @ Sat, 15 Sep 2018 10:16:32: #1 tags after filtering in treatment: 8549566 INFO @ Sat, 15 Sep 2018 10:16:32: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Sep 2018 10:16:32: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Sep 2018 10:16:32: #1 finished! INFO @ Sat, 15 Sep 2018 10:16:32: #1 finished! INFO @ Sat, 15 Sep 2018 10:16:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:16:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:16:33: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:16:33: 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 10:16:33: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 10:16:33: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:16:33: 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 10:16:33: Process for pairing-model is terminated! cat: SRX1743200.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1743200.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1743200.20_model.r'rm: cannot remove `SRX1743200.10_model.r': そのようなファイルやディレクトリはありません : 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 `SRX1743200.20_*.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 `SRX1743200.10_*.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 `SRX1743200.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1743200.10_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 CompletedMACS2peakCalling BigWig に変換しました。