Job ID = 11192899 sra ファイルのダウンロード中... Completed: 1249752K bytes transferred in 54 seconds (188630K 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 17615191 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771777/SRR5488932.sra Written 17615191 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771777/SRR5488932.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: 00:18:36 17615191 reads; of these: 17615191 (100.00%) were paired; of these: 1805531 (10.25%) aligned concordantly 0 times 13599472 (77.20%) aligned concordantly exactly 1 time 2210188 (12.55%) aligned concordantly >1 times ---- 1805531 pairs aligned concordantly 0 times; of these: 42625 (2.36%) aligned discordantly 1 time ---- 1762906 pairs aligned 0 times concordantly or discordantly; of these: 3525812 mates make up the pairs; of these: 3190553 (90.49%) aligned 0 times 262870 (7.46%) aligned exactly 1 time 72389 (2.05%) aligned >1 times 90.94% overall alignment rate Time searching: 00:18:36 Overall time: 00:18:36 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] 673098 / 15839231 = 0.0425 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 10:54:14: # Command line: callpeak -t SRX2771777.bam -f BAM -g 12100000 -n SRX2771777.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2771777.10 # format = BAM # ChIP-seq file = ['SRX2771777.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 10:54:14: # Command line: callpeak -t SRX2771777.bam -f BAM -g 12100000 -n SRX2771777.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2771777.05 # format = BAM # ChIP-seq file = ['SRX2771777.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 10:54:14: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:54:14: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:54:14: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:54:14: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:54:14: # Command line: callpeak -t SRX2771777.bam -f BAM -g 12100000 -n SRX2771777.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2771777.20 # format = BAM # ChIP-seq file = ['SRX2771777.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 10:54:14: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:54:14: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:54:22: 1000000 INFO @ Sat, 15 Sep 2018 10:54:22: 1000000 INFO @ Sat, 15 Sep 2018 10:54:22: 1000000 INFO @ Sat, 15 Sep 2018 10:54:29: 2000000 INFO @ Sat, 15 Sep 2018 10:54:29: 2000000 INFO @ Sat, 15 Sep 2018 10:54:29: 2000000 INFO @ Sat, 15 Sep 2018 10:54:35: 3000000 INFO @ Sat, 15 Sep 2018 10:54:35: 3000000 INFO @ Sat, 15 Sep 2018 10:54:36: 3000000 INFO @ Sat, 15 Sep 2018 10:54:43: 4000000 INFO @ Sat, 15 Sep 2018 10:54:43: 4000000 INFO @ Sat, 15 Sep 2018 10:54:43: 4000000 INFO @ Sat, 15 Sep 2018 10:54:50: 5000000 INFO @ Sat, 15 Sep 2018 10:54:50: 5000000 INFO @ Sat, 15 Sep 2018 10:54:51: 5000000 INFO @ Sat, 15 Sep 2018 10:54:57: 6000000 INFO @ Sat, 15 Sep 2018 10:54:57: 6000000 INFO @ Sat, 15 Sep 2018 10:54:59: 6000000 INFO @ Sat, 15 Sep 2018 10:55:05: 7000000 INFO @ Sat, 15 Sep 2018 10:55:05: 7000000 INFO @ Sat, 15 Sep 2018 10:55:07: 7000000 INFO @ Sat, 15 Sep 2018 10:55:13: 8000000 INFO @ Sat, 15 Sep 2018 10:55:14: 8000000 INFO @ Sat, 15 Sep 2018 10:55:15: 8000000 INFO @ Sat, 15 Sep 2018 10:55:21: 9000000 INFO @ Sat, 15 Sep 2018 10:55:22: 9000000 INFO @ Sat, 15 Sep 2018 10:55:22: 9000000 INFO @ Sat, 15 Sep 2018 10:55:28: 10000000 INFO @ Sat, 15 Sep 2018 10:55:30: 10000000 INFO @ Sat, 15 Sep 2018 10:55:31: 10000000 INFO @ Sat, 15 Sep 2018 10:55:36: 11000000 INFO @ Sat, 15 Sep 2018 10:55:38: 11000000 INFO @ Sat, 15 Sep 2018 10:55:39: 11000000 INFO @ Sat, 15 Sep 2018 10:55:45: 12000000 INFO @ Sat, 15 Sep 2018 10:55:46: 12000000 INFO @ Sat, 15 Sep 2018 10:55:47: 12000000 INFO @ Sat, 15 Sep 2018 10:55:52: 13000000 INFO @ Sat, 15 Sep 2018 10:55:54: 13000000 INFO @ Sat, 15 Sep 2018 10:55:55: 13000000 INFO @ Sat, 15 Sep 2018 10:56:00: 14000000 INFO @ Sat, 15 Sep 2018 10:56:02: 14000000 INFO @ Sat, 15 Sep 2018 10:56:03: 14000000 INFO @ Sat, 15 Sep 2018 10:56:08: 15000000 INFO @ Sat, 15 Sep 2018 10:56:10: 15000000 INFO @ Sat, 15 Sep 2018 10:56:10: 15000000 INFO @ Sat, 15 Sep 2018 10:56:17: 16000000 INFO @ Sat, 15 Sep 2018 10:56:18: 16000000 INFO @ Sat, 15 Sep 2018 10:56:19: 16000000 INFO @ Sat, 15 Sep 2018 10:56:26: 17000000 INFO @ Sat, 15 Sep 2018 10:56:26: 17000000 INFO @ Sat, 15 Sep 2018 10:56:28: 17000000 INFO @ Sat, 15 Sep 2018 10:56:35: 18000000 INFO @ Sat, 15 Sep 2018 10:56:35: 18000000 INFO @ Sat, 15 Sep 2018 10:56:37: 18000000 INFO @ Sat, 15 Sep 2018 10:56:43: 19000000 INFO @ Sat, 15 Sep 2018 10:56:43: 19000000 INFO @ Sat, 15 Sep 2018 10:56:45: 19000000 INFO @ Sat, 15 Sep 2018 10:56:51: 20000000 INFO @ Sat, 15 Sep 2018 10:56:52: 20000000 INFO @ Sat, 15 Sep 2018 10:56:54: 20000000 INFO @ Sat, 15 Sep 2018 10:56:59: 21000000 INFO @ Sat, 15 Sep 2018 10:57:01: 21000000 INFO @ Sat, 15 Sep 2018 10:57:03: 21000000 INFO @ Sat, 15 Sep 2018 10:57:06: 22000000 INFO @ Sat, 15 Sep 2018 10:57:10: 22000000 INFO @ Sat, 15 Sep 2018 10:57:12: 22000000 INFO @ Sat, 15 Sep 2018 10:57:14: 23000000 INFO @ Sat, 15 Sep 2018 10:57:19: 23000000 INFO @ Sat, 15 Sep 2018 10:57:21: 23000000 INFO @ Sat, 15 Sep 2018 10:57:21: 24000000 INFO @ Sat, 15 Sep 2018 10:57:28: 24000000 INFO @ Sat, 15 Sep 2018 10:57:29: 25000000 INFO @ Sat, 15 Sep 2018 10:57:30: 24000000 INFO @ Sat, 15 Sep 2018 10:57:37: 26000000 INFO @ Sat, 15 Sep 2018 10:57:37: 25000000 INFO @ Sat, 15 Sep 2018 10:57:39: 25000000 INFO @ Sat, 15 Sep 2018 10:57:44: 27000000 INFO @ Sat, 15 Sep 2018 10:57:46: 26000000 INFO @ Sat, 15 Sep 2018 10:57:48: 26000000 INFO @ Sat, 15 Sep 2018 10:57:52: 28000000 INFO @ Sat, 15 Sep 2018 10:57:55: 27000000 INFO @ Sat, 15 Sep 2018 10:57:58: 27000000 INFO @ Sat, 15 Sep 2018 10:58:01: 29000000 INFO @ Sat, 15 Sep 2018 10:58:05: 28000000 INFO @ Sat, 15 Sep 2018 10:58:07: 28000000 INFO @ Sat, 15 Sep 2018 10:58:09: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Sep 2018 10:58:15: 29000000 INFO @ Sat, 15 Sep 2018 10:58:15: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:58:15: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:58:15: #1 total tags in treatment: 15137206 INFO @ Sat, 15 Sep 2018 10:58:15: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:15: #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 10:58:16: #1 tags after filtering in treatment: 9854502 INFO @ Sat, 15 Sep 2018 10:58:16: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Sep 2018 10:58:16: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:16: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:17: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:58:17: 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 10:58:17: Process for pairing-model is terminated! cat: SRX2771777.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Sat, 15 Sep 2018 10:58:17: 29000000 pass1 - making usageList (0 chroms): 34 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2771777.05_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 `SRX2771777.05_*.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 `SRX2771777.05_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 10:58:24: 30000000 INFO @ Sat, 15 Sep 2018 10:58:26: 30000000 BigWig に変換しました。 INFO @ Sat, 15 Sep 2018 10:58:31: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:58:31: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:58:31: #1 total tags in treatment: 15137206 INFO @ Sat, 15 Sep 2018 10:58:31: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:31: #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 10:58:31: #1 tags after filtering in treatment: 9854502 INFO @ Sat, 15 Sep 2018 10:58:31: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Sep 2018 10:58:31: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:31: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:31: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:58:31: 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 10:58:31: Process for pairing-model is terminated! cat: SRX2771777.10_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 `SRX2771777.10_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 `SRX2771777.10_*.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 `SRX2771777.10_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 10:58:32: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:58:32: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:58:32: #1 total tags in treatment: 15137206 INFO @ Sat, 15 Sep 2018 10:58:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:32: #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 10:58:32: #1 tags after filtering in treatment: 9854502 INFO @ Sat, 15 Sep 2018 10:58:32: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Sep 2018 10:58:32: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:33: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:58:33: 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 10:58:33: Process for pairing-model is terminated! cat: SRX2771777.20_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 `SRX2771777.20_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 `SRX2771777.20_*.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 `SRX2771777.20_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