Job ID = 11192891 sra ファイルのダウンロード中... Completed: 758653K bytes transferred in 47 seconds (129538K 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 13743222 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771769/SRR5488924.sra Written 13743222 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771769/SRR5488924.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: 00:14:03 13743222 reads; of these: 13743222 (100.00%) were paired; of these: 936778 (6.82%) aligned concordantly 0 times 11026702 (80.23%) aligned concordantly exactly 1 time 1779742 (12.95%) aligned concordantly >1 times ---- 936778 pairs aligned concordantly 0 times; of these: 74422 (7.94%) aligned discordantly 1 time ---- 862356 pairs aligned 0 times concordantly or discordantly; of these: 1724712 mates make up the pairs; of these: 1420219 (82.35%) aligned 0 times 226730 (13.15%) aligned exactly 1 time 77763 (4.51%) aligned >1 times 94.83% overall alignment rate Time searching: 00:14:03 Overall time: 00:14:03 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] 579210 / 12870919 = 0.0450 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 10:40:37: # Command line: callpeak -t SRX2771769.bam -f BAM -g 12100000 -n SRX2771769.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2771769.10 # format = BAM # ChIP-seq file = ['SRX2771769.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 10:40:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:40:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:40:37: # Command line: callpeak -t SRX2771769.bam -f BAM -g 12100000 -n SRX2771769.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2771769.05 # format = BAM # ChIP-seq file = ['SRX2771769.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 10:40:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:40:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:40:37: # Command line: callpeak -t SRX2771769.bam -f BAM -g 12100000 -n SRX2771769.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2771769.20 # format = BAM # ChIP-seq file = ['SRX2771769.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 10:40:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:40:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:40:43: 1000000 INFO @ Sat, 15 Sep 2018 10:40:44: 1000000 INFO @ Sat, 15 Sep 2018 10:40:44: 1000000 INFO @ Sat, 15 Sep 2018 10:40:49: 2000000 INFO @ Sat, 15 Sep 2018 10:40:51: 2000000 INFO @ Sat, 15 Sep 2018 10:40:51: 2000000 INFO @ Sat, 15 Sep 2018 10:40:55: 3000000 INFO @ Sat, 15 Sep 2018 10:40:58: 3000000 INFO @ Sat, 15 Sep 2018 10:40:58: 3000000 INFO @ Sat, 15 Sep 2018 10:41:01: 4000000 INFO @ Sat, 15 Sep 2018 10:41:05: 4000000 INFO @ Sat, 15 Sep 2018 10:41:05: 4000000 INFO @ Sat, 15 Sep 2018 10:41:07: 5000000 INFO @ Sat, 15 Sep 2018 10:41:11: 5000000 INFO @ Sat, 15 Sep 2018 10:41:11: 5000000 INFO @ Sat, 15 Sep 2018 10:41:13: 6000000 INFO @ Sat, 15 Sep 2018 10:41:18: 6000000 INFO @ Sat, 15 Sep 2018 10:41:18: 6000000 INFO @ Sat, 15 Sep 2018 10:41:19: 7000000 INFO @ Sat, 15 Sep 2018 10:41:25: 7000000 INFO @ Sat, 15 Sep 2018 10:41:25: 7000000 INFO @ Sat, 15 Sep 2018 10:41:25: 8000000 INFO @ Sat, 15 Sep 2018 10:41:31: 9000000 INFO @ Sat, 15 Sep 2018 10:41:32: 8000000 INFO @ Sat, 15 Sep 2018 10:41:32: 8000000 INFO @ Sat, 15 Sep 2018 10:41:37: 10000000 INFO @ Sat, 15 Sep 2018 10:41:38: 9000000 INFO @ Sat, 15 Sep 2018 10:41:38: 9000000 INFO @ Sat, 15 Sep 2018 10:41:43: 11000000 INFO @ Sat, 15 Sep 2018 10:41:45: 10000000 INFO @ Sat, 15 Sep 2018 10:41:45: 10000000 INFO @ Sat, 15 Sep 2018 10:41:49: 12000000 INFO @ Sat, 15 Sep 2018 10:41:52: 11000000 INFO @ Sat, 15 Sep 2018 10:41:52: 11000000 INFO @ Sat, 15 Sep 2018 10:41:55: 13000000 INFO @ Sat, 15 Sep 2018 10:41:59: 12000000 INFO @ Sat, 15 Sep 2018 10:41:59: 12000000 INFO @ Sat, 15 Sep 2018 10:42:01: 14000000 INFO @ Sat, 15 Sep 2018 10:42:06: 13000000 INFO @ Sat, 15 Sep 2018 10:42:06: 13000000 INFO @ Sat, 15 Sep 2018 10:42:08: 15000000 INFO @ Sat, 15 Sep 2018 10:42:13: 14000000 INFO @ Sat, 15 Sep 2018 10:42:13: 14000000 INFO @ Sat, 15 Sep 2018 10:42:14: 16000000 INFO @ Sat, 15 Sep 2018 10:42:20: 15000000 INFO @ Sat, 15 Sep 2018 10:42:20: 15000000 INFO @ Sat, 15 Sep 2018 10:42:20: 17000000 INFO @ Sat, 15 Sep 2018 10:42:26: 16000000 INFO @ Sat, 15 Sep 2018 10:42:26: 16000000 INFO @ Sat, 15 Sep 2018 10:42:26: 18000000 INFO @ Sat, 15 Sep 2018 10:42:32: 17000000 INFO @ Sat, 15 Sep 2018 10:42:32: 17000000 INFO @ Sat, 15 Sep 2018 10:42:33: 19000000 INFO @ Sat, 15 Sep 2018 10:42:39: 18000000 INFO @ Sat, 15 Sep 2018 10:42:39: 18000000 INFO @ Sat, 15 Sep 2018 10:42:39: 20000000 INFO @ Sat, 15 Sep 2018 10:42:45: 21000000 INFO @ Sat, 15 Sep 2018 10:42:45: 19000000 INFO @ Sat, 15 Sep 2018 10:42:45: 19000000 INFO @ Sat, 15 Sep 2018 10:42:51: 22000000 INFO @ Sat, 15 Sep 2018 10:42:52: 20000000 INFO @ Sat, 15 Sep 2018 10:42:52: 20000000 INFO @ Sat, 15 Sep 2018 10:42:58: 23000000 INFO @ Sat, 15 Sep 2018 10:42:58: 21000000 INFO @ Sat, 15 Sep 2018 10:42:58: 21000000 INFO @ Sat, 15 Sep 2018 10:43:04: 24000000 INFO @ Sat, 15 Sep 2018 10:43:04: 22000000 INFO @ Sat, 15 Sep 2018 10:43:04: 22000000 INFO @ Sat, 15 Sep 2018 10:43:10: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:43:10: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:43:10: #1 total tags in treatment: 12228547 INFO @ Sat, 15 Sep 2018 10:43:10: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:10: #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 10:43:10: #1 tags after filtering in treatment: 8660785 INFO @ Sat, 15 Sep 2018 10:43:10: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Sep 2018 10:43:10: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:10: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:11: 23000000 INFO @ Sat, 15 Sep 2018 10:43:11: 23000000 INFO @ Sat, 15 Sep 2018 10:43:11: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:43:11: 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 10:43:11: Process for pairing-model is terminated! cat: SRX2771769.10_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 `SRX2771769.10_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 `SRX2771769.10_*.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 `SRX2771769.10_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 10:43:17: 24000000 INFO @ Sat, 15 Sep 2018 10:43:17: 24000000 INFO @ Sat, 15 Sep 2018 10:43:22: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:43:22: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:43:22: #1 total tags in treatment: 12228547 INFO @ Sat, 15 Sep 2018 10:43:22: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:22: #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 10:43:22: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:43:22: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:43:22: #1 total tags in treatment: 12228547 INFO @ Sat, 15 Sep 2018 10:43:22: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:22: #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 10:43:22: #1 tags after filtering in treatment: 8660785 INFO @ Sat, 15 Sep 2018 10:43:22: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Sep 2018 10:43:22: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:22: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:22: #1 tags after filtering in treatment: 8660785 INFO @ Sat, 15 Sep 2018 10:43:22: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Sep 2018 10:43:22: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:22: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:23: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:43:23: 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 10:43:23: Process for pairing-model is terminated! cat: SRX2771769.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2771769.05_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 `SRX2771769.05_*.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 `SRX2771769.05_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 10:43:23: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:43:23: 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 10:43:23: Process for pairing-model is terminated! cat: SRX2771769.20_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 `SRX2771769.20_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 `SRX2771769.20_*.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 `SRX2771769.20_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。