Job ID = 11192896 sra ファイルのダウンロード中... Completed: 786849K bytes transferred in 47 seconds (134605K 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 14226806 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771774/SRR5488929.sra Written 14226806 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771774/SRR5488929.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: 00:13:44 14226806 reads; of these: 14226806 (100.00%) were paired; of these: 861753 (6.06%) aligned concordantly 0 times 12029452 (84.55%) aligned concordantly exactly 1 time 1335601 (9.39%) aligned concordantly >1 times ---- 861753 pairs aligned concordantly 0 times; of these: 124663 (14.47%) aligned discordantly 1 time ---- 737090 pairs aligned 0 times concordantly or discordantly; of these: 1474180 mates make up the pairs; of these: 1157434 (78.51%) aligned 0 times 245706 (16.67%) aligned exactly 1 time 71040 (4.82%) aligned >1 times 95.93% overall alignment rate Time searching: 00:13:44 Overall time: 00:13:44 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] 513206 / 13474324 = 0.0381 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 10:41:17: # Command line: callpeak -t SRX2771774.bam -f BAM -g 12100000 -n SRX2771774.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2771774.20 # format = BAM # ChIP-seq file = ['SRX2771774.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 10:41:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:41:17: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:41:17: # Command line: callpeak -t SRX2771774.bam -f BAM -g 12100000 -n SRX2771774.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2771774.05 # format = BAM # ChIP-seq file = ['SRX2771774.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 10:41:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:41:17: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:41:17: # Command line: callpeak -t SRX2771774.bam -f BAM -g 12100000 -n SRX2771774.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2771774.10 # format = BAM # ChIP-seq file = ['SRX2771774.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 10:41:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:41:17: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:41:23: 1000000 INFO @ Sat, 15 Sep 2018 10:41:24: 1000000 INFO @ Sat, 15 Sep 2018 10:41:24: 1000000 INFO @ Sat, 15 Sep 2018 10:41:30: 2000000 INFO @ Sat, 15 Sep 2018 10:41:30: 2000000 INFO @ Sat, 15 Sep 2018 10:41:30: 2000000 INFO @ Sat, 15 Sep 2018 10:41:37: 3000000 INFO @ Sat, 15 Sep 2018 10:41:37: 3000000 INFO @ Sat, 15 Sep 2018 10:41:37: 3000000 INFO @ Sat, 15 Sep 2018 10:41:43: 4000000 INFO @ Sat, 15 Sep 2018 10:41:43: 4000000 INFO @ Sat, 15 Sep 2018 10:41:44: 4000000 INFO @ Sat, 15 Sep 2018 10:41:50: 5000000 INFO @ Sat, 15 Sep 2018 10:41:50: 5000000 INFO @ Sat, 15 Sep 2018 10:41:51: 5000000 INFO @ Sat, 15 Sep 2018 10:41:56: 6000000 INFO @ Sat, 15 Sep 2018 10:41:57: 6000000 INFO @ Sat, 15 Sep 2018 10:41:58: 6000000 INFO @ Sat, 15 Sep 2018 10:42:02: 7000000 INFO @ Sat, 15 Sep 2018 10:42:04: 7000000 INFO @ Sat, 15 Sep 2018 10:42:05: 7000000 INFO @ Sat, 15 Sep 2018 10:42:09: 8000000 INFO @ Sat, 15 Sep 2018 10:42:11: 8000000 INFO @ Sat, 15 Sep 2018 10:42:12: 8000000 INFO @ Sat, 15 Sep 2018 10:42:15: 9000000 INFO @ Sat, 15 Sep 2018 10:42:18: 9000000 INFO @ Sat, 15 Sep 2018 10:42:20: 9000000 INFO @ Sat, 15 Sep 2018 10:42:21: 10000000 INFO @ Sat, 15 Sep 2018 10:42:25: 10000000 INFO @ Sat, 15 Sep 2018 10:42:27: 10000000 INFO @ Sat, 15 Sep 2018 10:42:28: 11000000 INFO @ Sat, 15 Sep 2018 10:42:32: 11000000 INFO @ Sat, 15 Sep 2018 10:42:34: 12000000 INFO @ Sat, 15 Sep 2018 10:42:34: 11000000 INFO @ Sat, 15 Sep 2018 10:42:39: 12000000 INFO @ Sat, 15 Sep 2018 10:42:40: 13000000 INFO @ Sat, 15 Sep 2018 10:42:42: 12000000 INFO @ Sat, 15 Sep 2018 10:42:46: 13000000 INFO @ Sat, 15 Sep 2018 10:42:47: 14000000 INFO @ Sat, 15 Sep 2018 10:42:49: 13000000 INFO @ Sat, 15 Sep 2018 10:42:53: 14000000 INFO @ Sat, 15 Sep 2018 10:42:53: 15000000 INFO @ Sat, 15 Sep 2018 10:42:56: 14000000 INFO @ Sat, 15 Sep 2018 10:42:59: 15000000 INFO @ Sat, 15 Sep 2018 10:42:59: 16000000 INFO @ Sat, 15 Sep 2018 10:43:03: 15000000 INFO @ Sat, 15 Sep 2018 10:43:06: 16000000 INFO @ Sat, 15 Sep 2018 10:43:06: 17000000 INFO @ Sat, 15 Sep 2018 10:43:10: 16000000 INFO @ Sat, 15 Sep 2018 10:43:13: 18000000 INFO @ Sat, 15 Sep 2018 10:43:13: 17000000 INFO @ Sat, 15 Sep 2018 10:43:17: 17000000 INFO @ Sat, 15 Sep 2018 10:43:19: 19000000 INFO @ Sat, 15 Sep 2018 10:43:19: 18000000 INFO @ Sat, 15 Sep 2018 10:43:24: 18000000 INFO @ Sat, 15 Sep 2018 10:43:25: 20000000 INFO @ Sat, 15 Sep 2018 10:43:26: 19000000 INFO @ Sat, 15 Sep 2018 10:43:31: 21000000 INFO @ Sat, 15 Sep 2018 10:43:32: 19000000 INFO @ Sat, 15 Sep 2018 10:43:33: 20000000 INFO @ Sat, 15 Sep 2018 10:43:38: 22000000 INFO @ Sat, 15 Sep 2018 10:43:39: 20000000 INFO @ Sat, 15 Sep 2018 10:43:40: 21000000 INFO @ Sat, 15 Sep 2018 10:43:44: 23000000 INFO @ Sat, 15 Sep 2018 10:43:46: 21000000 INFO @ Sat, 15 Sep 2018 10:43:47: 22000000 INFO @ Sat, 15 Sep 2018 10:43:50: 24000000 INFO @ Sat, 15 Sep 2018 10:43:53: 22000000 INFO @ Sat, 15 Sep 2018 10:43:53: 23000000 INFO @ Sat, 15 Sep 2018 10:43:57: 25000000 INFO @ Sat, 15 Sep 2018 10:44:00: 24000000 INFO @ Sat, 15 Sep 2018 10:44:00: 23000000 INFO @ Sat, 15 Sep 2018 10:44:03: 26000000 INFO @ Sat, 15 Sep 2018 10:44:05: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:44:05: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:44:05: #1 total tags in treatment: 12853871 INFO @ Sat, 15 Sep 2018 10:44:05: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:44:05: #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 10:44:05: #1 tags after filtering in treatment: 9287783 INFO @ Sat, 15 Sep 2018 10:44:05: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Sep 2018 10:44:05: #1 finished! INFO @ Sat, 15 Sep 2018 10:44:05: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:44:06: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:44:06: 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 10:44:06: Process for pairing-model is terminated! cat: SRX2771774.05_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2771774.05_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 `SRX2771774.05_*.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 `SRX2771774.05_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 10:44:07: 25000000 INFO @ Sat, 15 Sep 2018 10:44:07: 24000000 INFO @ Sat, 15 Sep 2018 10:44:13: 26000000 INFO @ Sat, 15 Sep 2018 10:44:14: 25000000 INFO @ Sat, 15 Sep 2018 10:44:15: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:44:15: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:44:15: #1 total tags in treatment: 12853871 INFO @ Sat, 15 Sep 2018 10:44:15: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:44:15: #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 10:44:15: #1 tags after filtering in treatment: 9287783 INFO @ Sat, 15 Sep 2018 10:44:15: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Sep 2018 10:44:15: #1 finished! INFO @ Sat, 15 Sep 2018 10:44:15: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:44:16: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:44:16: 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 @ Sat, 15 Sep 2018 10:44:16: Process for pairing-model is terminated! cat: SRX2771774.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2771774.10_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 `SRX2771774.10_*.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 `SRX2771774.10_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 10:44:20: 26000000 INFO @ Sat, 15 Sep 2018 10:44:22: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:44:22: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:44:22: #1 total tags in treatment: 12853871 INFO @ Sat, 15 Sep 2018 10:44:22: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:44:22: #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 10:44:22: #1 tags after filtering in treatment: 9287783 INFO @ Sat, 15 Sep 2018 10:44:22: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Sep 2018 10:44:22: #1 finished! INFO @ Sat, 15 Sep 2018 10:44:22: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:44:23: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:44:23: 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 10:44:23: Process for pairing-model is terminated! cat: SRX2771774.20_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 `SRX2771774.20_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 `SRX2771774.20_*.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 `SRX2771774.20_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。