Job ID = 11192882 sra ファイルのダウンロード中... Completed: 1272845K bytes transferred in 37 seconds (280149K 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 17831333 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771760/SRR5488915.sra Written 17831333 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771760/SRR5488915.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: 00:17:41 17831333 reads; of these: 17831333 (100.00%) were paired; of these: 1738211 (9.75%) aligned concordantly 0 times 14038286 (78.73%) aligned concordantly exactly 1 time 2054836 (11.52%) aligned concordantly >1 times ---- 1738211 pairs aligned concordantly 0 times; of these: 38380 (2.21%) aligned discordantly 1 time ---- 1699831 pairs aligned 0 times concordantly or discordantly; of these: 3399662 mates make up the pairs; of these: 3061862 (90.06%) aligned 0 times 270110 (7.95%) aligned exactly 1 time 67690 (1.99%) aligned >1 times 91.41% overall alignment rate Time searching: 00:17:41 Overall time: 00:17:41 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] 699338 / 16114120 = 0.0434 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 10:48:04: # Command line: callpeak -t SRX2771760.bam -f BAM -g 12100000 -n SRX2771760.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2771760.20 # format = BAM # ChIP-seq file = ['SRX2771760.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 10:48:04: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:48:04: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:48:04: # Command line: callpeak -t SRX2771760.bam -f BAM -g 12100000 -n SRX2771760.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2771760.05 # format = BAM # ChIP-seq file = ['SRX2771760.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 10:48:04: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:48:04: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:48:04: # Command line: callpeak -t SRX2771760.bam -f BAM -g 12100000 -n SRX2771760.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2771760.10 # format = BAM # ChIP-seq file = ['SRX2771760.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 10:48:04: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:48:04: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:48:12: 1000000 INFO @ Sat, 15 Sep 2018 10:48:12: 1000000 INFO @ Sat, 15 Sep 2018 10:48:13: 1000000 INFO @ Sat, 15 Sep 2018 10:48:19: 2000000 INFO @ Sat, 15 Sep 2018 10:48:19: 2000000 INFO @ Sat, 15 Sep 2018 10:48:21: 2000000 INFO @ Sat, 15 Sep 2018 10:48:27: 3000000 INFO @ Sat, 15 Sep 2018 10:48:27: 3000000 INFO @ Sat, 15 Sep 2018 10:48:30: 3000000 INFO @ Sat, 15 Sep 2018 10:48:34: 4000000 INFO @ Sat, 15 Sep 2018 10:48:34: 4000000 INFO @ Sat, 15 Sep 2018 10:48:38: 4000000 INFO @ Sat, 15 Sep 2018 10:48:43: 5000000 INFO @ Sat, 15 Sep 2018 10:48:43: 5000000 INFO @ Sat, 15 Sep 2018 10:48:46: 5000000 INFO @ Sat, 15 Sep 2018 10:48:51: 6000000 INFO @ Sat, 15 Sep 2018 10:48:51: 6000000 INFO @ Sat, 15 Sep 2018 10:48:55: 6000000 INFO @ Sat, 15 Sep 2018 10:48:59: 7000000 INFO @ Sat, 15 Sep 2018 10:48:59: 7000000 INFO @ Sat, 15 Sep 2018 10:49:03: 7000000 INFO @ Sat, 15 Sep 2018 10:49:06: 8000000 INFO @ Sat, 15 Sep 2018 10:49:06: 8000000 INFO @ Sat, 15 Sep 2018 10:49:12: 8000000 INFO @ Sat, 15 Sep 2018 10:49:14: 9000000 INFO @ Sat, 15 Sep 2018 10:49:14: 9000000 INFO @ Sat, 15 Sep 2018 10:49:20: 9000000 INFO @ Sat, 15 Sep 2018 10:49:21: 10000000 INFO @ Sat, 15 Sep 2018 10:49:21: 10000000 INFO @ Sat, 15 Sep 2018 10:49:29: 10000000 INFO @ Sat, 15 Sep 2018 10:49:29: 11000000 INFO @ Sat, 15 Sep 2018 10:49:29: 11000000 INFO @ Sat, 15 Sep 2018 10:49:38: 12000000 INFO @ Sat, 15 Sep 2018 10:49:38: 12000000 INFO @ Sat, 15 Sep 2018 10:49:38: 11000000 INFO @ Sat, 15 Sep 2018 10:49:46: 13000000 INFO @ Sat, 15 Sep 2018 10:49:46: 13000000 INFO @ Sat, 15 Sep 2018 10:49:47: 12000000 INFO @ Sat, 15 Sep 2018 10:49:54: 14000000 INFO @ Sat, 15 Sep 2018 10:49:54: 14000000 INFO @ Sat, 15 Sep 2018 10:49:56: 13000000 INFO @ Sat, 15 Sep 2018 10:50:03: 15000000 INFO @ Sat, 15 Sep 2018 10:50:03: 15000000 INFO @ Sat, 15 Sep 2018 10:50:05: 14000000 INFO @ Sat, 15 Sep 2018 10:50:11: 16000000 INFO @ Sat, 15 Sep 2018 10:50:11: 16000000 INFO @ Sat, 15 Sep 2018 10:50:13: 15000000 INFO @ Sat, 15 Sep 2018 10:50:19: 17000000 INFO @ Sat, 15 Sep 2018 10:50:19: 17000000 INFO @ Sat, 15 Sep 2018 10:50:22: 16000000 INFO @ Sat, 15 Sep 2018 10:50:27: 18000000 INFO @ Sat, 15 Sep 2018 10:50:28: 18000000 INFO @ Sat, 15 Sep 2018 10:50:30: 17000000 INFO @ Sat, 15 Sep 2018 10:50:35: 19000000 INFO @ Sat, 15 Sep 2018 10:50:36: 19000000 INFO @ Sat, 15 Sep 2018 10:50:39: 18000000 INFO @ Sat, 15 Sep 2018 10:50:43: 20000000 INFO @ Sat, 15 Sep 2018 10:50:45: 20000000 INFO @ Sat, 15 Sep 2018 10:50:48: 19000000 INFO @ Sat, 15 Sep 2018 10:50:52: 21000000 INFO @ Sat, 15 Sep 2018 10:50:54: 21000000 INFO @ Sat, 15 Sep 2018 10:50:58: 20000000 INFO @ Sat, 15 Sep 2018 10:51:01: 22000000 INFO @ Sat, 15 Sep 2018 10:51:03: 22000000 INFO @ Sat, 15 Sep 2018 10:51:09: 21000000 INFO @ Sat, 15 Sep 2018 10:51:10: 23000000 INFO @ Sat, 15 Sep 2018 10:51:13: 23000000 INFO @ Sat, 15 Sep 2018 10:51:18: 22000000 INFO @ Sat, 15 Sep 2018 10:51:19: 24000000 INFO @ Sat, 15 Sep 2018 10:51:22: 24000000 INFO @ Sat, 15 Sep 2018 10:51:26: 23000000 INFO @ Sat, 15 Sep 2018 10:51:27: 25000000 INFO @ Sat, 15 Sep 2018 10:51:30: 25000000 INFO @ Sat, 15 Sep 2018 10:51:34: 26000000 INFO @ Sat, 15 Sep 2018 10:51:35: 24000000 INFO @ Sat, 15 Sep 2018 10:51:38: 26000000 INFO @ Sat, 15 Sep 2018 10:51:42: 27000000 INFO @ Sat, 15 Sep 2018 10:51:44: 25000000 INFO @ Sat, 15 Sep 2018 10:51:47: 27000000 INFO @ Sat, 15 Sep 2018 10:51:51: 28000000 INFO @ Sat, 15 Sep 2018 10:51:51: 26000000 INFO @ Sat, 15 Sep 2018 10:51:55: 28000000 INFO @ Sat, 15 Sep 2018 10:51:58: 29000000 INFO @ Sat, 15 Sep 2018 10:52:00: 27000000 INFO @ Sat, 15 Sep 2018 10:52:04: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Sep 2018 10:52:06: 30000000 INFO @ Sat, 15 Sep 2018 10:52:09: 28000000 INFO @ Sat, 15 Sep 2018 10:52:12: 30000000 INFO @ Sat, 15 Sep 2018 10:52:14: 31000000 INFO @ Sat, 15 Sep 2018 10:52:16: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:52:16: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:52:16: #1 total tags in treatment: 15394428 INFO @ Sat, 15 Sep 2018 10:52:16: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:16: #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 10:52:16: #1 tags after filtering in treatment: 9989599 INFO @ Sat, 15 Sep 2018 10:52:16: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Sep 2018 10:52:16: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:16: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:17: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:52:17: 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 10:52:17: Process for pairing-model is terminated! cat: SRX2771760.05_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 `SRX2771760.05_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 `SRX2771760.05_*.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 `SRX2771760.05_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 10:52:18: 29000000 INFO @ Sat, 15 Sep 2018 10:52:20: 31000000 INFO @ Sat, 15 Sep 2018 10:52:22: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:52:22: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:52:22: #1 total tags in treatment: 15394428 INFO @ Sat, 15 Sep 2018 10:52:22: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:22: #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 10:52:22: #1 tags after filtering in treatment: 9989599 INFO @ Sat, 15 Sep 2018 10:52:22: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Sep 2018 10:52:22: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:22: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:23: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:52:23: 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 10:52:23: Process for pairing-model is terminated! cat: SRX2771760.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2771760.20_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 `SRX2771760.20_*.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 `SRX2771760.20_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。 INFO @ Sat, 15 Sep 2018 10:52:25: 30000000 INFO @ Sat, 15 Sep 2018 10:52:33: 31000000 INFO @ Sat, 15 Sep 2018 10:52:35: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:52:35: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:52:35: #1 total tags in treatment: 15394428 INFO @ Sat, 15 Sep 2018 10:52:35: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:35: #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 10:52:35: #1 tags after filtering in treatment: 9989599 INFO @ Sat, 15 Sep 2018 10:52:35: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Sep 2018 10:52:35: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:36: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:52:36: 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 10:52:36: Process for pairing-model is terminated! cat: SRX2771760.10_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 `SRX2771760.10_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 `SRX2771760.10_*.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 `SRX2771760.10_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