Job ID = 11244891 sra ファイルのダウンロード中... Completed: 711483K bytes transferred in 12 seconds (461328K bits/sec), in 1 file. Completed: 698083K bytes transferred in 11 seconds (502828K 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 15093553 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065337/SRR7145394.sra Written 15093553 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065337/SRR7145394.sra Read 15160747 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065337/SRR7145393.sra Written 15160747 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065337/SRR7145393.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 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: 00:27:50 30254300 reads; of these: 30254300 (100.00%) were paired; of these: 6416671 (21.21%) aligned concordantly 0 times 16784648 (55.48%) aligned concordantly exactly 1 time 7052981 (23.31%) aligned concordantly >1 times ---- 6416671 pairs aligned concordantly 0 times; of these: 1592877 (24.82%) aligned discordantly 1 time ---- 4823794 pairs aligned 0 times concordantly or discordantly; of these: 9647588 mates make up the pairs; of these: 7423427 (76.95%) aligned 0 times 674437 (6.99%) aligned exactly 1 time 1549724 (16.06%) aligned >1 times 87.73% overall alignment rate Time searching: 00:27:50 Overall time: 00:27:50 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 24 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] 3066119 / 25258010 = 0.1214 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 @ Tue, 09 Oct 2018 23:20:21: # Command line: callpeak -t SRX4065337.bam -f BAM -g 12100000 -n SRX4065337.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4065337.20 # format = BAM # ChIP-seq file = ['SRX4065337.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 @ Tue, 09 Oct 2018 23:20:21: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:21: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:21: # Command line: callpeak -t SRX4065337.bam -f BAM -g 12100000 -n SRX4065337.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4065337.10 # format = BAM # ChIP-seq file = ['SRX4065337.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 @ Tue, 09 Oct 2018 23:20:21: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:21: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:21: # Command line: callpeak -t SRX4065337.bam -f BAM -g 12100000 -n SRX4065337.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4065337.05 # format = BAM # ChIP-seq file = ['SRX4065337.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 @ Tue, 09 Oct 2018 23:20:21: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:21: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:27: 1000000 INFO @ Tue, 09 Oct 2018 23:20:27: 1000000 INFO @ Tue, 09 Oct 2018 23:20:27: 1000000 INFO @ Tue, 09 Oct 2018 23:20:33: 2000000 INFO @ Tue, 09 Oct 2018 23:20:34: 2000000 INFO @ Tue, 09 Oct 2018 23:20:34: 2000000 INFO @ Tue, 09 Oct 2018 23:20:39: 3000000 INFO @ Tue, 09 Oct 2018 23:20:40: 3000000 INFO @ Tue, 09 Oct 2018 23:20:40: 3000000 INFO @ Tue, 09 Oct 2018 23:20:44: 4000000 INFO @ Tue, 09 Oct 2018 23:20:47: 4000000 INFO @ Tue, 09 Oct 2018 23:20:47: 4000000 INFO @ Tue, 09 Oct 2018 23:20:50: 5000000 INFO @ Tue, 09 Oct 2018 23:20:53: 5000000 INFO @ Tue, 09 Oct 2018 23:20:53: 5000000 INFO @ Tue, 09 Oct 2018 23:20:56: 6000000 INFO @ Tue, 09 Oct 2018 23:21:00: 6000000 INFO @ Tue, 09 Oct 2018 23:21:00: 6000000 INFO @ Tue, 09 Oct 2018 23:21:01: 7000000 INFO @ Tue, 09 Oct 2018 23:21:06: 7000000 INFO @ Tue, 09 Oct 2018 23:21:06: 7000000 INFO @ Tue, 09 Oct 2018 23:21:07: 8000000 INFO @ Tue, 09 Oct 2018 23:21:13: 8000000 INFO @ Tue, 09 Oct 2018 23:21:13: 8000000 INFO @ Tue, 09 Oct 2018 23:21:13: 9000000 INFO @ Tue, 09 Oct 2018 23:21:18: 10000000 INFO @ Tue, 09 Oct 2018 23:21:19: 9000000 INFO @ Tue, 09 Oct 2018 23:21:19: 9000000 INFO @ Tue, 09 Oct 2018 23:21:24: 11000000 INFO @ Tue, 09 Oct 2018 23:21:25: 10000000 INFO @ Tue, 09 Oct 2018 23:21:25: 10000000 INFO @ Tue, 09 Oct 2018 23:21:30: 12000000 INFO @ Tue, 09 Oct 2018 23:21:32: 11000000 INFO @ Tue, 09 Oct 2018 23:21:32: 11000000 INFO @ Tue, 09 Oct 2018 23:21:35: 13000000 INFO @ Tue, 09 Oct 2018 23:21:38: 12000000 INFO @ Tue, 09 Oct 2018 23:21:38: 12000000 INFO @ Tue, 09 Oct 2018 23:21:41: 14000000 INFO @ Tue, 09 Oct 2018 23:21:45: 13000000 INFO @ Tue, 09 Oct 2018 23:21:45: 13000000 INFO @ Tue, 09 Oct 2018 23:21:47: 15000000 INFO @ Tue, 09 Oct 2018 23:21:52: 14000000 INFO @ Tue, 09 Oct 2018 23:21:52: 14000000 INFO @ Tue, 09 Oct 2018 23:21:53: 16000000 INFO @ Tue, 09 Oct 2018 23:21:58: 15000000 INFO @ Tue, 09 Oct 2018 23:21:59: 15000000 INFO @ Tue, 09 Oct 2018 23:21:59: 17000000 INFO @ Tue, 09 Oct 2018 23:22:05: 18000000 INFO @ Tue, 09 Oct 2018 23:22:05: 16000000 INFO @ Tue, 09 Oct 2018 23:22:05: 16000000 INFO @ Tue, 09 Oct 2018 23:22:11: 19000000 INFO @ Tue, 09 Oct 2018 23:22:12: 17000000 INFO @ Tue, 09 Oct 2018 23:22:12: 17000000 INFO @ Tue, 09 Oct 2018 23:22:17: 20000000 INFO @ Tue, 09 Oct 2018 23:22:18: 18000000 INFO @ Tue, 09 Oct 2018 23:22:19: 18000000 INFO @ Tue, 09 Oct 2018 23:22:23: 21000000 INFO @ Tue, 09 Oct 2018 23:22:25: 19000000 INFO @ Tue, 09 Oct 2018 23:22:25: 19000000 INFO @ Tue, 09 Oct 2018 23:22:28: 22000000 INFO @ Tue, 09 Oct 2018 23:22:32: 20000000 INFO @ Tue, 09 Oct 2018 23:22:32: 20000000 INFO @ Tue, 09 Oct 2018 23:22:34: 23000000 INFO @ Tue, 09 Oct 2018 23:22:38: 21000000 INFO @ Tue, 09 Oct 2018 23:22:39: 21000000 INFO @ Tue, 09 Oct 2018 23:22:40: 24000000 INFO @ Tue, 09 Oct 2018 23:22:45: 22000000 INFO @ Tue, 09 Oct 2018 23:22:45: 22000000 INFO @ Tue, 09 Oct 2018 23:22:46: 25000000 INFO @ Tue, 09 Oct 2018 23:22:52: 26000000 INFO @ Tue, 09 Oct 2018 23:22:52: 23000000 INFO @ Tue, 09 Oct 2018 23:22:52: 23000000 INFO @ Tue, 09 Oct 2018 23:22:58: 27000000 INFO @ Tue, 09 Oct 2018 23:22:59: 24000000 INFO @ Tue, 09 Oct 2018 23:22:59: 24000000 INFO @ Tue, 09 Oct 2018 23:23:05: 25000000 INFO @ Tue, 09 Oct 2018 23:23:05: 25000000 INFO @ Tue, 09 Oct 2018 23:23:06: 28000000 INFO @ Tue, 09 Oct 2018 23:23:12: 26000000 INFO @ Tue, 09 Oct 2018 23:23:12: 26000000 INFO @ Tue, 09 Oct 2018 23:23:15: 29000000 INFO @ Tue, 09 Oct 2018 23:23:19: 27000000 INFO @ Tue, 09 Oct 2018 23:23:19: 27000000 INFO @ Tue, 09 Oct 2018 23:23:23: 30000000 INFO @ Tue, 09 Oct 2018 23:23:26: 28000000 INFO @ Tue, 09 Oct 2018 23:23:26: 28000000 INFO @ Tue, 09 Oct 2018 23:23:30: 31000000 INFO @ Tue, 09 Oct 2018 23:23:33: 29000000 INFO @ Tue, 09 Oct 2018 23:23:33: 29000000 INFO @ Tue, 09 Oct 2018 23:23:38: 32000000 INFO @ Tue, 09 Oct 2018 23:23:39: 30000000 INFO @ Tue, 09 Oct 2018 23:23:39: 30000000 INFO @ Tue, 09 Oct 2018 23:23:46: 31000000 INFO @ Tue, 09 Oct 2018 23:23:46: 31000000 INFO @ Tue, 09 Oct 2018 23:23:46: 33000000 INFO @ Tue, 09 Oct 2018 23:23:53: 32000000 INFO @ Tue, 09 Oct 2018 23:23:53: 32000000 INFO @ Tue, 09 Oct 2018 23:23:54: 34000000 INFO @ Tue, 09 Oct 2018 23:24:00: 33000000 INFO @ Tue, 09 Oct 2018 23:24:00: 33000000 INFO @ Tue, 09 Oct 2018 23:24:02: 35000000 INFO @ Tue, 09 Oct 2018 23:24:06: 34000000 INFO @ Tue, 09 Oct 2018 23:24:06: 34000000 INFO @ Tue, 09 Oct 2018 23:24:10: 36000000 INFO @ Tue, 09 Oct 2018 23:24:13: 35000000 INFO @ Tue, 09 Oct 2018 23:24:14: 35000000 INFO @ Tue, 09 Oct 2018 23:24:18: 37000000 INFO @ Tue, 09 Oct 2018 23:24:20: 36000000 INFO @ Tue, 09 Oct 2018 23:24:21: 36000000 INFO @ Tue, 09 Oct 2018 23:24:26: 38000000 INFO @ Tue, 09 Oct 2018 23:24:27: 37000000 INFO @ Tue, 09 Oct 2018 23:24:28: 37000000 INFO @ Tue, 09 Oct 2018 23:24:34: 39000000 INFO @ Tue, 09 Oct 2018 23:24:34: 38000000 INFO @ Tue, 09 Oct 2018 23:24:34: 38000000 INFO @ Tue, 09 Oct 2018 23:24:41: 39000000 INFO @ Tue, 09 Oct 2018 23:24:41: 39000000 INFO @ Tue, 09 Oct 2018 23:24:42: 40000000 INFO @ Tue, 09 Oct 2018 23:24:48: 40000000 INFO @ Tue, 09 Oct 2018 23:24:48: 40000000 INFO @ Tue, 09 Oct 2018 23:24:50: 41000000 INFO @ Tue, 09 Oct 2018 23:24:55: 41000000 INFO @ Tue, 09 Oct 2018 23:24:55: 41000000 INFO @ Tue, 09 Oct 2018 23:24:58: 42000000 INFO @ Tue, 09 Oct 2018 23:25:02: 42000000 INFO @ Tue, 09 Oct 2018 23:25:02: 42000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 09 Oct 2018 23:25:06: 43000000 INFO @ Tue, 09 Oct 2018 23:25:08: 43000000 INFO @ Tue, 09 Oct 2018 23:25:09: 43000000 INFO @ Tue, 09 Oct 2018 23:25:13: 44000000 INFO @ Tue, 09 Oct 2018 23:25:15: 44000000 INFO @ Tue, 09 Oct 2018 23:25:16: 44000000 INFO @ Tue, 09 Oct 2018 23:25:21: 45000000 INFO @ Tue, 09 Oct 2018 23:25:22: 45000000 INFO @ Tue, 09 Oct 2018 23:25:24: 45000000 BigWig に変換しました。 INFO @ Tue, 09 Oct 2018 23:25:29: 46000000 INFO @ Tue, 09 Oct 2018 23:25:29: 46000000 INFO @ Tue, 09 Oct 2018 23:25:31: 46000000 INFO @ Tue, 09 Oct 2018 23:25:36: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:25:36: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:25:36: #1 total tags in treatment: 20799541 INFO @ Tue, 09 Oct 2018 23:25:36: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:25:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:25:37: #1 tags after filtering in treatment: 10294481 INFO @ Tue, 09 Oct 2018 23:25:37: #1 Redundant rate of treatment: 0.51 INFO @ Tue, 09 Oct 2018 23:25:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:25:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:25:37: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:25:37: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:25:37: #1 total tags in treatment: 20799541 INFO @ Tue, 09 Oct 2018 23:25:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:25:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:25:37: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:25:37: 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 @ Tue, 09 Oct 2018 23:25:37: Process for pairing-model is terminated! cat: SRX4065337.05_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 `SRX4065337.05_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 `SRX4065337.05_*.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 `SRX4065337.05_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 @ Tue, 09 Oct 2018 23:25:38: #1 tags after filtering in treatment: 10294481 INFO @ Tue, 09 Oct 2018 23:25:38: #1 Redundant rate of treatment: 0.51 INFO @ Tue, 09 Oct 2018 23:25:38: #1 finished! INFO @ Tue, 09 Oct 2018 23:25:38: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:25:38: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:25:38: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:25:38: #1 total tags in treatment: 20799541 INFO @ Tue, 09 Oct 2018 23:25:38: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:25:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:25:38: #1 tags after filtering in treatment: 10294481 INFO @ Tue, 09 Oct 2018 23:25:38: #1 Redundant rate of treatment: 0.51 INFO @ Tue, 09 Oct 2018 23:25:38: #1 finished! INFO @ Tue, 09 Oct 2018 23:25:38: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:25:38: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:25:38: 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 @ Tue, 09 Oct 2018 23:25:38: Process for pairing-model is terminated! cat: SRX4065337.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4065337.20_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 `SRX4065337.20_*.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 `SRX4065337.20_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 INFO @ Tue, 09 Oct 2018 23:25:39: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:25:39: 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 @ Tue, 09 Oct 2018 23:25:39: Process for pairing-model is terminated! cat: SRX4065337.10_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 `SRX4065337.10_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 `SRX4065337.10_*.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 `SRX4065337.10_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