Job ID = 10536373 sra ファイルのダウンロード中... Completed: 1327695K bytes transferred in 33 seconds (329402K 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... Written 34509498 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433234/SRR6333875.sra Written 34509498 spots total 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: 00:36:23 34509498 reads; of these: 34509498 (100.00%) were paired; of these: 2942149 (8.53%) aligned concordantly 0 times 26725936 (77.45%) aligned concordantly exactly 1 time 4841413 (14.03%) aligned concordantly >1 times ---- 2942149 pairs aligned concordantly 0 times; of these: 58409 (1.99%) aligned discordantly 1 time ---- 2883740 pairs aligned 0 times concordantly or discordantly; of these: 5767480 mates make up the pairs; of these: 5310452 (92.08%) aligned 0 times 299325 (5.19%) aligned exactly 1 time 157703 (2.73%) aligned >1 times 92.31% overall alignment rate Time searching: 00:36:23 Overall time: 00:36:23 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 28 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] 10100303 / 31586225 = 0.3198 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 @ Thu, 05 Apr 2018 09:54:58: # Command line: callpeak -t SRX3433234.bam -f BAM -g 12100000 -n SRX3433234.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433234.10 # format = BAM # ChIP-seq file = ['SRX3433234.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 @ Thu, 05 Apr 2018 09:54:58: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:58: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:54:58: # Command line: callpeak -t SRX3433234.bam -f BAM -g 12100000 -n SRX3433234.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433234.05 # format = BAM # ChIP-seq file = ['SRX3433234.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 @ Thu, 05 Apr 2018 09:54:58: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:58: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:54:58: # Command line: callpeak -t SRX3433234.bam -f BAM -g 12100000 -n SRX3433234.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433234.20 # format = BAM # ChIP-seq file = ['SRX3433234.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 @ Thu, 05 Apr 2018 09:54:58: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:58: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:55:04: 1000000 INFO @ Thu, 05 Apr 2018 09:55:04: 1000000 INFO @ Thu, 05 Apr 2018 09:55:04: 1000000 INFO @ Thu, 05 Apr 2018 09:55:10: 2000000 INFO @ Thu, 05 Apr 2018 09:55:10: 2000000 INFO @ Thu, 05 Apr 2018 09:55:10: 2000000 INFO @ Thu, 05 Apr 2018 09:55:16: 3000000 INFO @ Thu, 05 Apr 2018 09:55:16: 3000000 INFO @ Thu, 05 Apr 2018 09:55:16: 3000000 INFO @ Thu, 05 Apr 2018 09:55:22: 4000000 INFO @ Thu, 05 Apr 2018 09:55:22: 4000000 INFO @ Thu, 05 Apr 2018 09:55:22: 4000000 INFO @ Thu, 05 Apr 2018 09:55:28: 5000000 INFO @ Thu, 05 Apr 2018 09:55:28: 5000000 INFO @ Thu, 05 Apr 2018 09:55:29: 5000000 INFO @ Thu, 05 Apr 2018 09:55:34: 6000000 INFO @ Thu, 05 Apr 2018 09:55:34: 6000000 INFO @ Thu, 05 Apr 2018 09:55:35: 6000000 INFO @ Thu, 05 Apr 2018 09:55:40: 7000000 INFO @ Thu, 05 Apr 2018 09:55:41: 7000000 INFO @ Thu, 05 Apr 2018 09:55:41: 7000000 INFO @ Thu, 05 Apr 2018 09:55:46: 8000000 INFO @ Thu, 05 Apr 2018 09:55:47: 8000000 INFO @ Thu, 05 Apr 2018 09:55:47: 8000000 INFO @ Thu, 05 Apr 2018 09:55:52: 9000000 INFO @ Thu, 05 Apr 2018 09:55:53: 9000000 INFO @ Thu, 05 Apr 2018 09:55:54: 9000000 INFO @ Thu, 05 Apr 2018 09:55:57: 10000000 INFO @ Thu, 05 Apr 2018 09:56:00: 10000000 INFO @ Thu, 05 Apr 2018 09:56:00: 10000000 INFO @ Thu, 05 Apr 2018 09:56:03: 11000000 INFO @ Thu, 05 Apr 2018 09:56:06: 11000000 INFO @ Thu, 05 Apr 2018 09:56:06: 11000000 INFO @ Thu, 05 Apr 2018 09:56:09: 12000000 INFO @ Thu, 05 Apr 2018 09:56:12: 12000000 INFO @ Thu, 05 Apr 2018 09:56:12: 12000000 INFO @ Thu, 05 Apr 2018 09:56:15: 13000000 INFO @ Thu, 05 Apr 2018 09:56:19: 13000000 INFO @ Thu, 05 Apr 2018 09:56:19: 13000000 INFO @ Thu, 05 Apr 2018 09:56:20: 14000000 INFO @ Thu, 05 Apr 2018 09:56:25: 14000000 INFO @ Thu, 05 Apr 2018 09:56:25: 14000000 INFO @ Thu, 05 Apr 2018 09:56:26: 15000000 INFO @ Thu, 05 Apr 2018 09:56:31: 15000000 INFO @ Thu, 05 Apr 2018 09:56:31: 15000000 INFO @ Thu, 05 Apr 2018 09:56:32: 16000000 INFO @ Thu, 05 Apr 2018 09:56:37: 16000000 INFO @ Thu, 05 Apr 2018 09:56:38: 16000000 INFO @ Thu, 05 Apr 2018 09:56:38: 17000000 INFO @ Thu, 05 Apr 2018 09:56:43: 17000000 INFO @ Thu, 05 Apr 2018 09:56:44: 17000000 INFO @ Thu, 05 Apr 2018 09:56:44: 18000000 INFO @ Thu, 05 Apr 2018 09:56:49: 18000000 INFO @ Thu, 05 Apr 2018 09:56:50: 18000000 INFO @ Thu, 05 Apr 2018 09:56:50: 19000000 INFO @ Thu, 05 Apr 2018 09:56:55: 19000000 INFO @ Thu, 05 Apr 2018 09:56:56: 19000000 INFO @ Thu, 05 Apr 2018 09:56:56: 20000000 INFO @ Thu, 05 Apr 2018 09:57:02: 20000000 INFO @ Thu, 05 Apr 2018 09:57:02: 21000000 INFO @ Thu, 05 Apr 2018 09:57:02: 20000000 INFO @ Thu, 05 Apr 2018 09:57:08: 22000000 INFO @ Thu, 05 Apr 2018 09:57:08: 21000000 INFO @ Thu, 05 Apr 2018 09:57:08: 21000000 INFO @ Thu, 05 Apr 2018 09:57:14: 23000000 INFO @ Thu, 05 Apr 2018 09:57:14: 22000000 INFO @ Thu, 05 Apr 2018 09:57:14: 22000000 INFO @ Thu, 05 Apr 2018 09:57:20: 23000000 INFO @ Thu, 05 Apr 2018 09:57:20: 24000000 INFO @ Thu, 05 Apr 2018 09:57:20: 23000000 INFO @ Thu, 05 Apr 2018 09:57:26: 24000000 INFO @ Thu, 05 Apr 2018 09:57:26: 25000000 INFO @ Thu, 05 Apr 2018 09:57:26: 24000000 INFO @ Thu, 05 Apr 2018 09:57:32: 26000000 INFO @ Thu, 05 Apr 2018 09:57:32: 25000000 INFO @ Thu, 05 Apr 2018 09:57:32: 25000000 INFO @ Thu, 05 Apr 2018 09:57:38: 26000000 INFO @ Thu, 05 Apr 2018 09:57:38: 27000000 INFO @ Thu, 05 Apr 2018 09:57:38: 26000000 INFO @ Thu, 05 Apr 2018 09:57:43: 28000000 INFO @ Thu, 05 Apr 2018 09:57:44: 27000000 INFO @ Thu, 05 Apr 2018 09:57:44: 27000000 INFO @ Thu, 05 Apr 2018 09:57:49: 29000000 INFO @ Thu, 05 Apr 2018 09:57:50: 28000000 INFO @ Thu, 05 Apr 2018 09:57:51: 28000000 INFO @ Thu, 05 Apr 2018 09:57:55: 30000000 INFO @ Thu, 05 Apr 2018 09:57:57: 29000000 INFO @ Thu, 05 Apr 2018 09:57:57: 29000000 INFO @ Thu, 05 Apr 2018 09:58:01: 31000000 INFO @ Thu, 05 Apr 2018 09:58:03: 30000000 INFO @ Thu, 05 Apr 2018 09:58:04: 30000000 INFO @ Thu, 05 Apr 2018 09:58:07: 32000000 INFO @ Thu, 05 Apr 2018 09:58:09: 31000000 INFO @ Thu, 05 Apr 2018 09:58:10: 31000000 INFO @ Thu, 05 Apr 2018 09:58:13: 33000000 INFO @ Thu, 05 Apr 2018 09:58:15: 32000000 INFO @ Thu, 05 Apr 2018 09:58:16: 32000000 INFO @ Thu, 05 Apr 2018 09:58:19: 34000000 INFO @ Thu, 05 Apr 2018 09:58:22: 33000000 INFO @ Thu, 05 Apr 2018 09:58:22: 33000000 INFO @ Thu, 05 Apr 2018 09:58:25: 35000000 INFO @ Thu, 05 Apr 2018 09:58:28: 34000000 INFO @ Thu, 05 Apr 2018 09:58:28: 34000000 INFO @ Thu, 05 Apr 2018 09:58:31: 36000000 INFO @ Thu, 05 Apr 2018 09:58:34: 35000000 INFO @ Thu, 05 Apr 2018 09:58:34: 35000000 INFO @ Thu, 05 Apr 2018 09:58:37: 37000000 INFO @ Thu, 05 Apr 2018 09:58:40: 36000000 INFO @ Thu, 05 Apr 2018 09:58:40: 36000000 INFO @ Thu, 05 Apr 2018 09:58:44: 38000000 INFO @ Thu, 05 Apr 2018 09:58:46: 37000000 INFO @ Thu, 05 Apr 2018 09:58:47: 37000000 INFO @ Thu, 05 Apr 2018 09:58:50: 39000000 INFO @ Thu, 05 Apr 2018 09:58:52: 38000000 INFO @ Thu, 05 Apr 2018 09:58:53: 38000000 INFO @ Thu, 05 Apr 2018 09:58:56: 40000000 INFO @ Thu, 05 Apr 2018 09:58:58: 39000000 INFO @ Thu, 05 Apr 2018 09:58:59: 39000000 INFO @ Thu, 05 Apr 2018 09:59:02: 41000000 INFO @ Thu, 05 Apr 2018 09:59:04: 40000000 INFO @ Thu, 05 Apr 2018 09:59:05: 40000000 INFO @ Thu, 05 Apr 2018 09:59:08: 42000000 INFO @ Thu, 05 Apr 2018 09:59:10: 41000000 INFO @ Thu, 05 Apr 2018 09:59:11: 41000000 INFO @ Thu, 05 Apr 2018 09:59:14: 43000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:59:16: 42000000 INFO @ Thu, 05 Apr 2018 09:59:17: 42000000 INFO @ Thu, 05 Apr 2018 09:59:18: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:59:18: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:59:18: #1 total tags in treatment: 21473054 INFO @ Thu, 05 Apr 2018 09:59:18: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:59:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:59:18: #1 tags after filtering in treatment: 10505310 INFO @ Thu, 05 Apr 2018 09:59:18: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 05 Apr 2018 09:59:18: #1 finished! INFO @ Thu, 05 Apr 2018 09:59:18: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:59:19: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:59:19: 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 @ Thu, 05 Apr 2018 09:59:19: Process for pairing-model is terminated! cat: SRX3433234.10_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 `SRX3433234.10_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 `SRX3433234.10_*.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 `SRX3433234.10_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 @ Thu, 05 Apr 2018 09:59:22: 43000000 INFO @ Thu, 05 Apr 2018 09:59:23: 43000000 INFO @ Thu, 05 Apr 2018 09:59:25: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:59:25: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:59:25: #1 total tags in treatment: 21473054 INFO @ Thu, 05 Apr 2018 09:59:25: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:59:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:59:26: #1 tags after filtering in treatment: 10505310 INFO @ Thu, 05 Apr 2018 09:59:26: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 05 Apr 2018 09:59:26: #1 finished! INFO @ Thu, 05 Apr 2018 09:59:26: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:59:26: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:59:26: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:59:26: #1 total tags in treatment: 21473054 INFO @ Thu, 05 Apr 2018 09:59:26: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:59:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:59:26: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:59:26: 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 @ Thu, 05 Apr 2018 09:59:26: Process for pairing-model is terminated! cat: SRX3433234.05_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 `SRX3433234.05_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 `SRX3433234.05_*.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 `SRX3433234.05_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 @ Thu, 05 Apr 2018 09:59:27: #1 tags after filtering in treatment: 10505310 INFO @ Thu, 05 Apr 2018 09:59:27: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 05 Apr 2018 09:59:27: #1 finished! INFO @ Thu, 05 Apr 2018 09:59:27: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:59:27: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:59:27: 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 @ Thu, 05 Apr 2018 09:59:27: Process for pairing-model is terminated! cat: SRX3433234.20_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 `SRX3433234.20_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 `SRX3433234.20_*.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 `SRX3433234.20_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。