Job ID = 11388939 sra ファイルのダウンロード中... Completed: 1810618K bytes transferred in 37 seconds (390892K 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 32781279 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017458/SRR8198081.sra Written 32781279 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017458/SRR8198081.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: 01:04:00 32781279 reads; of these: 32781279 (100.00%) were paired; of these: 2614485 (7.98%) aligned concordantly 0 times 27164183 (82.86%) aligned concordantly exactly 1 time 3002611 (9.16%) aligned concordantly >1 times ---- 2614485 pairs aligned concordantly 0 times; of these: 493929 (18.89%) aligned discordantly 1 time ---- 2120556 pairs aligned 0 times concordantly or discordantly; of these: 4241112 mates make up the pairs; of these: 3718110 (87.67%) aligned 0 times 333584 (7.87%) aligned exactly 1 time 189418 (4.47%) aligned >1 times 94.33% overall alignment rate Time searching: 01:04:00 Overall time: 01:04:00 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] 4723503 / 30421943 = 0.1553 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, 13 Dec 2018 01:52:01: # Command line: callpeak -t SRX5017458.bam -f BAM -g 12100000 -n SRX5017458.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017458.10 # format = BAM # ChIP-seq file = ['SRX5017458.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, 13 Dec 2018 01:52:01: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:52:01: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:52:01: # Command line: callpeak -t SRX5017458.bam -f BAM -g 12100000 -n SRX5017458.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017458.20 # format = BAM # ChIP-seq file = ['SRX5017458.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, 13 Dec 2018 01:52:01: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:52:01: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:52:01: # Command line: callpeak -t SRX5017458.bam -f BAM -g 12100000 -n SRX5017458.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017458.05 # format = BAM # ChIP-seq file = ['SRX5017458.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, 13 Dec 2018 01:52:01: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:52:01: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:52:14: 1000000 INFO @ Thu, 13 Dec 2018 01:52:19: 1000000 INFO @ Thu, 13 Dec 2018 01:52:22: 1000000 INFO @ Thu, 13 Dec 2018 01:52:26: 2000000 INFO @ Thu, 13 Dec 2018 01:52:36: 2000000 INFO @ Thu, 13 Dec 2018 01:52:41: 2000000 INFO @ Thu, 13 Dec 2018 01:52:42: 3000000 INFO @ Thu, 13 Dec 2018 01:52:50: 3000000 INFO @ Thu, 13 Dec 2018 01:52:57: 4000000 INFO @ Thu, 13 Dec 2018 01:53:04: 3000000 INFO @ Thu, 13 Dec 2018 01:53:06: 4000000 INFO @ Thu, 13 Dec 2018 01:53:11: 5000000 INFO @ Thu, 13 Dec 2018 01:53:19: 4000000 INFO @ Thu, 13 Dec 2018 01:53:21: 5000000 INFO @ Thu, 13 Dec 2018 01:53:29: 6000000 INFO @ Thu, 13 Dec 2018 01:53:33: 6000000 INFO @ Thu, 13 Dec 2018 01:53:36: 5000000 INFO @ Thu, 13 Dec 2018 01:53:44: 7000000 INFO @ Thu, 13 Dec 2018 01:53:47: 7000000 INFO @ Thu, 13 Dec 2018 01:53:56: 6000000 INFO @ Thu, 13 Dec 2018 01:54:00: 8000000 INFO @ Thu, 13 Dec 2018 01:54:03: 8000000 INFO @ Thu, 13 Dec 2018 01:54:11: 7000000 INFO @ Thu, 13 Dec 2018 01:54:13: 9000000 INFO @ Thu, 13 Dec 2018 01:54:21: 9000000 INFO @ Thu, 13 Dec 2018 01:54:25: 10000000 INFO @ Thu, 13 Dec 2018 01:54:29: 8000000 INFO @ Thu, 13 Dec 2018 01:54:36: 10000000 INFO @ Thu, 13 Dec 2018 01:54:38: 11000000 INFO @ Thu, 13 Dec 2018 01:54:43: 9000000 INFO @ Thu, 13 Dec 2018 01:54:51: 12000000 INFO @ Thu, 13 Dec 2018 01:54:51: 11000000 INFO @ Thu, 13 Dec 2018 01:54:58: 10000000 INFO @ Thu, 13 Dec 2018 01:55:05: 13000000 INFO @ Thu, 13 Dec 2018 01:55:05: 12000000 INFO @ Thu, 13 Dec 2018 01:55:08: 11000000 INFO @ Thu, 13 Dec 2018 01:55:18: 14000000 INFO @ Thu, 13 Dec 2018 01:55:18: 13000000 INFO @ Thu, 13 Dec 2018 01:55:22: 12000000 INFO @ Thu, 13 Dec 2018 01:55:29: 15000000 INFO @ Thu, 13 Dec 2018 01:55:34: 14000000 INFO @ Thu, 13 Dec 2018 01:55:38: 13000000 INFO @ Thu, 13 Dec 2018 01:55:41: 16000000 INFO @ Thu, 13 Dec 2018 01:55:52: 15000000 INFO @ Thu, 13 Dec 2018 01:55:54: 14000000 INFO @ Thu, 13 Dec 2018 01:55:56: 17000000 INFO @ Thu, 13 Dec 2018 01:56:06: 16000000 INFO @ Thu, 13 Dec 2018 01:56:10: 15000000 INFO @ Thu, 13 Dec 2018 01:56:12: 18000000 INFO @ Thu, 13 Dec 2018 01:56:19: 17000000 INFO @ Thu, 13 Dec 2018 01:56:27: 16000000 INFO @ Thu, 13 Dec 2018 01:56:30: 18000000 INFO @ Thu, 13 Dec 2018 01:56:30: 19000000 INFO @ Thu, 13 Dec 2018 01:56:41: 17000000 INFO @ Thu, 13 Dec 2018 01:56:41: 19000000 INFO @ Thu, 13 Dec 2018 01:56:50: 20000000 INFO @ Thu, 13 Dec 2018 01:56:55: 20000000 INFO @ Thu, 13 Dec 2018 01:57:01: 18000000 INFO @ Thu, 13 Dec 2018 01:57:08: 21000000 INFO @ Thu, 13 Dec 2018 01:57:12: 21000000 INFO @ Thu, 13 Dec 2018 01:57:13: 19000000 INFO @ Thu, 13 Dec 2018 01:57:23: 22000000 INFO @ Thu, 13 Dec 2018 01:57:27: 22000000 INFO @ Thu, 13 Dec 2018 01:57:30: 20000000 INFO @ Thu, 13 Dec 2018 01:57:45: 23000000 INFO @ Thu, 13 Dec 2018 01:57:45: 21000000 INFO @ Thu, 13 Dec 2018 01:57:46: 23000000 INFO @ Thu, 13 Dec 2018 01:58:03: 22000000 INFO @ Thu, 13 Dec 2018 01:58:03: 24000000 INFO @ Thu, 13 Dec 2018 01:58:08: 24000000 INFO @ Thu, 13 Dec 2018 01:58:23: 25000000 INFO @ Thu, 13 Dec 2018 01:58:23: 23000000 INFO @ Thu, 13 Dec 2018 01:58:32: 25000000 INFO @ Thu, 13 Dec 2018 01:58:46: 24000000 INFO @ Thu, 13 Dec 2018 01:58:47: 26000000 INFO @ Thu, 13 Dec 2018 01:58:52: 26000000 INFO @ Thu, 13 Dec 2018 01:59:07: 25000000 INFO @ Thu, 13 Dec 2018 01:59:07: 27000000 INFO @ Thu, 13 Dec 2018 01:59:09: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 01:59:19: 28000000 INFO @ Thu, 13 Dec 2018 01:59:24: 28000000 INFO @ Thu, 13 Dec 2018 01:59:29: 26000000 INFO @ Thu, 13 Dec 2018 01:59:36: 29000000 INFO @ Thu, 13 Dec 2018 01:59:39: 29000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 01:59:44: 27000000 INFO @ Thu, 13 Dec 2018 01:59:52: 30000000 INFO @ Thu, 13 Dec 2018 01:59:57: 30000000 INFO @ Thu, 13 Dec 2018 01:59:59: 28000000 INFO @ Thu, 13 Dec 2018 02:00:07: 31000000 INFO @ Thu, 13 Dec 2018 02:00:14: 31000000 INFO @ Thu, 13 Dec 2018 02:00:17: 29000000 INFO @ Thu, 13 Dec 2018 02:00:24: 32000000 INFO @ Thu, 13 Dec 2018 02:00:32: 32000000 INFO @ Thu, 13 Dec 2018 02:00:36: 30000000 INFO @ Thu, 13 Dec 2018 02:00:36: 33000000 INFO @ Thu, 13 Dec 2018 02:00:50: 33000000 INFO @ Thu, 13 Dec 2018 02:00:50: 34000000 INFO @ Thu, 13 Dec 2018 02:00:54: 31000000 INFO @ Thu, 13 Dec 2018 02:01:05: 34000000 INFO @ Thu, 13 Dec 2018 02:01:10: 35000000 INFO @ Thu, 13 Dec 2018 02:01:12: 32000000 INFO @ Thu, 13 Dec 2018 02:01:22: 35000000 INFO @ Thu, 13 Dec 2018 02:01:25: 36000000 INFO @ Thu, 13 Dec 2018 02:01:32: 33000000 INFO @ Thu, 13 Dec 2018 02:01:39: 36000000 INFO @ Thu, 13 Dec 2018 02:01:43: 37000000 INFO @ Thu, 13 Dec 2018 02:01:44: 34000000 INFO @ Thu, 13 Dec 2018 02:01:51: 37000000 INFO @ Thu, 13 Dec 2018 02:02:00: 38000000 INFO @ Thu, 13 Dec 2018 02:02:01: 35000000 INFO @ Thu, 13 Dec 2018 02:02:02: 38000000 INFO @ Thu, 13 Dec 2018 02:02:14: 39000000 INFO @ Thu, 13 Dec 2018 02:02:16: 39000000 INFO @ Thu, 13 Dec 2018 02:02:18: 36000000 INFO @ Thu, 13 Dec 2018 02:02:30: 40000000 INFO @ Thu, 13 Dec 2018 02:02:31: 40000000 INFO @ Thu, 13 Dec 2018 02:02:40: 37000000 INFO @ Thu, 13 Dec 2018 02:02:49: 41000000 INFO @ Thu, 13 Dec 2018 02:02:51: 41000000 INFO @ Thu, 13 Dec 2018 02:02:56: 38000000 INFO @ Thu, 13 Dec 2018 02:03:06: 42000000 INFO @ Thu, 13 Dec 2018 02:03:08: 42000000 INFO @ Thu, 13 Dec 2018 02:03:14: 39000000 INFO @ Thu, 13 Dec 2018 02:03:20: 43000000 INFO @ Thu, 13 Dec 2018 02:03:22: 43000000 INFO @ Thu, 13 Dec 2018 02:03:32: 40000000 INFO @ Thu, 13 Dec 2018 02:03:36: 44000000 INFO @ Thu, 13 Dec 2018 02:03:37: 44000000 INFO @ Thu, 13 Dec 2018 02:03:47: 41000000 INFO @ Thu, 13 Dec 2018 02:03:47: 45000000 INFO @ Thu, 13 Dec 2018 02:03:59: 45000000 INFO @ Thu, 13 Dec 2018 02:04:00: 46000000 INFO @ Thu, 13 Dec 2018 02:04:06: 42000000 INFO @ Thu, 13 Dec 2018 02:04:16: 46000000 INFO @ Thu, 13 Dec 2018 02:04:20: 47000000 INFO @ Thu, 13 Dec 2018 02:04:25: 43000000 INFO @ Thu, 13 Dec 2018 02:04:34: 47000000 INFO @ Thu, 13 Dec 2018 02:04:42: 48000000 INFO @ Thu, 13 Dec 2018 02:04:47: 48000000 INFO @ Thu, 13 Dec 2018 02:04:48: 44000000 INFO @ Thu, 13 Dec 2018 02:04:55: 49000000 INFO @ Thu, 13 Dec 2018 02:05:06: 50000000 INFO @ Thu, 13 Dec 2018 02:05:09: 49000000 INFO @ Thu, 13 Dec 2018 02:05:10: 45000000 INFO @ Thu, 13 Dec 2018 02:05:17: 51000000 INFO @ Thu, 13 Dec 2018 02:05:28: 52000000 INFO @ Thu, 13 Dec 2018 02:05:29: 50000000 INFO @ Thu, 13 Dec 2018 02:05:30: 46000000 INFO @ Thu, 13 Dec 2018 02:05:34: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:05:34: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:05:34: #1 total tags in treatment: 25469689 INFO @ Thu, 13 Dec 2018 02:05:34: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:05:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 02:05:35: #1 tags after filtering in treatment: 13421682 INFO @ Thu, 13 Dec 2018 02:05:35: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:05:35: #1 finished! INFO @ Thu, 13 Dec 2018 02:05:35: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:05:36: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:05:36: 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 @ Thu, 13 Dec 2018 02:05:36: Process for pairing-model is terminated! cat: SRX5017458.10_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): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017458.10_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 `SRX5017458.10_*.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 `SRX5017458.10_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, 13 Dec 2018 02:05:41: 47000000 INFO @ Thu, 13 Dec 2018 02:05:42: 51000000 INFO @ Thu, 13 Dec 2018 02:05:55: 52000000 INFO @ Thu, 13 Dec 2018 02:05:56: 48000000 INFO @ Thu, 13 Dec 2018 02:06:00: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:06:00: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:06:00: #1 total tags in treatment: 25469689 INFO @ Thu, 13 Dec 2018 02:06:00: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:06:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 02:06:01: #1 tags after filtering in treatment: 13421682 INFO @ Thu, 13 Dec 2018 02:06:01: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:06:01: #1 finished! INFO @ Thu, 13 Dec 2018 02:06:01: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:06:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:06:02: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:06:02: 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, 13 Dec 2018 02:06:02: Process for pairing-model is terminated! cat: SRX5017458.20_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017458.20_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 `SRX5017458.20_*.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 `SRX5017458.20_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 @ Thu, 13 Dec 2018 02:06:12: 49000000 INFO @ Thu, 13 Dec 2018 02:06:23: 50000000 INFO @ Thu, 13 Dec 2018 02:06:33: 51000000 INFO @ Thu, 13 Dec 2018 02:06:43: 52000000 INFO @ Thu, 13 Dec 2018 02:06:47: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:06:47: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:06:47: #1 total tags in treatment: 25469689 INFO @ Thu, 13 Dec 2018 02:06:47: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:06:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 02:06:48: #1 tags after filtering in treatment: 13421682 INFO @ Thu, 13 Dec 2018 02:06:48: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:06:48: #1 finished! INFO @ Thu, 13 Dec 2018 02:06:48: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:06:49: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:06:49: 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, 13 Dec 2018 02:06:49: Process for pairing-model is terminated! cat: SRX5017458.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017458.05_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 `SRX5017458.05_*.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 `SRX5017458.05_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