Job ID = 11388932 sra ファイルのダウンロード中... Completed: 2269985K bytes transferred in 40 seconds (454364K 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 40190150 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017451/SRR8198074.sra Written 40190150 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017451/SRR8198074.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: 01:07:32 40190150 reads; of these: 40190150 (100.00%) were paired; of these: 5054005 (12.58%) aligned concordantly 0 times 29973424 (74.58%) aligned concordantly exactly 1 time 5162721 (12.85%) aligned concordantly >1 times ---- 5054005 pairs aligned concordantly 0 times; of these: 1430812 (28.31%) aligned discordantly 1 time ---- 3623193 pairs aligned 0 times concordantly or discordantly; of these: 7246386 mates make up the pairs; of these: 5533589 (76.36%) aligned 0 times 1043089 (14.39%) aligned exactly 1 time 669708 (9.24%) aligned >1 times 93.12% overall alignment rate Time searching: 01:07:32 Overall time: 01:07:32 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 32 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] 5769242 / 35846647 = 0.1609 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 01:57:35: # Command line: callpeak -t SRX5017451.bam -f BAM -g 12100000 -n SRX5017451.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017451.20 # format = BAM # ChIP-seq file = ['SRX5017451.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 01:57:35: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:57:35: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:57:35: # Command line: callpeak -t SRX5017451.bam -f BAM -g 12100000 -n SRX5017451.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017451.10 # format = BAM # ChIP-seq file = ['SRX5017451.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 01:57:35: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:57:35: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:57:35: # Command line: callpeak -t SRX5017451.bam -f BAM -g 12100000 -n SRX5017451.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017451.05 # format = BAM # ChIP-seq file = ['SRX5017451.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 01:57:35: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:57:35: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:57:46: 1000000 INFO @ Thu, 13 Dec 2018 01:57:50: 1000000 INFO @ Thu, 13 Dec 2018 01:57:54: 1000000 INFO @ Thu, 13 Dec 2018 01:57:58: 2000000 INFO @ Thu, 13 Dec 2018 01:58:04: 2000000 INFO @ Thu, 13 Dec 2018 01:58:13: 3000000 INFO @ Thu, 13 Dec 2018 01:58:14: 2000000 INFO @ Thu, 13 Dec 2018 01:58:19: 3000000 INFO @ Thu, 13 Dec 2018 01:58:30: 4000000 INFO @ Thu, 13 Dec 2018 01:58:30: 3000000 INFO @ Thu, 13 Dec 2018 01:58:34: 4000000 INFO @ Thu, 13 Dec 2018 01:58:45: 5000000 INFO @ Thu, 13 Dec 2018 01:58:45: 4000000 INFO @ Thu, 13 Dec 2018 01:58:48: 5000000 INFO @ Thu, 13 Dec 2018 01:58:59: 6000000 INFO @ Thu, 13 Dec 2018 01:58:59: 5000000 INFO @ Thu, 13 Dec 2018 01:59:02: 6000000 INFO @ Thu, 13 Dec 2018 01:59:13: 6000000 INFO @ Thu, 13 Dec 2018 01:59:14: 7000000 INFO @ Thu, 13 Dec 2018 01:59:18: 7000000 INFO @ Thu, 13 Dec 2018 01:59:28: 7000000 INFO @ Thu, 13 Dec 2018 01:59:28: 8000000 INFO @ Thu, 13 Dec 2018 01:59:35: 8000000 INFO @ Thu, 13 Dec 2018 01:59:41: 8000000 INFO @ Thu, 13 Dec 2018 01:59:43: 9000000 INFO @ Thu, 13 Dec 2018 01:59:52: 9000000 INFO @ Thu, 13 Dec 2018 01:59:55: 9000000 INFO @ Thu, 13 Dec 2018 01:59:58: 10000000 INFO @ Thu, 13 Dec 2018 02:00:08: 10000000 INFO @ Thu, 13 Dec 2018 02:00:12: 10000000 INFO @ Thu, 13 Dec 2018 02:00:13: 11000000 INFO @ Thu, 13 Dec 2018 02:00:27: 11000000 INFO @ Thu, 13 Dec 2018 02:00:30: 12000000 INFO @ Thu, 13 Dec 2018 02:00:30: 11000000 INFO @ Thu, 13 Dec 2018 02:00:42: 12000000 INFO @ Thu, 13 Dec 2018 02:00:44: 13000000 INFO @ Thu, 13 Dec 2018 02:00:45: 12000000 INFO @ Thu, 13 Dec 2018 02:00:54: 13000000 INFO @ Thu, 13 Dec 2018 02:01:00: 14000000 INFO @ Thu, 13 Dec 2018 02:01:02: 13000000 INFO @ Thu, 13 Dec 2018 02:01:07: 14000000 INFO @ Thu, 13 Dec 2018 02:01:18: 14000000 INFO @ Thu, 13 Dec 2018 02:01:18: 15000000 INFO @ Thu, 13 Dec 2018 02:01:23: 15000000 INFO @ Thu, 13 Dec 2018 02:01:30: 16000000 INFO @ Thu, 13 Dec 2018 02:01:35: 15000000 INFO @ Thu, 13 Dec 2018 02:01:41: 16000000 INFO @ Thu, 13 Dec 2018 02:01:43: 17000000 INFO @ Thu, 13 Dec 2018 02:01:53: 16000000 INFO @ Thu, 13 Dec 2018 02:01:57: 18000000 INFO @ Thu, 13 Dec 2018 02:01:59: 17000000 INFO @ Thu, 13 Dec 2018 02:02:12: 17000000 INFO @ Thu, 13 Dec 2018 02:02:15: 19000000 INFO @ Thu, 13 Dec 2018 02:02:17: 18000000 INFO @ Thu, 13 Dec 2018 02:02:26: 18000000 INFO @ Thu, 13 Dec 2018 02:02:27: 20000000 INFO @ Thu, 13 Dec 2018 02:02:28: 19000000 INFO @ Thu, 13 Dec 2018 02:02:39: 19000000 INFO @ Thu, 13 Dec 2018 02:02:41: 20000000 INFO @ Thu, 13 Dec 2018 02:02:42: 21000000 INFO @ Thu, 13 Dec 2018 02:02:55: 21000000 INFO @ Thu, 13 Dec 2018 02:02:56: 20000000 INFO @ Thu, 13 Dec 2018 02:02:59: 22000000 INFO @ Thu, 13 Dec 2018 02:03:09: 22000000 INFO @ Thu, 13 Dec 2018 02:03:12: 21000000 INFO @ Thu, 13 Dec 2018 02:03:12: 23000000 INFO @ Thu, 13 Dec 2018 02:03:22: 24000000 INFO @ Thu, 13 Dec 2018 02:03:25: 23000000 INFO @ Thu, 13 Dec 2018 02:03:27: 22000000 INFO @ Thu, 13 Dec 2018 02:03:32: 25000000 INFO @ Thu, 13 Dec 2018 02:03:39: 23000000 INFO @ Thu, 13 Dec 2018 02:03:39: 24000000 INFO @ Thu, 13 Dec 2018 02:03:46: 26000000 INFO @ Thu, 13 Dec 2018 02:03:49: 24000000 INFO @ Thu, 13 Dec 2018 02:03:52: 25000000 INFO @ Thu, 13 Dec 2018 02:03:58: 27000000 INFO @ Thu, 13 Dec 2018 02:03:59: 25000000 INFO @ Thu, 13 Dec 2018 02:04:05: 26000000 INFO @ Thu, 13 Dec 2018 02:04:06: 28000000 INFO @ Thu, 13 Dec 2018 02:04:08: 26000000 INFO @ Thu, 13 Dec 2018 02:04:15: 29000000 INFO @ Thu, 13 Dec 2018 02:04:18: 27000000 INFO @ Thu, 13 Dec 2018 02:04:20: 27000000 INFO @ Thu, 13 Dec 2018 02:04:25: 30000000 INFO @ Thu, 13 Dec 2018 02:04:35: 31000000 INFO @ Thu, 13 Dec 2018 02:04:36: 28000000 INFO @ Thu, 13 Dec 2018 02:04:40: 28000000 INFO @ Thu, 13 Dec 2018 02:04:45: 32000000 INFO @ Thu, 13 Dec 2018 02:04:53: 29000000 INFO @ Thu, 13 Dec 2018 02:04:54: 29000000 INFO @ Thu, 13 Dec 2018 02:04:56: 33000000 INFO @ Thu, 13 Dec 2018 02:05:02: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 02:05:07: 34000000 INFO @ Thu, 13 Dec 2018 02:05:08: 30000000 INFO @ Thu, 13 Dec 2018 02:05:13: 31000000 INFO @ Thu, 13 Dec 2018 02:05:17: 35000000 INFO @ Thu, 13 Dec 2018 02:05:23: 31000000 INFO @ Thu, 13 Dec 2018 02:05:23: 32000000 INFO @ Thu, 13 Dec 2018 02:05:28: 36000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 02:05:34: 33000000 INFO @ Thu, 13 Dec 2018 02:05:36: 32000000 INFO @ Thu, 13 Dec 2018 02:05:39: 37000000 INFO @ Thu, 13 Dec 2018 02:05:44: 34000000 INFO @ Thu, 13 Dec 2018 02:05:51: 33000000 INFO @ Thu, 13 Dec 2018 02:05:54: 38000000 INFO @ Thu, 13 Dec 2018 02:05:54: 35000000 INFO @ Thu, 13 Dec 2018 02:06:02: 34000000 INFO @ Thu, 13 Dec 2018 02:06:04: 36000000 INFO @ Thu, 13 Dec 2018 02:06:07: 39000000 INFO @ Thu, 13 Dec 2018 02:06:12: 35000000 INFO @ Thu, 13 Dec 2018 02:06:13: 37000000 INFO @ Thu, 13 Dec 2018 02:06:19: 40000000 INFO @ Thu, 13 Dec 2018 02:06:24: 36000000 INFO @ Thu, 13 Dec 2018 02:06:26: 38000000 INFO @ Thu, 13 Dec 2018 02:06:33: 41000000 INFO @ Thu, 13 Dec 2018 02:06:35: 37000000 INFO @ Thu, 13 Dec 2018 02:06:36: 39000000 INFO @ Thu, 13 Dec 2018 02:06:46: 40000000 INFO @ Thu, 13 Dec 2018 02:06:46: 38000000 INFO @ Thu, 13 Dec 2018 02:06:46: 42000000 INFO @ Thu, 13 Dec 2018 02:06:57: 39000000 INFO @ Thu, 13 Dec 2018 02:06:59: 41000000 INFO @ Thu, 13 Dec 2018 02:07:03: 43000000 INFO @ Thu, 13 Dec 2018 02:07:08: 40000000 INFO @ Thu, 13 Dec 2018 02:07:12: 42000000 INFO @ Thu, 13 Dec 2018 02:07:15: 44000000 INFO @ Thu, 13 Dec 2018 02:07:19: 41000000 INFO @ Thu, 13 Dec 2018 02:07:26: 43000000 INFO @ Thu, 13 Dec 2018 02:07:29: 45000000 INFO @ Thu, 13 Dec 2018 02:07:31: 42000000 INFO @ Thu, 13 Dec 2018 02:07:38: 44000000 INFO @ Thu, 13 Dec 2018 02:07:42: 46000000 INFO @ Thu, 13 Dec 2018 02:07:42: 43000000 INFO @ Thu, 13 Dec 2018 02:07:49: 45000000 INFO @ Thu, 13 Dec 2018 02:07:53: 44000000 INFO @ Thu, 13 Dec 2018 02:07:56: 47000000 INFO @ Thu, 13 Dec 2018 02:08:00: 46000000 INFO @ Thu, 13 Dec 2018 02:08:05: 45000000 INFO @ Thu, 13 Dec 2018 02:08:11: 48000000 INFO @ Thu, 13 Dec 2018 02:08:12: 47000000 INFO @ Thu, 13 Dec 2018 02:08:16: 46000000 INFO @ Thu, 13 Dec 2018 02:08:24: 48000000 INFO @ Thu, 13 Dec 2018 02:08:25: 49000000 INFO @ Thu, 13 Dec 2018 02:08:28: 47000000 INFO @ Thu, 13 Dec 2018 02:08:35: 49000000 INFO @ Thu, 13 Dec 2018 02:08:40: 50000000 INFO @ Thu, 13 Dec 2018 02:08:41: 48000000 INFO @ Thu, 13 Dec 2018 02:08:47: 50000000 INFO @ Thu, 13 Dec 2018 02:08:54: 51000000 INFO @ Thu, 13 Dec 2018 02:08:54: 49000000 INFO @ Thu, 13 Dec 2018 02:08:59: 51000000 INFO @ Thu, 13 Dec 2018 02:09:08: 52000000 INFO @ Thu, 13 Dec 2018 02:09:10: 50000000 INFO @ Thu, 13 Dec 2018 02:09:14: 52000000 INFO @ Thu, 13 Dec 2018 02:09:21: 53000000 INFO @ Thu, 13 Dec 2018 02:09:25: 51000000 INFO @ Thu, 13 Dec 2018 02:09:30: 53000000 INFO @ Thu, 13 Dec 2018 02:09:37: 54000000 INFO @ Thu, 13 Dec 2018 02:09:40: 52000000 INFO @ Thu, 13 Dec 2018 02:09:45: 54000000 INFO @ Thu, 13 Dec 2018 02:09:54: 55000000 INFO @ Thu, 13 Dec 2018 02:09:55: 53000000 INFO @ Thu, 13 Dec 2018 02:10:00: 55000000 INFO @ Thu, 13 Dec 2018 02:10:08: 54000000 INFO @ Thu, 13 Dec 2018 02:10:09: 56000000 INFO @ Thu, 13 Dec 2018 02:10:10: 56000000 INFO @ Thu, 13 Dec 2018 02:10:19: 57000000 INFO @ Thu, 13 Dec 2018 02:10:24: 57000000 INFO @ Thu, 13 Dec 2018 02:10:26: 55000000 INFO @ Thu, 13 Dec 2018 02:10:29: 58000000 INFO @ Thu, 13 Dec 2018 02:10:38: 59000000 INFO @ Thu, 13 Dec 2018 02:10:39: 58000000 INFO @ Thu, 13 Dec 2018 02:10:44: 56000000 INFO @ Thu, 13 Dec 2018 02:10:47: 60000000 INFO @ Thu, 13 Dec 2018 02:10:55: 59000000 INFO @ Thu, 13 Dec 2018 02:10:57: 61000000 INFO @ Thu, 13 Dec 2018 02:11:02: 57000000 INFO @ Thu, 13 Dec 2018 02:11:06: 60000000 INFO @ Thu, 13 Dec 2018 02:11:09: 62000000 INFO @ Thu, 13 Dec 2018 02:11:16: 58000000 INFO @ Thu, 13 Dec 2018 02:11:18: 63000000 INFO @ Thu, 13 Dec 2018 02:11:21: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:11:21: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:11:21: #1 total tags in treatment: 29421024 INFO @ Thu, 13 Dec 2018 02:11:21: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:11:21: #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 02:11:22: 61000000 INFO @ Thu, 13 Dec 2018 02:11:22: #1 tags after filtering in treatment: 14460107 INFO @ Thu, 13 Dec 2018 02:11:22: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 13 Dec 2018 02:11:22: #1 finished! INFO @ Thu, 13 Dec 2018 02:11:22: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:11:23: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:11:23: 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 @ Thu, 13 Dec 2018 02:11:23: Process for pairing-model is terminated! cat: SRX5017451.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017451.05_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 `SRX5017451.05_*.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 `SRX5017451.05_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, 13 Dec 2018 02:11:32: 59000000 INFO @ Thu, 13 Dec 2018 02:11:38: 62000000 INFO @ Thu, 13 Dec 2018 02:11:47: 60000000 INFO @ Thu, 13 Dec 2018 02:11:55: 63000000 INFO @ Thu, 13 Dec 2018 02:12:00: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:12:00: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:12:00: #1 total tags in treatment: 29421024 INFO @ Thu, 13 Dec 2018 02:12:00: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:12:00: #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 02:12:01: #1 tags after filtering in treatment: 14460107 INFO @ Thu, 13 Dec 2018 02:12:01: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 13 Dec 2018 02:12:01: #1 finished! INFO @ Thu, 13 Dec 2018 02:12:01: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:12:01: 61000000 INFO @ Thu, 13 Dec 2018 02:12:02: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:12:02: 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 02:12:02: Process for pairing-model is terminated! cat: SRX5017451.20_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 `SRX5017451.20_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 `SRX5017451.20_*.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 `SRX5017451.20_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 02:12:14: 62000000 INFO @ Thu, 13 Dec 2018 02:12:28: 63000000 INFO @ Thu, 13 Dec 2018 02:12:32: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:12:32: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:12:32: #1 total tags in treatment: 29421024 INFO @ Thu, 13 Dec 2018 02:12:32: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:12:32: #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 02:12:34: #1 tags after filtering in treatment: 14460107 INFO @ Thu, 13 Dec 2018 02:12:34: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 13 Dec 2018 02:12:34: #1 finished! INFO @ Thu, 13 Dec 2018 02:12:34: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:12:35: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:12:35: 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 02:12:35: Process for pairing-model is terminated! cat: SRX5017451.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017451.10_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 `SRX5017451.10_*.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 `SRX5017451.10_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