Job ID = 11388931 sra ファイルのダウンロード中... Completed: 1920088K bytes transferred in 33 seconds (466308K 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 34370175 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017450/SRR8198073.sra Written 34370175 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017450/SRR8198073.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: 01:13:19 34370175 reads; of these: 34370175 (100.00%) were paired; of these: 2794623 (8.13%) aligned concordantly 0 times 28179572 (81.99%) aligned concordantly exactly 1 time 3395980 (9.88%) aligned concordantly >1 times ---- 2794623 pairs aligned concordantly 0 times; of these: 477092 (17.07%) aligned discordantly 1 time ---- 2317531 pairs aligned 0 times concordantly or discordantly; of these: 4635062 mates make up the pairs; of these: 4080747 (88.04%) aligned 0 times 346375 (7.47%) aligned exactly 1 time 207940 (4.49%) aligned >1 times 94.06% overall alignment rate Time searching: 01:13:19 Overall time: 01:13:19 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] 4769388 / 31776074 = 0.1501 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 01:59:17: # Command line: callpeak -t SRX5017450.bam -f BAM -g 12100000 -n SRX5017450.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017450.05 # format = BAM # ChIP-seq file = ['SRX5017450.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 01:59:17: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:59:17: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:59:17: # Command line: callpeak -t SRX5017450.bam -f BAM -g 12100000 -n SRX5017450.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017450.10 # format = BAM # ChIP-seq file = ['SRX5017450.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 01:59:17: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:59:17: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:59:17: # Command line: callpeak -t SRX5017450.bam -f BAM -g 12100000 -n SRX5017450.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017450.20 # format = BAM # ChIP-seq file = ['SRX5017450.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 01:59:17: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:59:17: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:59:32: 1000000 INFO @ Thu, 13 Dec 2018 01:59:33: 1000000 INFO @ Thu, 13 Dec 2018 01:59:33: 1000000 INFO @ Thu, 13 Dec 2018 01:59:48: 2000000 INFO @ Thu, 13 Dec 2018 01:59:49: 2000000 INFO @ Thu, 13 Dec 2018 01:59:49: 2000000 INFO @ Thu, 13 Dec 2018 02:00:04: 3000000 INFO @ Thu, 13 Dec 2018 02:00:05: 3000000 INFO @ Thu, 13 Dec 2018 02:00:06: 3000000 INFO @ Thu, 13 Dec 2018 02:00:20: 4000000 INFO @ Thu, 13 Dec 2018 02:00:23: 4000000 INFO @ Thu, 13 Dec 2018 02:00:23: 4000000 INFO @ Thu, 13 Dec 2018 02:00:36: 5000000 INFO @ Thu, 13 Dec 2018 02:00:40: 5000000 INFO @ Thu, 13 Dec 2018 02:00:40: 5000000 INFO @ Thu, 13 Dec 2018 02:00:52: 6000000 INFO @ Thu, 13 Dec 2018 02:00:57: 6000000 INFO @ Thu, 13 Dec 2018 02:00:58: 6000000 INFO @ Thu, 13 Dec 2018 02:01:08: 7000000 INFO @ Thu, 13 Dec 2018 02:01:15: 7000000 INFO @ Thu, 13 Dec 2018 02:01:15: 7000000 INFO @ Thu, 13 Dec 2018 02:01:23: 8000000 INFO @ Thu, 13 Dec 2018 02:01:32: 8000000 INFO @ Thu, 13 Dec 2018 02:01:32: 8000000 INFO @ Thu, 13 Dec 2018 02:01:38: 9000000 INFO @ Thu, 13 Dec 2018 02:01:48: 9000000 INFO @ Thu, 13 Dec 2018 02:01:48: 9000000 INFO @ Thu, 13 Dec 2018 02:01:52: 10000000 INFO @ Thu, 13 Dec 2018 02:02:06: 10000000 INFO @ Thu, 13 Dec 2018 02:02:06: 10000000 INFO @ Thu, 13 Dec 2018 02:02:09: 11000000 INFO @ Thu, 13 Dec 2018 02:02:23: 11000000 INFO @ Thu, 13 Dec 2018 02:02:24: 11000000 INFO @ Thu, 13 Dec 2018 02:02:25: 12000000 INFO @ Thu, 13 Dec 2018 02:02:39: 12000000 INFO @ Thu, 13 Dec 2018 02:02:41: 13000000 INFO @ Thu, 13 Dec 2018 02:02:42: 12000000 INFO @ Thu, 13 Dec 2018 02:02:57: 13000000 INFO @ Thu, 13 Dec 2018 02:02:58: 14000000 INFO @ Thu, 13 Dec 2018 02:02:59: 13000000 INFO @ Thu, 13 Dec 2018 02:03:14: 14000000 INFO @ Thu, 13 Dec 2018 02:03:16: 14000000 INFO @ Thu, 13 Dec 2018 02:03:16: 15000000 INFO @ Thu, 13 Dec 2018 02:03:31: 15000000 INFO @ Thu, 13 Dec 2018 02:03:33: 15000000 INFO @ Thu, 13 Dec 2018 02:03:34: 16000000 INFO @ Thu, 13 Dec 2018 02:03:49: 16000000 INFO @ Thu, 13 Dec 2018 02:03:50: 16000000 INFO @ Thu, 13 Dec 2018 02:03:53: 17000000 INFO @ Thu, 13 Dec 2018 02:04:07: 17000000 INFO @ Thu, 13 Dec 2018 02:04:10: 18000000 INFO @ Thu, 13 Dec 2018 02:04:10: 17000000 INFO @ Thu, 13 Dec 2018 02:04:25: 18000000 INFO @ Thu, 13 Dec 2018 02:04:27: 19000000 INFO @ Thu, 13 Dec 2018 02:04:28: 18000000 INFO @ Thu, 13 Dec 2018 02:04:43: 19000000 INFO @ Thu, 13 Dec 2018 02:04:44: 20000000 INFO @ Thu, 13 Dec 2018 02:04:46: 19000000 INFO @ Thu, 13 Dec 2018 02:04:59: 20000000 INFO @ Thu, 13 Dec 2018 02:05:00: 21000000 INFO @ Thu, 13 Dec 2018 02:05:01: 20000000 INFO @ Thu, 13 Dec 2018 02:05:16: 21000000 INFO @ Thu, 13 Dec 2018 02:05:17: 22000000 INFO @ Thu, 13 Dec 2018 02:05:20: 21000000 INFO @ Thu, 13 Dec 2018 02:05:34: 22000000 INFO @ Thu, 13 Dec 2018 02:05:34: 23000000 INFO @ Thu, 13 Dec 2018 02:05:38: 22000000 INFO @ Thu, 13 Dec 2018 02:05:51: 24000000 INFO @ Thu, 13 Dec 2018 02:05:52: 23000000 INFO @ Thu, 13 Dec 2018 02:05:56: 23000000 INFO @ Thu, 13 Dec 2018 02:06:08: 25000000 INFO @ Thu, 13 Dec 2018 02:06:10: 24000000 INFO @ Thu, 13 Dec 2018 02:06:13: 24000000 INFO @ Thu, 13 Dec 2018 02:06:22: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 02:06:25: 25000000 INFO @ Thu, 13 Dec 2018 02:06:30: 25000000 INFO @ Thu, 13 Dec 2018 02:06:38: 27000000 INFO @ Thu, 13 Dec 2018 02:06:43: 26000000 INFO @ Thu, 13 Dec 2018 02:06:46: 26000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 02:06:54: 28000000 INFO @ Thu, 13 Dec 2018 02:07:01: 27000000 INFO @ Thu, 13 Dec 2018 02:07:05: 27000000 INFO @ Thu, 13 Dec 2018 02:07:11: 29000000 INFO @ Thu, 13 Dec 2018 02:07:20: 28000000 INFO @ Thu, 13 Dec 2018 02:07:23: 28000000 INFO @ Thu, 13 Dec 2018 02:07:28: 30000000 INFO @ Thu, 13 Dec 2018 02:07:38: 29000000 INFO @ Thu, 13 Dec 2018 02:07:41: 29000000 INFO @ Thu, 13 Dec 2018 02:07:45: 31000000 INFO @ Thu, 13 Dec 2018 02:07:56: 30000000 INFO @ Thu, 13 Dec 2018 02:08:00: 30000000 INFO @ Thu, 13 Dec 2018 02:08:02: 32000000 INFO @ Thu, 13 Dec 2018 02:08:14: 31000000 INFO @ Thu, 13 Dec 2018 02:08:18: 31000000 INFO @ Thu, 13 Dec 2018 02:08:19: 33000000 INFO @ Thu, 13 Dec 2018 02:08:30: 32000000 INFO @ Thu, 13 Dec 2018 02:08:36: 34000000 INFO @ Thu, 13 Dec 2018 02:08:36: 32000000 INFO @ Thu, 13 Dec 2018 02:08:48: 33000000 INFO @ Thu, 13 Dec 2018 02:08:52: 35000000 INFO @ Thu, 13 Dec 2018 02:08:53: 33000000 INFO @ Thu, 13 Dec 2018 02:09:05: 34000000 INFO @ Thu, 13 Dec 2018 02:09:08: 36000000 INFO @ Thu, 13 Dec 2018 02:09:10: 34000000 INFO @ Thu, 13 Dec 2018 02:09:23: 35000000 INFO @ Thu, 13 Dec 2018 02:09:26: 37000000 INFO @ Thu, 13 Dec 2018 02:09:29: 35000000 INFO @ Thu, 13 Dec 2018 02:09:41: 36000000 INFO @ Thu, 13 Dec 2018 02:09:43: 38000000 INFO @ Thu, 13 Dec 2018 02:09:48: 36000000 INFO @ Thu, 13 Dec 2018 02:09:59: 39000000 INFO @ Thu, 13 Dec 2018 02:10:00: 37000000 INFO @ Thu, 13 Dec 2018 02:10:05: 37000000 INFO @ Thu, 13 Dec 2018 02:10:17: 40000000 INFO @ Thu, 13 Dec 2018 02:10:18: 38000000 INFO @ Thu, 13 Dec 2018 02:10:23: 38000000 INFO @ Thu, 13 Dec 2018 02:10:34: 41000000 INFO @ Thu, 13 Dec 2018 02:10:37: 39000000 INFO @ Thu, 13 Dec 2018 02:10:41: 39000000 INFO @ Thu, 13 Dec 2018 02:10:52: 42000000 INFO @ Thu, 13 Dec 2018 02:10:54: 40000000 INFO @ Thu, 13 Dec 2018 02:10:59: 40000000 INFO @ Thu, 13 Dec 2018 02:11:08: 43000000 INFO @ Thu, 13 Dec 2018 02:11:12: 41000000 INFO @ Thu, 13 Dec 2018 02:11:17: 41000000 INFO @ Thu, 13 Dec 2018 02:11:26: 44000000 INFO @ Thu, 13 Dec 2018 02:11:31: 42000000 INFO @ Thu, 13 Dec 2018 02:11:36: 42000000 INFO @ Thu, 13 Dec 2018 02:11:44: 45000000 INFO @ Thu, 13 Dec 2018 02:11:49: 43000000 INFO @ Thu, 13 Dec 2018 02:11:55: 43000000 INFO @ Thu, 13 Dec 2018 02:12:02: 46000000 INFO @ Thu, 13 Dec 2018 02:12:07: 44000000 INFO @ Thu, 13 Dec 2018 02:12:12: 44000000 INFO @ Thu, 13 Dec 2018 02:12:19: 47000000 INFO @ Thu, 13 Dec 2018 02:12:25: 45000000 INFO @ Thu, 13 Dec 2018 02:12:30: 45000000 INFO @ Thu, 13 Dec 2018 02:12:35: 48000000 INFO @ Thu, 13 Dec 2018 02:12:42: 46000000 INFO @ Thu, 13 Dec 2018 02:12:46: 46000000 INFO @ Thu, 13 Dec 2018 02:12:51: 49000000 INFO @ Thu, 13 Dec 2018 02:12:59: 47000000 INFO @ Thu, 13 Dec 2018 02:13:03: 47000000 INFO @ Thu, 13 Dec 2018 02:13:08: 50000000 INFO @ Thu, 13 Dec 2018 02:13:16: 48000000 INFO @ Thu, 13 Dec 2018 02:13:21: 48000000 INFO @ Thu, 13 Dec 2018 02:13:25: 51000000 INFO @ Thu, 13 Dec 2018 02:13:34: 49000000 INFO @ Thu, 13 Dec 2018 02:13:38: 49000000 INFO @ Thu, 13 Dec 2018 02:13:44: 52000000 INFO @ Thu, 13 Dec 2018 02:13:52: 50000000 INFO @ Thu, 13 Dec 2018 02:13:56: 50000000 INFO @ Thu, 13 Dec 2018 02:14:01: 53000000 INFO @ Thu, 13 Dec 2018 02:14:11: 51000000 INFO @ Thu, 13 Dec 2018 02:14:13: 51000000 INFO @ Thu, 13 Dec 2018 02:14:19: 54000000 INFO @ Thu, 13 Dec 2018 02:14:29: 52000000 INFO @ Thu, 13 Dec 2018 02:14:30: 52000000 INFO @ Thu, 13 Dec 2018 02:14:36: 55000000 INFO @ Thu, 13 Dec 2018 02:14:38: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:14:38: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:14:38: #1 total tags in treatment: 26825240 INFO @ Thu, 13 Dec 2018 02:14:38: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:14:38: #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 02:14:39: #1 tags after filtering in treatment: 14084332 INFO @ Thu, 13 Dec 2018 02:14:39: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:14:39: #1 finished! INFO @ Thu, 13 Dec 2018 02:14:39: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:14:40: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:14:40: 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 02:14:40: Process for pairing-model is terminated! cat: SRX5017450.10_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): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017450.10_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 `SRX5017450.10_*.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 `SRX5017450.10_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 02:14:46: 53000000 INFO @ Thu, 13 Dec 2018 02:14:47: 53000000 INFO @ Thu, 13 Dec 2018 02:15:04: 54000000 INFO @ Thu, 13 Dec 2018 02:15:04: 54000000 INFO @ Thu, 13 Dec 2018 02:15:21: 55000000 INFO @ Thu, 13 Dec 2018 02:15:21: 55000000 INFO @ Thu, 13 Dec 2018 02:15:23: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:15:23: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:15:23: #1 total tags in treatment: 26825240 INFO @ Thu, 13 Dec 2018 02:15:23: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:15:23: #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 02:15:24: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:15:24: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:15:24: #1 total tags in treatment: 26825240 INFO @ Thu, 13 Dec 2018 02:15:24: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:15:24: #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 02:15:24: #1 tags after filtering in treatment: 14084332 INFO @ Thu, 13 Dec 2018 02:15:24: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:15:24: #1 finished! INFO @ Thu, 13 Dec 2018 02:15:24: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:15:25: #1 tags after filtering in treatment: 14084332 INFO @ Thu, 13 Dec 2018 02:15:25: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:15:25: #1 finished! INFO @ Thu, 13 Dec 2018 02:15:25: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:15:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:15:25: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:15:25: 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 02:15:25: Process for pairing-model is terminated! cat: SRX5017450.20_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017450.20_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 `SRX5017450.20_*.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 `SRX5017450.20_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 02:15:26: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:15:26: 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, 13 Dec 2018 02:15:26: Process for pairing-model is terminated! cat: SRX5017450.05_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): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017450.05_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 `SRX5017450.05_*.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 `SRX5017450.05_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