Job ID = 10608976 sra ファイルのダウンロード中... Completed: 2765288K bytes transferred in 315 seconds (71786K 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 21899239 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741983/SRR5453817.sra Written 21899239 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: 00:38:02 21899239 reads; of these: 21899239 (100.00%) were paired; of these: 1392779 (6.36%) aligned concordantly 0 times 18508131 (84.51%) aligned concordantly exactly 1 time 1998329 (9.13%) aligned concordantly >1 times ---- 1392779 pairs aligned concordantly 0 times; of these: 216027 (15.51%) aligned discordantly 1 time ---- 1176752 pairs aligned 0 times concordantly or discordantly; of these: 2353504 mates make up the pairs; of these: 1384731 (58.84%) aligned 0 times 727132 (30.90%) aligned exactly 1 time 241641 (10.27%) aligned >1 times 96.84% overall alignment rate Time searching: 00:38:02 Overall time: 00:38:02 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 20 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] 6038254 / 20695406 = 0.2918 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, 03 May 2018 23:54:03: # Command line: callpeak -t SRX2741983.bam -f BAM -g 12100000 -n SRX2741983.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741983.05 # format = BAM # ChIP-seq file = ['SRX2741983.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, 03 May 2018 23:54:03: #1 read tag files... INFO @ Thu, 03 May 2018 23:54:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:54:03: # Command line: callpeak -t SRX2741983.bam -f BAM -g 12100000 -n SRX2741983.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741983.10 # format = BAM # ChIP-seq file = ['SRX2741983.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, 03 May 2018 23:54:03: #1 read tag files... INFO @ Thu, 03 May 2018 23:54:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:54:03: # Command line: callpeak -t SRX2741983.bam -f BAM -g 12100000 -n SRX2741983.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741983.20 # format = BAM # ChIP-seq file = ['SRX2741983.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, 03 May 2018 23:54:03: #1 read tag files... INFO @ Thu, 03 May 2018 23:54:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:54:10: 1000000 INFO @ Thu, 03 May 2018 23:54:10: 1000000 INFO @ Thu, 03 May 2018 23:54:10: 1000000 INFO @ Thu, 03 May 2018 23:54:17: 2000000 INFO @ Thu, 03 May 2018 23:54:17: 2000000 INFO @ Thu, 03 May 2018 23:54:17: 2000000 INFO @ Thu, 03 May 2018 23:54:24: 3000000 INFO @ Thu, 03 May 2018 23:54:24: 3000000 INFO @ Thu, 03 May 2018 23:54:24: 3000000 INFO @ Thu, 03 May 2018 23:54:31: 4000000 INFO @ Thu, 03 May 2018 23:54:31: 4000000 INFO @ Thu, 03 May 2018 23:54:31: 4000000 INFO @ Thu, 03 May 2018 23:54:38: 5000000 INFO @ Thu, 03 May 2018 23:54:38: 5000000 INFO @ Thu, 03 May 2018 23:54:39: 5000000 INFO @ Thu, 03 May 2018 23:54:45: 6000000 INFO @ Thu, 03 May 2018 23:54:45: 6000000 INFO @ Thu, 03 May 2018 23:54:46: 6000000 INFO @ Thu, 03 May 2018 23:54:52: 7000000 INFO @ Thu, 03 May 2018 23:54:52: 7000000 INFO @ Thu, 03 May 2018 23:54:54: 7000000 INFO @ Thu, 03 May 2018 23:54:59: 8000000 INFO @ Thu, 03 May 2018 23:55:00: 8000000 INFO @ Thu, 03 May 2018 23:55:01: 8000000 INFO @ Thu, 03 May 2018 23:55:06: 9000000 INFO @ Thu, 03 May 2018 23:55:07: 9000000 INFO @ Thu, 03 May 2018 23:55:09: 9000000 INFO @ Thu, 03 May 2018 23:55:13: 10000000 INFO @ Thu, 03 May 2018 23:55:14: 10000000 INFO @ Thu, 03 May 2018 23:55:16: 10000000 INFO @ Thu, 03 May 2018 23:55:19: 11000000 INFO @ Thu, 03 May 2018 23:55:21: 11000000 INFO @ Thu, 03 May 2018 23:55:23: 11000000 INFO @ Thu, 03 May 2018 23:55:26: 12000000 INFO @ Thu, 03 May 2018 23:55:28: 12000000 INFO @ Thu, 03 May 2018 23:55:31: 12000000 INFO @ Thu, 03 May 2018 23:55:33: 13000000 INFO @ Thu, 03 May 2018 23:55:35: 13000000 INFO @ Thu, 03 May 2018 23:55:38: 13000000 INFO @ Thu, 03 May 2018 23:55:40: 14000000 INFO @ Thu, 03 May 2018 23:55:42: 14000000 INFO @ Thu, 03 May 2018 23:55:46: 14000000 INFO @ Thu, 03 May 2018 23:55:47: 15000000 INFO @ Thu, 03 May 2018 23:55:49: 15000000 INFO @ Thu, 03 May 2018 23:55:53: 15000000 INFO @ Thu, 03 May 2018 23:55:53: 16000000 INFO @ Thu, 03 May 2018 23:55:56: 16000000 INFO @ Thu, 03 May 2018 23:56:00: 17000000 INFO @ Thu, 03 May 2018 23:56:00: 16000000 INFO @ Thu, 03 May 2018 23:56:03: 17000000 INFO @ Thu, 03 May 2018 23:56:07: 18000000 INFO @ Thu, 03 May 2018 23:56:08: 17000000 INFO @ Thu, 03 May 2018 23:56:10: 18000000 INFO @ Thu, 03 May 2018 23:56:14: 19000000 INFO @ Thu, 03 May 2018 23:56:15: 18000000 INFO @ Thu, 03 May 2018 23:56:17: 19000000 INFO @ Thu, 03 May 2018 23:56:21: 20000000 INFO @ Thu, 03 May 2018 23:56:23: 19000000 INFO @ Thu, 03 May 2018 23:56:24: 20000000 INFO @ Thu, 03 May 2018 23:56:28: 21000000 INFO @ Thu, 03 May 2018 23:56:30: 20000000 INFO @ Thu, 03 May 2018 23:56:32: 21000000 INFO @ Thu, 03 May 2018 23:56:35: 22000000 INFO @ Thu, 03 May 2018 23:56:37: 21000000 INFO @ Thu, 03 May 2018 23:56:39: 22000000 INFO @ Thu, 03 May 2018 23:56:42: 23000000 INFO @ Thu, 03 May 2018 23:56:44: 22000000 INFO @ Thu, 03 May 2018 23:56:47: 23000000 INFO @ Thu, 03 May 2018 23:56:49: 24000000 INFO @ Thu, 03 May 2018 23:56:51: 23000000 INFO @ Thu, 03 May 2018 23:56:54: 24000000 INFO @ Thu, 03 May 2018 23:56:56: 25000000 INFO @ Thu, 03 May 2018 23:56:58: 24000000 INFO @ Thu, 03 May 2018 23:57:02: 25000000 INFO @ Thu, 03 May 2018 23:57:04: 26000000 INFO @ Thu, 03 May 2018 23:57:05: 25000000 INFO @ Thu, 03 May 2018 23:57:10: 26000000 INFO @ Thu, 03 May 2018 23:57:11: 27000000 INFO @ Thu, 03 May 2018 23:57:12: 26000000 INFO @ Thu, 03 May 2018 23:57:17: 27000000 INFO @ Thu, 03 May 2018 23:57:18: 28000000 INFO @ Thu, 03 May 2018 23:57:19: 27000000 INFO @ Thu, 03 May 2018 23:57:24: 28000000 INFO @ Thu, 03 May 2018 23:57:26: 29000000 INFO @ Thu, 03 May 2018 23:57:26: 28000000 INFO @ Thu, 03 May 2018 23:57:32: 29000000 INFO @ Thu, 03 May 2018 23:57:33: 30000000 INFO @ Thu, 03 May 2018 23:57:33: 29000000 INFO @ Thu, 03 May 2018 23:57:36: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:57:36: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:57:36: #1 total tags in treatment: 14476533 INFO @ Thu, 03 May 2018 23:57:36: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:57:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:57:36: #1 tags after filtering in treatment: 7309408 INFO @ Thu, 03 May 2018 23:57:36: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 03 May 2018 23:57:36: #1 finished! INFO @ Thu, 03 May 2018 23:57:36: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:57:36: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:57:36: 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, 03 May 2018 23:57:36: Process for pairing-model is terminated! cat: SRX2741983.20_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 `SRX2741983.20_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 `SRX2741983.20_*.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 `SRX2741983.20_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, 03 May 2018 23:57:39: 30000000 INFO @ Thu, 03 May 2018 23:57:40: 30000000 INFO @ Thu, 03 May 2018 23:57:42: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:57:42: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:57:42: #1 total tags in treatment: 14476533 INFO @ Thu, 03 May 2018 23:57:42: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:57:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:57:42: #1 tags after filtering in treatment: 7309408 INFO @ Thu, 03 May 2018 23:57:42: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 03 May 2018 23:57:42: #1 finished! INFO @ Thu, 03 May 2018 23:57:42: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:57:42: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:57:42: 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, 03 May 2018 23:57:42: Process for pairing-model is terminated! cat: SRX2741983.10_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 `SRX2741983.10_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 `SRX2741983.10_*.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 `SRX2741983.10_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, 03 May 2018 23:57:42: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:57:42: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:57:42: #1 total tags in treatment: 14476533 INFO @ Thu, 03 May 2018 23:57:42: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:57:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:57:43: #1 tags after filtering in treatment: 7309408 INFO @ Thu, 03 May 2018 23:57:43: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 03 May 2018 23:57:43: #1 finished! INFO @ Thu, 03 May 2018 23:57:43: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:57:43: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:57:43: 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, 03 May 2018 23:57:43: Process for pairing-model is terminated! cat: SRX2741983.05_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 `SRX2741983.05_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 `SRX2741983.05_*.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 `SRX2741983.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。