Job ID = 11388930 sra ファイルのダウンロード中... Completed: 1070871K bytes transferred in 18 seconds (464094K 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 19090381 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017449/SRR8198072.sra Written 19090381 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017449/SRR8198072.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: 00:34:15 19090381 reads; of these: 19090381 (100.00%) were paired; of these: 1347851 (7.06%) aligned concordantly 0 times 15698717 (82.23%) aligned concordantly exactly 1 time 2043813 (10.71%) aligned concordantly >1 times ---- 1347851 pairs aligned concordantly 0 times; of these: 274847 (20.39%) aligned discordantly 1 time ---- 1073004 pairs aligned 0 times concordantly or discordantly; of these: 2146008 mates make up the pairs; of these: 1832690 (85.40%) aligned 0 times 188642 (8.79%) aligned exactly 1 time 124676 (5.81%) aligned >1 times 95.20% overall alignment rate Time searching: 00:34:15 Overall time: 00:34:15 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 16 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] 2222378 / 17869861 = 0.1244 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 01:04:57: # Command line: callpeak -t SRX5017449.bam -f BAM -g 12100000 -n SRX5017449.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017449.20 # format = BAM # ChIP-seq file = ['SRX5017449.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 01:04:57: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:04:57: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:04:57: # Command line: callpeak -t SRX5017449.bam -f BAM -g 12100000 -n SRX5017449.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017449.10 # format = BAM # ChIP-seq file = ['SRX5017449.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 01:04:57: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:04:57: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:04:57: # Command line: callpeak -t SRX5017449.bam -f BAM -g 12100000 -n SRX5017449.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017449.05 # format = BAM # ChIP-seq file = ['SRX5017449.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 01:04:57: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:04:57: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:05:06: 1000000 INFO @ Thu, 13 Dec 2018 01:05:07: 1000000 INFO @ Thu, 13 Dec 2018 01:05:08: 1000000 INFO @ Thu, 13 Dec 2018 01:05:16: 2000000 INFO @ Thu, 13 Dec 2018 01:05:17: 2000000 INFO @ Thu, 13 Dec 2018 01:05:17: 2000000 INFO @ Thu, 13 Dec 2018 01:05:26: 3000000 INFO @ Thu, 13 Dec 2018 01:05:27: 3000000 INFO @ Thu, 13 Dec 2018 01:05:28: 3000000 INFO @ Thu, 13 Dec 2018 01:05:34: 4000000 INFO @ Thu, 13 Dec 2018 01:05:37: 4000000 INFO @ Thu, 13 Dec 2018 01:05:40: 4000000 INFO @ Thu, 13 Dec 2018 01:05:42: 5000000 INFO @ Thu, 13 Dec 2018 01:05:48: 5000000 INFO @ Thu, 13 Dec 2018 01:05:50: 6000000 INFO @ Thu, 13 Dec 2018 01:05:51: 5000000 INFO @ Thu, 13 Dec 2018 01:05:59: 6000000 INFO @ Thu, 13 Dec 2018 01:05:59: 7000000 INFO @ Thu, 13 Dec 2018 01:06:02: 6000000 INFO @ Thu, 13 Dec 2018 01:06:07: 7000000 INFO @ Thu, 13 Dec 2018 01:06:10: 7000000 INFO @ Thu, 13 Dec 2018 01:06:11: 8000000 INFO @ Thu, 13 Dec 2018 01:06:16: 8000000 INFO @ Thu, 13 Dec 2018 01:06:18: 8000000 INFO @ Thu, 13 Dec 2018 01:06:22: 9000000 INFO @ Thu, 13 Dec 2018 01:06:24: 9000000 INFO @ Thu, 13 Dec 2018 01:06:26: 9000000 INFO @ Thu, 13 Dec 2018 01:06:31: 10000000 INFO @ Thu, 13 Dec 2018 01:06:34: 10000000 INFO @ Thu, 13 Dec 2018 01:06:36: 10000000 INFO @ Thu, 13 Dec 2018 01:06:39: 11000000 INFO @ Thu, 13 Dec 2018 01:06:41: 11000000 INFO @ Thu, 13 Dec 2018 01:06:47: 12000000 INFO @ Thu, 13 Dec 2018 01:06:49: 12000000 INFO @ Thu, 13 Dec 2018 01:06:52: 11000000 INFO @ Thu, 13 Dec 2018 01:06:55: 13000000 INFO @ Thu, 13 Dec 2018 01:06:57: 13000000 INFO @ Thu, 13 Dec 2018 01:07:02: 12000000 INFO @ Thu, 13 Dec 2018 01:07:03: 14000000 INFO @ Thu, 13 Dec 2018 01:07:05: 14000000 INFO @ Thu, 13 Dec 2018 01:07:12: 15000000 INFO @ Thu, 13 Dec 2018 01:07:12: 15000000 INFO @ Thu, 13 Dec 2018 01:07:12: 13000000 INFO @ Thu, 13 Dec 2018 01:07:20: 16000000 INFO @ Thu, 13 Dec 2018 01:07:21: 16000000 INFO @ Thu, 13 Dec 2018 01:07:23: 14000000 INFO @ Thu, 13 Dec 2018 01:07:29: 17000000 INFO @ Thu, 13 Dec 2018 01:07:30: 17000000 INFO @ Thu, 13 Dec 2018 01:07:36: 15000000 INFO @ Thu, 13 Dec 2018 01:07:38: 18000000 INFO @ Thu, 13 Dec 2018 01:07:41: 18000000 INFO @ Thu, 13 Dec 2018 01:07:48: 19000000 INFO @ Thu, 13 Dec 2018 01:07:52: 16000000 INFO @ Thu, 13 Dec 2018 01:07:59: 19000000 INFO @ Thu, 13 Dec 2018 01:07:59: 20000000 INFO @ Thu, 13 Dec 2018 01:08:08: 21000000 INFO @ Thu, 13 Dec 2018 01:08:10: 17000000 INFO @ Thu, 13 Dec 2018 01:08:15: 20000000 INFO @ Thu, 13 Dec 2018 01:08:16: 22000000 INFO @ Thu, 13 Dec 2018 01:08:20: 18000000 INFO @ Thu, 13 Dec 2018 01:08:26: 23000000 INFO @ Thu, 13 Dec 2018 01:08:31: 21000000 INFO @ Thu, 13 Dec 2018 01:08:32: 19000000 INFO @ Thu, 13 Dec 2018 01:08:40: 24000000 INFO @ Thu, 13 Dec 2018 01:08:46: 20000000 INFO @ Thu, 13 Dec 2018 01:08:48: 22000000 INFO @ Thu, 13 Dec 2018 01:08:54: 25000000 INFO @ Thu, 13 Dec 2018 01:08:57: 21000000 INFO @ Thu, 13 Dec 2018 01:08:59: 23000000 INFO @ Thu, 13 Dec 2018 01:09:04: 26000000 INFO @ Thu, 13 Dec 2018 01:09:08: 22000000 INFO @ Thu, 13 Dec 2018 01:09:10: 24000000 INFO @ Thu, 13 Dec 2018 01:09:16: 27000000 INFO @ Thu, 13 Dec 2018 01:09:18: 23000000 INFO @ Thu, 13 Dec 2018 01:09:21: 25000000 INFO @ Thu, 13 Dec 2018 01:09:28: 24000000 INFO @ Thu, 13 Dec 2018 01:09:28: 28000000 INFO @ Thu, 13 Dec 2018 01:09:30: 26000000 INFO @ Thu, 13 Dec 2018 01:09:37: 25000000 INFO @ Thu, 13 Dec 2018 01:09:40: 27000000 INFO @ Thu, 13 Dec 2018 01:09:40: 29000000 INFO @ Thu, 13 Dec 2018 01:09:47: 26000000 INFO @ Thu, 13 Dec 2018 01:09:51: 30000000 INFO @ Thu, 13 Dec 2018 01:09:52: 28000000 INFO @ Thu, 13 Dec 2018 01:09:58: 27000000 INFO @ Thu, 13 Dec 2018 01:10:01: 31000000 INFO @ Thu, 13 Dec 2018 01:10:05: 29000000 INFO @ Thu, 13 Dec 2018 01:10:08: 28000000 INFO @ Thu, 13 Dec 2018 01:10:09: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:10:09: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:10:09: #1 total tags in treatment: 15530473 INFO @ Thu, 13 Dec 2018 01:10:09: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:10:09: #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 01:10:09: #1 tags after filtering in treatment: 10161266 INFO @ Thu, 13 Dec 2018 01:10:09: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 13 Dec 2018 01:10:09: #1 finished! INFO @ Thu, 13 Dec 2018 01:10:09: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:10:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:10:10: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:10:10: 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 01:10:10: Process for pairing-model is terminated! cat: SRX5017449.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017449.10_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 `SRX5017449.10_*.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 `SRX5017449.10_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 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 01:10:17: 29000000 INFO @ Thu, 13 Dec 2018 01:10:20: 30000000 INFO @ Thu, 13 Dec 2018 01:10:29: 30000000 INFO @ Thu, 13 Dec 2018 01:10:32: 31000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 01:10:41: 31000000 INFO @ Thu, 13 Dec 2018 01:10:42: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:10:42: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:10:42: #1 total tags in treatment: 15530473 INFO @ Thu, 13 Dec 2018 01:10:42: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:10:42: #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 01:10:43: #1 tags after filtering in treatment: 10161266 INFO @ Thu, 13 Dec 2018 01:10:43: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 13 Dec 2018 01:10:43: #1 finished! INFO @ Thu, 13 Dec 2018 01:10:43: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:10:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:10:44: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:10:44: 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 01:10:44: Process for pairing-model is terminated! cat: SRX5017449.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017449.05_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 `SRX5017449.05_*.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 `SRX5017449.05_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 01:10:51: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:10:51: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:10:51: #1 total tags in treatment: 15530473 INFO @ Thu, 13 Dec 2018 01:10:51: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:10:51: #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 01:10:51: #1 tags after filtering in treatment: 10161266 INFO @ Thu, 13 Dec 2018 01:10:51: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 13 Dec 2018 01:10:51: #1 finished! INFO @ Thu, 13 Dec 2018 01:10:51: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:10:52: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:10:52: 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 01:10:52: Process for pairing-model is terminated! cat: SRX5017449.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017449.20_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 `SRX5017449.20_*.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 `SRX5017449.20_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