Job ID = 2010550 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,957,470 reads read : 5,914,940 reads written : 5,914,940 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:01:48 2957470 reads; of these: 2957470 (100.00%) were paired; of these: 1416804 (47.91%) aligned concordantly 0 times 1150988 (38.92%) aligned concordantly exactly 1 time 389678 (13.18%) aligned concordantly >1 times ---- 1416804 pairs aligned concordantly 0 times; of these: 87827 (6.20%) aligned discordantly 1 time ---- 1328977 pairs aligned 0 times concordantly or discordantly; of these: 2657954 mates make up the pairs; of these: 2564209 (96.47%) aligned 0 times 28446 (1.07%) aligned exactly 1 time 65299 (2.46%) aligned >1 times 56.65% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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_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] 92314 / 1614509 = 0.0572 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 @ Fri, 05 Jul 2019 23:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.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 @ Fri, 05 Jul 2019 23:01:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:01:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.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 @ Fri, 05 Jul 2019 23:01:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:01:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:01:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.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 @ Fri, 05 Jul 2019 23:01:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:01:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:01:54: 1000000 INFO @ Fri, 05 Jul 2019 23:01:55: 1000000 INFO @ Fri, 05 Jul 2019 23:01:56: 1000000 INFO @ Fri, 05 Jul 2019 23:02:03: 2000000 INFO @ Fri, 05 Jul 2019 23:02:04: 2000000 INFO @ Fri, 05 Jul 2019 23:02:06: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:02:11: 3000000 INFO @ Fri, 05 Jul 2019 23:02:13: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:02:13: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:02:13: #1 total tags in treatment: 1453450 INFO @ Fri, 05 Jul 2019 23:02:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:02:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:02:13: #1 tags after filtering in treatment: 862436 INFO @ Fri, 05 Jul 2019 23:02:13: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:02:13: #1 finished! INFO @ Fri, 05 Jul 2019 23:02:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:02:13: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:02:13: #2 number of paired peaks: 274 WARNING @ Fri, 05 Jul 2019 23:02:13: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 05 Jul 2019 23:02:13: start model_add_line... INFO @ Fri, 05 Jul 2019 23:02:13: start X-correlation... Traceback (most recent call last): File "/usr/local/bin/macs2", line 4, in __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2') File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 617, in File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 57, in main File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 178, in run File "MACS2/PeakModel.pyx", line 108, in MACS2.PeakModel.PeakModel.__init__ (MACS2/PeakModel.c:2438) File "MACS2/PeakModel.pyx", line 150, in MACS2.PeakModel.PeakModel.build (MACS2/PeakModel.c:3010) File "MACS2/PeakModel.pyx", line 230, in MACS2.PeakModel.PeakModel.__paired_peak_model (MACS2/PeakModel.c:4266) ValueError: max() arg is an empty sequence cut: /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:02:13: 3000000 INFO @ Fri, 05 Jul 2019 23:02:14: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:02:14: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:02:14: #1 total tags in treatment: 1453450 INFO @ Fri, 05 Jul 2019 23:02:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:02:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:02:14: #1 tags after filtering in treatment: 862436 INFO @ Fri, 05 Jul 2019 23:02:14: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:02:14: #1 finished! INFO @ Fri, 05 Jul 2019 23:02:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:02:15: #2 number of paired peaks: 274 WARNING @ Fri, 05 Jul 2019 23:02:15: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 05 Jul 2019 23:02:15: start model_add_line... INFO @ Fri, 05 Jul 2019 23:02:15: start X-correlation... Traceback (most recent call last): File "/usr/local/bin/macs2", line 4, in __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2') File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 617, in File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 57, in main File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 178, in run File "MACS2/PeakModel.pyx", line 108, in MACS2.PeakModel.PeakModel.__init__ (MACS2/PeakModel.c:2438) File "MACS2/PeakModel.pyx", line 150, in MACS2.PeakModel.PeakModel.build (MACS2/PeakModel.c:3010) File "MACS2/PeakModel.pyx", line 230, in MACS2.PeakModel.PeakModel.__paired_peak_model (MACS2/PeakModel.c:4266) ValueError: max() arg is an empty sequence cut: /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:02:15: 3000000 INFO @ Fri, 05 Jul 2019 23:02:16: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:02:16: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:02:16: #1 total tags in treatment: 1453450 INFO @ Fri, 05 Jul 2019 23:02:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:02:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:02:16: #1 tags after filtering in treatment: 862436 INFO @ Fri, 05 Jul 2019 23:02:16: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:02:16: #1 finished! INFO @ Fri, 05 Jul 2019 23:02:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:02:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:02:17: #2 number of paired peaks: 274 WARNING @ Fri, 05 Jul 2019 23:02:17: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 05 Jul 2019 23:02:17: start model_add_line... INFO @ Fri, 05 Jul 2019 23:02:17: start X-correlation... Traceback (most recent call last): File "/usr/local/bin/macs2", line 4, in __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2') File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 617, in File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 57, in main File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 178, in run File "MACS2/PeakModel.pyx", line 108, in MACS2.PeakModel.PeakModel.__init__ (MACS2/PeakModel.c:2438) File "MACS2/PeakModel.pyx", line 150, in MACS2.PeakModel.PeakModel.build (MACS2/PeakModel.c:3010) File "MACS2/PeakModel.pyx", line 230, in MACS2.PeakModel.PeakModel.__paired_peak_model (MACS2/PeakModel.c:4266) ValueError: max() arg is an empty sequence cut: /home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381251/SRX381251.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling