Job ID = 11296967 sra ファイルのダウンロード中... Completed: 229401K bytes transferred in 5 seconds (342176K 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: SINGLE fastq に変換中... Read 7951713 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4212609/SRR7310241.sra Written 7951713 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4212609/SRR7310241.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: 00:01:48 7951713 reads; of these: 7951713 (100.00%) were unpaired; of these: 4046156 (50.88%) aligned 0 times 3675432 (46.22%) aligned exactly 1 time 230125 (2.89%) aligned >1 times 49.12% 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_rmdupse_core] 1913393 / 3905557 = 0.4899 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 @ Mon, 05 Nov 2018 18:05:01: # Command line: callpeak -t SRX4212609.bam -f BAM -g 12100000 -n SRX4212609.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4212609.10 # format = BAM # ChIP-seq file = ['SRX4212609.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 @ Mon, 05 Nov 2018 18:05:01: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:01: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:01: # Command line: callpeak -t SRX4212609.bam -f BAM -g 12100000 -n SRX4212609.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4212609.20 # format = BAM # ChIP-seq file = ['SRX4212609.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 @ Mon, 05 Nov 2018 18:05:01: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:01: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:01: # Command line: callpeak -t SRX4212609.bam -f BAM -g 12100000 -n SRX4212609.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4212609.05 # format = BAM # ChIP-seq file = ['SRX4212609.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 @ Mon, 05 Nov 2018 18:05:01: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:05:01: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:05:10: 1000000 INFO @ Mon, 05 Nov 2018 18:05:10: 1000000 INFO @ Mon, 05 Nov 2018 18:05:10: 1000000 INFO @ Mon, 05 Nov 2018 18:05:19: #1 tag size is determined as 60 bps INFO @ Mon, 05 Nov 2018 18:05:19: #1 tag size is determined as 60 bps INFO @ Mon, 05 Nov 2018 18:05:19: #1 tag size = 60 INFO @ Mon, 05 Nov 2018 18:05:19: #1 tag size = 60 INFO @ Mon, 05 Nov 2018 18:05:19: #1 total tags in treatment: 1992164 INFO @ Mon, 05 Nov 2018 18:05:19: #1 total tags in treatment: 1992164 INFO @ Mon, 05 Nov 2018 18:05:19: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:19: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:05:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:05:19: #1 tags after filtering in treatment: 1992164 INFO @ Mon, 05 Nov 2018 18:05:19: #1 tags after filtering in treatment: 1992164 INFO @ Mon, 05 Nov 2018 18:05:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:19: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:19: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:19: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:19: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:19: #2 number of paired peaks: 271 WARNING @ Mon, 05 Nov 2018 18:05:19: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 05 Nov 2018 18:05:19: start model_add_line... INFO @ Mon, 05 Nov 2018 18:05:19: #2 number of paired peaks: 271 WARNING @ Mon, 05 Nov 2018 18:05:19: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 05 Nov 2018 18:05:19: start model_add_line... INFO @ Mon, 05 Nov 2018 18:05:19: start X-correlation... INFO @ Mon, 05 Nov 2018 18:05:19: start X-correlation... Traceback (most recent call last): Traceback (most recent call last): File "/usr/local/bin/macs2", line 5, in File "/usr/local/bin/macs2", line 5, in pkg_resources.run_script('MACS2==2.1.1.20160309', 'macs2') pkg_resources.run_script('MACS2==2.1.1.20160309', 'macs2') File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1214, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1214, 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 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/EGG-INFO/scripts/macs2", line 57, in main File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 178, in run File "build/bdist.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 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 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) File "MACS2/PeakModel.pyx", line 230, in MACS2.PeakModel.PeakModel.__paired_peak_model (MACS2/PeakModel.c:4266) ValueError: max() arg is an empty sequence ValueError: max() arg is an empty sequence cat: SRX4212609.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4212609.20_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 pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4212609.20_model.r'rm: cannot remove `SRX4212609.10_model.r': そのようなファイルやディレクトリはありません : 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 `SRX4212609.20_*.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 `SRX4212609.10_*.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 `SRX4212609.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4212609.10_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 CompletedMACS2peakCalling INFO @ Mon, 05 Nov 2018 18:05:20: #1 tag size is determined as 60 bps INFO @ Mon, 05 Nov 2018 18:05:20: #1 tag size = 60 INFO @ Mon, 05 Nov 2018 18:05:20: #1 total tags in treatment: 1992164 INFO @ Mon, 05 Nov 2018 18:05:20: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:05:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:05:20: #1 tags after filtering in treatment: 1992164 INFO @ Mon, 05 Nov 2018 18:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:05:20: #1 finished! INFO @ Mon, 05 Nov 2018 18:05:20: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:05:20: #2 number of paired peaks: 271 WARNING @ Mon, 05 Nov 2018 18:05:20: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 05 Nov 2018 18:05:20: start model_add_line... INFO @ Mon, 05 Nov 2018 18:05:20: start X-correlation... Traceback (most recent call last): File "/usr/local/bin/macs2", line 5, in pkg_resources.run_script('MACS2==2.1.1.20160309', 'macs2') File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1214, 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 "build/bdist.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 cat: SRX4212609.05_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 `SRX4212609.05_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 `SRX4212609.05_*.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 `SRX4212609.05_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。