Job ID = 6458859 SRX = SRX5717030 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:40:47 prefetch.2.10.7: 1) Downloading 'SRR8936390'... 2020-06-21T12:40:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:48:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:48:10 prefetch.2.10.7: 1) 'SRR8936390' was downloaded successfully Read 32631187 spots for SRR8936390/SRR8936390.sra Written 32631187 spots for SRR8936390/SRR8936390.sra 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: 00:10:00 32631187 reads; of these: 32631187 (100.00%) were unpaired; of these: 5487924 (16.82%) aligned 0 times 11556013 (35.41%) aligned exactly 1 time 15587250 (47.77%) aligned >1 times 83.18% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 11249280 / 27143263 = 0.4144 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 22:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:04:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:58: 1000000 INFO @ Sun, 21 Jun 2020 22:05:03: 2000000 INFO @ Sun, 21 Jun 2020 22:05:08: 3000000 INFO @ Sun, 21 Jun 2020 22:05:13: 4000000 INFO @ Sun, 21 Jun 2020 22:05:19: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 22:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:05:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:24: 6000000 INFO @ Sun, 21 Jun 2020 22:05:27: 1000000 INFO @ Sun, 21 Jun 2020 22:05:29: 7000000 INFO @ Sun, 21 Jun 2020 22:05:32: 2000000 INFO @ Sun, 21 Jun 2020 22:05:35: 8000000 INFO @ Sun, 21 Jun 2020 22:05:37: 3000000 INFO @ Sun, 21 Jun 2020 22:05:40: 9000000 INFO @ Sun, 21 Jun 2020 22:05:41: 4000000 INFO @ Sun, 21 Jun 2020 22:05:45: 10000000 INFO @ Sun, 21 Jun 2020 22:05:46: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 22:05:50: 11000000 INFO @ Sun, 21 Jun 2020 22:05:51: 6000000 INFO @ Sun, 21 Jun 2020 22:05:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:05:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:55: 7000000 INFO @ Sun, 21 Jun 2020 22:05:56: 12000000 INFO @ Sun, 21 Jun 2020 22:05:57: 1000000 INFO @ Sun, 21 Jun 2020 22:06:00: 8000000 INFO @ Sun, 21 Jun 2020 22:06:01: 13000000 INFO @ Sun, 21 Jun 2020 22:06:02: 2000000 INFO @ Sun, 21 Jun 2020 22:06:05: 9000000 INFO @ Sun, 21 Jun 2020 22:06:06: 14000000 INFO @ Sun, 21 Jun 2020 22:06:07: 3000000 INFO @ Sun, 21 Jun 2020 22:06:09: 10000000 INFO @ Sun, 21 Jun 2020 22:06:12: 15000000 INFO @ Sun, 21 Jun 2020 22:06:12: 4000000 INFO @ Sun, 21 Jun 2020 22:06:14: 11000000 INFO @ Sun, 21 Jun 2020 22:06:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:06:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:06:17: #1 total tags in treatment: 15893983 INFO @ Sun, 21 Jun 2020 22:06:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:06:17: 5000000 INFO @ Sun, 21 Jun 2020 22:06:17: #1 tags after filtering in treatment: 15893942 INFO @ Sun, 21 Jun 2020 22:06:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:18: #2 number of paired peaks: 1015 INFO @ Sun, 21 Jun 2020 22:06:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:18: 12000000 INFO @ Sun, 21 Jun 2020 22:06:19: 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/dm6/SRX5717030/SRX5717030.05_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/dm6/SRX5717030/SRX5717030.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:22: 6000000 INFO @ Sun, 21 Jun 2020 22:06:23: 13000000 INFO @ Sun, 21 Jun 2020 22:06:27: 7000000 INFO @ Sun, 21 Jun 2020 22:06:28: 14000000 INFO @ Sun, 21 Jun 2020 22:06:32: 8000000 INFO @ Sun, 21 Jun 2020 22:06:33: 15000000 INFO @ Sun, 21 Jun 2020 22:06:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:06:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:06:37: #1 total tags in treatment: 15893983 INFO @ Sun, 21 Jun 2020 22:06:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:06:37: 9000000 INFO @ Sun, 21 Jun 2020 22:06:38: #1 tags after filtering in treatment: 15893942 INFO @ Sun, 21 Jun 2020 22:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:38: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:39: #2 number of paired peaks: 1015 INFO @ Sun, 21 Jun 2020 22:06:39: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:39: 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/dm6/SRX5717030/SRX5717030.10_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/dm6/SRX5717030/SRX5717030.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:43: 10000000 INFO @ Sun, 21 Jun 2020 22:06:48: 11000000 INFO @ Sun, 21 Jun 2020 22:06:54: 12000000 INFO @ Sun, 21 Jun 2020 22:07:00: 13000000 INFO @ Sun, 21 Jun 2020 22:07:05: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:07:10: 15000000 INFO @ Sun, 21 Jun 2020 22:07:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:07:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:07:16: #1 total tags in treatment: 15893983 INFO @ Sun, 21 Jun 2020 22:07:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:07:16: #1 tags after filtering in treatment: 15893942 INFO @ Sun, 21 Jun 2020 22:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:16: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:18: #2 number of paired peaks: 1015 INFO @ Sun, 21 Jun 2020 22:07:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:18: 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/dm6/SRX5717030/SRX5717030.20_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/dm6/SRX5717030/SRX5717030.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm6/SRX5717030/SRX5717030.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。