Job ID = 6498774 SRX = SRX760493 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:03:25 prefetch.2.10.7: 1) Downloading 'SRR1653724'... 2020-06-26T00:03:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:06:05 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:06:05 prefetch.2.10.7: 1) 'SRR1653724' was downloaded successfully Read 18724525 spots for SRR1653724/SRR1653724.sra Written 18724525 spots for SRR1653724/SRR1653724.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: 00:04:31 18724525 reads; of these: 18724525 (100.00%) were unpaired; of these: 5115036 (27.32%) aligned 0 times 12137813 (64.82%) aligned exactly 1 time 1471676 (7.86%) aligned >1 times 72.68% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3411505 / 13609489 = 0.2507 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 @ Fri, 26 Jun 2020 09:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.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 @ Fri, 26 Jun 2020 09:15:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:15:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:15:40: 1000000 INFO @ Fri, 26 Jun 2020 09:15:46: 2000000 INFO @ Fri, 26 Jun 2020 09:15:53: 3000000 INFO @ Fri, 26 Jun 2020 09:16:00: 4000000 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 @ Fri, 26 Jun 2020 09:16:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.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 @ Fri, 26 Jun 2020 09:16:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:16:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:16:07: 5000000 INFO @ Fri, 26 Jun 2020 09:16:10: 1000000 INFO @ Fri, 26 Jun 2020 09:16:15: 6000000 INFO @ Fri, 26 Jun 2020 09:16:17: 2000000 INFO @ Fri, 26 Jun 2020 09:16:22: 7000000 INFO @ Fri, 26 Jun 2020 09:16:24: 3000000 INFO @ Fri, 26 Jun 2020 09:16:30: 8000000 INFO @ Fri, 26 Jun 2020 09:16:31: 4000000 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 @ Fri, 26 Jun 2020 09:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.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 @ Fri, 26 Jun 2020 09:16:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:16:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:16:37: 9000000 INFO @ Fri, 26 Jun 2020 09:16:38: 5000000 INFO @ Fri, 26 Jun 2020 09:16:40: 1000000 INFO @ Fri, 26 Jun 2020 09:16:44: 10000000 INFO @ Fri, 26 Jun 2020 09:16:45: 6000000 INFO @ Fri, 26 Jun 2020 09:16:46: #1 tag size is determined as 49 bps INFO @ Fri, 26 Jun 2020 09:16:46: #1 tag size = 49 INFO @ Fri, 26 Jun 2020 09:16:46: #1 total tags in treatment: 10197984 INFO @ Fri, 26 Jun 2020 09:16:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:16:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:16:46: #1 tags after filtering in treatment: 10197984 INFO @ Fri, 26 Jun 2020 09:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:16:46: #1 finished! INFO @ Fri, 26 Jun 2020 09:16:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:16:47: 2000000 INFO @ Fri, 26 Jun 2020 09:16:47: #2 number of paired peaks: 3253 INFO @ Fri, 26 Jun 2020 09:16:47: start model_add_line... INFO @ Fri, 26 Jun 2020 09:16:47: 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/dm3/SRX760493/SRX760493.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:16:52: 7000000 INFO @ Fri, 26 Jun 2020 09:16:54: 3000000 INFO @ Fri, 26 Jun 2020 09:16:59: 8000000 INFO @ Fri, 26 Jun 2020 09:17:00: 4000000 INFO @ Fri, 26 Jun 2020 09:17:05: 9000000 INFO @ Fri, 26 Jun 2020 09:17:07: 5000000 INFO @ Fri, 26 Jun 2020 09:17:12: 10000000 INFO @ Fri, 26 Jun 2020 09:17:13: #1 tag size is determined as 49 bps INFO @ Fri, 26 Jun 2020 09:17:13: #1 tag size = 49 INFO @ Fri, 26 Jun 2020 09:17:13: #1 total tags in treatment: 10197984 INFO @ Fri, 26 Jun 2020 09:17:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:17:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:17:13: #1 tags after filtering in treatment: 10197984 INFO @ Fri, 26 Jun 2020 09:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:17:13: #1 finished! INFO @ Fri, 26 Jun 2020 09:17:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:17:14: 6000000 INFO @ Fri, 26 Jun 2020 09:17:15: #2 number of paired peaks: 3253 INFO @ Fri, 26 Jun 2020 09:17:15: start model_add_line... INFO @ Fri, 26 Jun 2020 09:17:15: 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/dm3/SRX760493/SRX760493.10_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/dm3/SRX760493/SRX760493.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:17:20: 7000000 INFO @ Fri, 26 Jun 2020 09:17:26: 8000000 INFO @ Fri, 26 Jun 2020 09:17:32: 9000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:17:38: 10000000 INFO @ Fri, 26 Jun 2020 09:17:39: #1 tag size is determined as 49 bps INFO @ Fri, 26 Jun 2020 09:17:39: #1 tag size = 49 INFO @ Fri, 26 Jun 2020 09:17:39: #1 total tags in treatment: 10197984 INFO @ Fri, 26 Jun 2020 09:17:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:17:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:17:39: #1 tags after filtering in treatment: 10197984 INFO @ Fri, 26 Jun 2020 09:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:17:39: #1 finished! INFO @ Fri, 26 Jun 2020 09:17:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:17:40: #2 number of paired peaks: 3253 INFO @ Fri, 26 Jun 2020 09:17:40: start model_add_line... INFO @ Fri, 26 Jun 2020 09:17:40: 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/dm3/SRX760493/SRX760493.20_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/dm3/SRX760493/SRX760493.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760493/SRX760493.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling