Job ID = 6528491 SRX = SRX760492 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:19:22 prefetch.2.10.7: 1) Downloading 'SRR1653723'... 2020-06-29T15:19:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:21:46 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:21:46 prefetch.2.10.7: 1) 'SRR1653723' was downloaded successfully Read 19443486 spots for SRR1653723/SRR1653723.sra Written 19443486 spots for SRR1653723/SRR1653723.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 19443486 reads; of these: 19443486 (100.00%) were unpaired; of these: 4913753 (25.27%) aligned 0 times 12854542 (66.11%) aligned exactly 1 time 1675191 (8.62%) aligned >1 times 74.73% 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] 3731479 / 14529733 = 0.2568 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 @ Tue, 30 Jun 2020 00:37:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.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 @ Tue, 30 Jun 2020 00:37:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:37:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:38:01: 1000000 INFO @ Tue, 30 Jun 2020 00:38:07: 2000000 INFO @ Tue, 30 Jun 2020 00:38:12: 3000000 INFO @ Tue, 30 Jun 2020 00:38:18: 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 @ Tue, 30 Jun 2020 00:38:24: 5000000 INFO @ Tue, 30 Jun 2020 00:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.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 @ Tue, 30 Jun 2020 00:38:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:38:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:38:30: 6000000 INFO @ Tue, 30 Jun 2020 00:38:31: 1000000 INFO @ Tue, 30 Jun 2020 00:38:35: 7000000 INFO @ Tue, 30 Jun 2020 00:38:36: 2000000 INFO @ Tue, 30 Jun 2020 00:38:41: 8000000 INFO @ Tue, 30 Jun 2020 00:38:42: 3000000 INFO @ Tue, 30 Jun 2020 00:38:47: 9000000 INFO @ Tue, 30 Jun 2020 00:38:48: 4000000 INFO @ Tue, 30 Jun 2020 00:38:53: 10000000 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 @ Tue, 30 Jun 2020 00:38:53: 5000000 INFO @ Tue, 30 Jun 2020 00:38:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.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 @ Tue, 30 Jun 2020 00:38:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:38:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:38:57: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 00:38:57: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 00:38:57: #1 total tags in treatment: 10798254 INFO @ Tue, 30 Jun 2020 00:38:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:38:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:38:57: #1 tags after filtering in treatment: 10798254 INFO @ Tue, 30 Jun 2020 00:38:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:38:57: #1 finished! INFO @ Tue, 30 Jun 2020 00:38:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:38:59: #2 number of paired peaks: 2567 INFO @ Tue, 30 Jun 2020 00:38:59: start model_add_line... INFO @ Tue, 30 Jun 2020 00:38:59: 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 INFO @ Tue, 30 Jun 2020 00:38:59: 6000000 cut: /home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.05_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/dm3/SRX760492/SRX760492.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:39:01: 1000000 INFO @ Tue, 30 Jun 2020 00:39:05: 7000000 INFO @ Tue, 30 Jun 2020 00:39:08: 2000000 INFO @ Tue, 30 Jun 2020 00:39:10: 8000000 INFO @ Tue, 30 Jun 2020 00:39:14: 3000000 INFO @ Tue, 30 Jun 2020 00:39:16: 9000000 INFO @ Tue, 30 Jun 2020 00:39:20: 4000000 INFO @ Tue, 30 Jun 2020 00:39:22: 10000000 INFO @ Tue, 30 Jun 2020 00:39:25: 5000000 INFO @ Tue, 30 Jun 2020 00:39:27: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 00:39:27: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 00:39:27: #1 total tags in treatment: 10798254 INFO @ Tue, 30 Jun 2020 00:39:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:39:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:39:27: #1 tags after filtering in treatment: 10798254 INFO @ Tue, 30 Jun 2020 00:39:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:39:27: #1 finished! INFO @ Tue, 30 Jun 2020 00:39:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:39:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:39:28: #2 number of paired peaks: 2567 INFO @ Tue, 30 Jun 2020 00:39:28: start model_add_line... INFO @ Tue, 30 Jun 2020 00:39:28: 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/SRX760492/SRX760492.10_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/SRX760492/SRX760492.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:39:31: 6000000 INFO @ Tue, 30 Jun 2020 00:39:36: 7000000 INFO @ Tue, 30 Jun 2020 00:39:42: 8000000 INFO @ Tue, 30 Jun 2020 00:39:47: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:39:52: 10000000 INFO @ Tue, 30 Jun 2020 00:39:57: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 00:39:57: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 00:39:57: #1 total tags in treatment: 10798254 INFO @ Tue, 30 Jun 2020 00:39:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:39:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:39:57: #1 tags after filtering in treatment: 10798254 INFO @ Tue, 30 Jun 2020 00:39:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:39:57: #1 finished! INFO @ Tue, 30 Jun 2020 00:39:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:39:58: #2 number of paired peaks: 2567 INFO @ Tue, 30 Jun 2020 00:39:58: start model_add_line... INFO @ Tue, 30 Jun 2020 00:39:58: 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/SRX760492/SRX760492.20_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/SRX760492/SRX760492.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX760492/SRX760492.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。