Job ID = 2640879 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:40:42 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 20,154,163 reads read : 40,308,326 reads written : 20,154,163 reads 0-length : 20,154,163 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: 00:03:15 20154163 reads; of these: 20154163 (100.00%) were unpaired; of these: 2688763 (13.34%) aligned 0 times 15247161 (75.65%) aligned exactly 1 time 2218239 (11.01%) aligned >1 times 86.66% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7054980 / 17465400 = 0.4039 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:50:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.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 @ Sat, 24 Aug 2019 19:50:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:50:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:50:28: 1000000 INFO @ Sat, 24 Aug 2019 19:50:35: 2000000 INFO @ Sat, 24 Aug 2019 19:50:42: 3000000 INFO @ Sat, 24 Aug 2019 19:50:48: 4000000 INFO @ Sat, 24 Aug 2019 19:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.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 @ Sat, 24 Aug 2019 19:50:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:50:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:50:55: 5000000 INFO @ Sat, 24 Aug 2019 19:51:00: 1000000 INFO @ Sat, 24 Aug 2019 19:51:02: 6000000 INFO @ Sat, 24 Aug 2019 19:51:07: 2000000 INFO @ Sat, 24 Aug 2019 19:51:09: 7000000 INFO @ Sat, 24 Aug 2019 19:51:15: 3000000 INFO @ Sat, 24 Aug 2019 19:51:15: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.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 @ Sat, 24 Aug 2019 19:51:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:51:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:51:22: 4000000 INFO @ Sat, 24 Aug 2019 19:51:22: 9000000 INFO @ Sat, 24 Aug 2019 19:51:29: 10000000 INFO @ Sat, 24 Aug 2019 19:51:30: 1000000 INFO @ Sat, 24 Aug 2019 19:51:30: 5000000 INFO @ Sat, 24 Aug 2019 19:51:32: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:51:32: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:51:32: #1 total tags in treatment: 10410420 INFO @ Sat, 24 Aug 2019 19:51:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:51:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:51:32: #1 tags after filtering in treatment: 10410420 INFO @ Sat, 24 Aug 2019 19:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:51:32: #1 finished! INFO @ Sat, 24 Aug 2019 19:51:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:51:33: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:51:33: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 19:51:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.05_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/SRX3944370/SRX3944370.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:51:37: 2000000 INFO @ Sat, 24 Aug 2019 19:51:37: 6000000 INFO @ Sat, 24 Aug 2019 19:51:45: 3000000 INFO @ Sat, 24 Aug 2019 19:51:45: 7000000 INFO @ Sat, 24 Aug 2019 19:51:52: 4000000 INFO @ Sat, 24 Aug 2019 19:51:52: 8000000 INFO @ Sat, 24 Aug 2019 19:52:00: 5000000 INFO @ Sat, 24 Aug 2019 19:52:00: 9000000 INFO @ Sat, 24 Aug 2019 19:52:07: 10000000 INFO @ Sat, 24 Aug 2019 19:52:08: 6000000 INFO @ Sat, 24 Aug 2019 19:52:10: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:52:10: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:52:10: #1 total tags in treatment: 10410420 INFO @ Sat, 24 Aug 2019 19:52:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:52:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:52:11: #1 tags after filtering in treatment: 10410420 INFO @ Sat, 24 Aug 2019 19:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:52:11: #1 finished! INFO @ Sat, 24 Aug 2019 19:52:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:52:11: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:52:11: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 19:52:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.10_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/sacCer3/SRX3944370/SRX3944370.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:52:15: 7000000 INFO @ Sat, 24 Aug 2019 19:52:22: 8000000 INFO @ Sat, 24 Aug 2019 19:52:30: 9000000 INFO @ Sat, 24 Aug 2019 19:52:37: 10000000 INFO @ Sat, 24 Aug 2019 19:52:40: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:52:40: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:52:40: #1 total tags in treatment: 10410420 INFO @ Sat, 24 Aug 2019 19:52:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:52:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:52:40: #1 tags after filtering in treatment: 10410420 INFO @ Sat, 24 Aug 2019 19:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:52:40: #1 finished! INFO @ Sat, 24 Aug 2019 19:52:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:52:41: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:52:41: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 19:52:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.20_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/SRX3944370/SRX3944370.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944370/SRX3944370.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。