Job ID = 2010781 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:37:10 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 ) 2019-07-05T15:37:10 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 : 12,332,332 reads read : 24,664,664 reads written : 12,332,332 reads 0-length : 12,332,332 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: 00:01:56 12332332 reads; of these: 12332332 (100.00%) were unpaired; of these: 2349013 (19.05%) aligned 0 times 7626052 (61.84%) aligned exactly 1 time 2357267 (19.11%) aligned >1 times 80.95% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 5559769 / 9983319 = 0.5569 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 @ Sat, 06 Jul 2019 00:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.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, 06 Jul 2019 00:47:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:47:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:47:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.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, 06 Jul 2019 00:47:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:47:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:47:48: 1000000 INFO @ Sat, 06 Jul 2019 00:47:49: 1000000 INFO @ Sat, 06 Jul 2019 00:47:55: 2000000 INFO @ Sat, 06 Jul 2019 00:47:56: 2000000 INFO @ Sat, 06 Jul 2019 00:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.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, 06 Jul 2019 00:48:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:48:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:48:02: 3000000 INFO @ Sat, 06 Jul 2019 00:48:04: 3000000 INFO @ Sat, 06 Jul 2019 00:48:08: 1000000 INFO @ Sat, 06 Jul 2019 00:48:09: 4000000 INFO @ Sat, 06 Jul 2019 00:48:11: 4000000 INFO @ Sat, 06 Jul 2019 00:48:12: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:48:12: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:48:12: #1 total tags in treatment: 4423550 INFO @ Sat, 06 Jul 2019 00:48:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:48:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:48:12: #1 tags after filtering in treatment: 4423550 INFO @ Sat, 06 Jul 2019 00:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:48:12: #1 finished! INFO @ Sat, 06 Jul 2019 00:48:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:48:13: #2 number of paired peaks: 10 WARNING @ Sat, 06 Jul 2019 00:48:13: Too few paired peaks (10) 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, 06 Jul 2019 00:48:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.05_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/sacCer3/SRX399186/SRX399186.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:48:14: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:48:14: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:48:14: #1 total tags in treatment: 4423550 INFO @ Sat, 06 Jul 2019 00:48:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:48:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:48:14: #1 tags after filtering in treatment: 4423550 INFO @ Sat, 06 Jul 2019 00:48:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:48:14: #1 finished! INFO @ Sat, 06 Jul 2019 00:48:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:48:14: 2000000 INFO @ Sat, 06 Jul 2019 00:48:15: #2 number of paired peaks: 10 WARNING @ Sat, 06 Jul 2019 00:48:15: Too few paired peaks (10) 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, 06 Jul 2019 00:48:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.10_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/SRX399186/SRX399186.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:48:21: 3000000 INFO @ Sat, 06 Jul 2019 00:48:28: 4000000 INFO @ Sat, 06 Jul 2019 00:48:31: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:48:31: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:48:31: #1 total tags in treatment: 4423550 INFO @ Sat, 06 Jul 2019 00:48:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:48:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:48:32: #1 tags after filtering in treatment: 4423550 INFO @ Sat, 06 Jul 2019 00:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:48:32: #1 finished! INFO @ Sat, 06 Jul 2019 00:48:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:48:32: #2 number of paired peaks: 10 WARNING @ Sat, 06 Jul 2019 00:48:32: Too few paired peaks (10) 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, 06 Jul 2019 00:48:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.20_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/SRX399186/SRX399186.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399186/SRX399186.20_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。