Job ID = 4289107 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:39:15 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 : 28,079,508 reads read : 56,159,016 reads written : 28,079,508 reads 0-length : 28,079,508 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: 00:06:22 28079508 reads; of these: 28079508 (100.00%) were unpaired; of these: 2142842 (7.63%) aligned 0 times 10312257 (36.73%) aligned exactly 1 time 15624409 (55.64%) aligned >1 times 92.37% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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 12 files... [bam_rmdupse_core] 19733335 / 25936666 = 0.7608 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.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 @ Tue, 10 Dec 2019 13:51:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:51:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:52:01: 1000000 INFO @ Tue, 10 Dec 2019 13:52:14: 2000000 INFO @ Tue, 10 Dec 2019 13:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.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 @ Tue, 10 Dec 2019 13:52:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:52:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:52:27: 3000000 INFO @ Tue, 10 Dec 2019 13:52:32: 1000000 INFO @ Tue, 10 Dec 2019 13:52:41: 4000000 INFO @ Tue, 10 Dec 2019 13:52:46: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.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 @ Tue, 10 Dec 2019 13:52:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:52:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:52:56: 5000000 INFO @ Tue, 10 Dec 2019 13:53:01: 3000000 INFO @ Tue, 10 Dec 2019 13:53:06: 1000000 INFO @ Tue, 10 Dec 2019 13:53:13: 6000000 INFO @ Tue, 10 Dec 2019 13:53:15: #1 tag size is determined as 76 bps INFO @ Tue, 10 Dec 2019 13:53:15: #1 tag size = 76 INFO @ Tue, 10 Dec 2019 13:53:15: #1 total tags in treatment: 6203331 INFO @ Tue, 10 Dec 2019 13:53:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:53:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:53:15: #1 tags after filtering in treatment: 6203331 INFO @ Tue, 10 Dec 2019 13:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:53:15: #1 finished! INFO @ Tue, 10 Dec 2019 13:53:15: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:53:16: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:53:16: 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 @ Tue, 10 Dec 2019 13:53:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.05_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/SRX5086844/SRX5086844.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:53:17: 4000000 INFO @ Tue, 10 Dec 2019 13:53:22: 2000000 INFO @ Tue, 10 Dec 2019 13:53:32: 5000000 INFO @ Tue, 10 Dec 2019 13:53:36: 3000000 INFO @ Tue, 10 Dec 2019 13:53:47: 6000000 INFO @ Tue, 10 Dec 2019 13:53:48: 4000000 INFO @ Tue, 10 Dec 2019 13:53:49: #1 tag size is determined as 76 bps INFO @ Tue, 10 Dec 2019 13:53:49: #1 tag size = 76 INFO @ Tue, 10 Dec 2019 13:53:49: #1 total tags in treatment: 6203331 INFO @ Tue, 10 Dec 2019 13:53:49: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:53:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:53:49: #1 tags after filtering in treatment: 6203331 INFO @ Tue, 10 Dec 2019 13:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:53:49: #1 finished! INFO @ Tue, 10 Dec 2019 13:53:49: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:53:49: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:53:49: 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 @ Tue, 10 Dec 2019 13:53:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.10_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/SRX5086844/SRX5086844.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:54:01: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 13:54:13: 6000000 INFO @ Tue, 10 Dec 2019 13:54:15: #1 tag size is determined as 76 bps INFO @ Tue, 10 Dec 2019 13:54:15: #1 tag size = 76 INFO @ Tue, 10 Dec 2019 13:54:15: #1 total tags in treatment: 6203331 INFO @ Tue, 10 Dec 2019 13:54:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:54:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:54:16: #1 tags after filtering in treatment: 6203331 INFO @ Tue, 10 Dec 2019 13:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:54:16: #1 finished! INFO @ Tue, 10 Dec 2019 13:54:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:54:16: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 13:54:16: 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 @ Tue, 10 Dec 2019 13:54:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.20_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/sacCer3/SRX5086844/SRX5086844.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5086844/SRX5086844.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。