Job ID = 2640861 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:37:40 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 : 20,580,928 reads read : 41,161,856 reads written : 20,580,928 reads 0-length : 20,580,928 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: 00:03:09 20580928 reads; of these: 20580928 (100.00%) were unpaired; of these: 4133973 (20.09%) aligned 0 times 14723401 (71.54%) aligned exactly 1 time 1723554 (8.37%) aligned >1 times 79.91% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 7641513 / 16446955 = 0.4646 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:48:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.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 19:48:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:48:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:48:21: 1000000 INFO @ Sat, 24 Aug 2019 19:48:30: 2000000 INFO @ Sat, 24 Aug 2019 19:48:38: 3000000 INFO @ Sat, 24 Aug 2019 19:48:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.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 19:48:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:48:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:48:47: 4000000 INFO @ Sat, 24 Aug 2019 19:48:51: 1000000 INFO @ Sat, 24 Aug 2019 19:48:57: 5000000 INFO @ Sat, 24 Aug 2019 19:48:59: 2000000 INFO @ Sat, 24 Aug 2019 19:49:06: 6000000 INFO @ Sat, 24 Aug 2019 19:49:08: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.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 19:49:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:49:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:49:15: 7000000 INFO @ Sat, 24 Aug 2019 19:49:15: 4000000 INFO @ Sat, 24 Aug 2019 19:49:23: 5000000 INFO @ Sat, 24 Aug 2019 19:49:23: 1000000 INFO @ Sat, 24 Aug 2019 19:49:24: 8000000 INFO @ Sat, 24 Aug 2019 19:49:31: 6000000 INFO @ Sat, 24 Aug 2019 19:49:31: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:49:31: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:49:31: #1 total tags in treatment: 8805442 INFO @ Sat, 24 Aug 2019 19:49:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:49:31: #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 19:49:31: #1 tags after filtering in treatment: 8805442 INFO @ Sat, 24 Aug 2019 19:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:49:31: #1 finished! INFO @ Sat, 24 Aug 2019 19:49:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:49:32: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:49:32: 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 19:49:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.05_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/SRX3944357/SRX3944357.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:49:35: 2000000 INFO @ Sat, 24 Aug 2019 19:49:38: 7000000 INFO @ Sat, 24 Aug 2019 19:49:45: 8000000 INFO @ Sat, 24 Aug 2019 19:49:46: 3000000 INFO @ Sat, 24 Aug 2019 19:49:51: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:49:51: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:49:51: #1 total tags in treatment: 8805442 INFO @ Sat, 24 Aug 2019 19:49:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:49:51: #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 19:49:51: #1 tags after filtering in treatment: 8805442 INFO @ Sat, 24 Aug 2019 19:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:49:51: #1 finished! INFO @ Sat, 24 Aug 2019 19:49:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:49:52: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:49:52: 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 19:49:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.10_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/SRX3944357/SRX3944357.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:49:58: 4000000 INFO @ Sat, 24 Aug 2019 19:50:09: 5000000 INFO @ Sat, 24 Aug 2019 19:50:21: 6000000 INFO @ Sat, 24 Aug 2019 19:50:32: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 19:50:44: 8000000 INFO @ Sat, 24 Aug 2019 19:50:53: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:50:53: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:50:53: #1 total tags in treatment: 8805442 INFO @ Sat, 24 Aug 2019 19:50:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:50:53: #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 19:50:53: #1 tags after filtering in treatment: 8805442 INFO @ Sat, 24 Aug 2019 19:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:50:53: #1 finished! INFO @ Sat, 24 Aug 2019 19:50:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:50:53: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:50:53: 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 19:50:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.20_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/SRX3944357/SRX3944357.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3944357/SRX3944357.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。