Job ID = 2641076 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:15:07 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 ) 1900-01-00T00:00:00 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 ) 2019-08-24T12:15:07 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 : 26,099,868 reads read : 52,199,736 reads written : 26,099,868 reads 0-length : 26,099,868 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: 00:04:31 26099868 reads; of these: 26099868 (100.00%) were unpaired; of these: 700440 (2.68%) aligned 0 times 22788492 (87.31%) aligned exactly 1 time 2610936 (10.00%) aligned >1 times 97.32% 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: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14419770 / 25399428 = 0.5677 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.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 21:27:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:27:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:27:26: 1000000 INFO @ Sat, 24 Aug 2019 21:27:34: 2000000 INFO @ Sat, 24 Aug 2019 21:27:41: 3000000 INFO @ Sat, 24 Aug 2019 21:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.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 21:27:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:27:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:27:49: 4000000 INFO @ Sat, 24 Aug 2019 21:27:55: 1000000 INFO @ Sat, 24 Aug 2019 21:27:57: 5000000 INFO @ Sat, 24 Aug 2019 21:28:02: 2000000 INFO @ Sat, 24 Aug 2019 21:28:04: 6000000 INFO @ Sat, 24 Aug 2019 21:28:09: 3000000 INFO @ Sat, 24 Aug 2019 21:28:12: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:28:15: 4000000 INFO @ Sat, 24 Aug 2019 21:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.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 21:28:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:28:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:28:19: 8000000 INFO @ Sat, 24 Aug 2019 21:28:22: 5000000 INFO @ Sat, 24 Aug 2019 21:28:27: 9000000 INFO @ Sat, 24 Aug 2019 21:28:28: 1000000 INFO @ Sat, 24 Aug 2019 21:28:29: 6000000 INFO @ Sat, 24 Aug 2019 21:28:35: 10000000 INFO @ Sat, 24 Aug 2019 21:28:36: 7000000 INFO @ Sat, 24 Aug 2019 21:28:37: 2000000 INFO @ Sat, 24 Aug 2019 21:28:42: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:28:42: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:28:42: #1 total tags in treatment: 10979658 INFO @ Sat, 24 Aug 2019 21:28:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:28:42: #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 21:28:43: #1 tags after filtering in treatment: 10979658 INFO @ Sat, 24 Aug 2019 21:28:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:28:43: #1 finished! INFO @ Sat, 24 Aug 2019 21:28:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:28:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:28:43: 8000000 INFO @ Sat, 24 Aug 2019 21:28:43: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:28:43: 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 21:28:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.05_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/SRX5257270/SRX5257270.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:28:46: 3000000 INFO @ Sat, 24 Aug 2019 21:28:50: 9000000 INFO @ Sat, 24 Aug 2019 21:28:55: 4000000 INFO @ Sat, 24 Aug 2019 21:28:57: 10000000 INFO @ Sat, 24 Aug 2019 21:29:04: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:29:04: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:29:04: #1 total tags in treatment: 10979658 INFO @ Sat, 24 Aug 2019 21:29:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:29:04: #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 21:29:04: #1 tags after filtering in treatment: 10979658 INFO @ Sat, 24 Aug 2019 21:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:29:04: #1 finished! INFO @ Sat, 24 Aug 2019 21:29:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:29:05: 5000000 INFO @ Sat, 24 Aug 2019 21:29:05: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:29:05: 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 21:29:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.10_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/SRX5257270/SRX5257270.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:29:13: 6000000 INFO @ Sat, 24 Aug 2019 21:29:22: 7000000 INFO @ Sat, 24 Aug 2019 21:29:31: 8000000 INFO @ Sat, 24 Aug 2019 21:29:40: 9000000 INFO @ Sat, 24 Aug 2019 21:29:49: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:29:58: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:29:58: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:29:58: #1 total tags in treatment: 10979658 INFO @ Sat, 24 Aug 2019 21:29:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:29:58: #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 21:29:58: #1 tags after filtering in treatment: 10979658 INFO @ Sat, 24 Aug 2019 21:29:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:29:58: #1 finished! INFO @ Sat, 24 Aug 2019 21:29:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:29:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:29:59: 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 21:29:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.20_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/SRX5257270/SRX5257270.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257270/SRX5257270.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。