Job ID = 2641021 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T11:31:34 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 ) 2019-08-24T11:31:34 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 ) 2019-08-24T11:31:57 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 ) 2019-08-24T11:31:57 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 : 19,070,456 reads read : 19,070,456 reads written : 19,070,456 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: 00:00:01 Multiseed full-index search: 00:03:36 19070456 reads; of these: 19070456 (100.00%) were unpaired; of these: 1172280 (6.15%) aligned 0 times 15987818 (83.84%) aligned exactly 1 time 1910358 (10.02%) aligned >1 times 93.85% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 8729899 / 17898176 = 0.4878 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.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 20:47:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:47:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:47:49: 1000000 INFO @ Sat, 24 Aug 2019 20:47:56: 2000000 INFO @ Sat, 24 Aug 2019 20:48:03: 3000000 INFO @ Sat, 24 Aug 2019 20:48:10: 4000000 INFO @ Sat, 24 Aug 2019 20:48:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.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 20:48:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:48:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:48:17: 5000000 INFO @ Sat, 24 Aug 2019 20:48:18: 1000000 INFO @ Sat, 24 Aug 2019 20:48:24: 6000000 INFO @ Sat, 24 Aug 2019 20:48:25: 2000000 INFO @ Sat, 24 Aug 2019 20:48:31: 7000000 INFO @ Sat, 24 Aug 2019 20:48:32: 3000000 INFO @ Sat, 24 Aug 2019 20:48:38: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:48:39: 4000000 INFO @ Sat, 24 Aug 2019 20:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.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 20:48:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:48:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:48:45: 9000000 INFO @ Sat, 24 Aug 2019 20:48:46: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 20:48:46: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 20:48:46: #1 total tags in treatment: 9168277 INFO @ Sat, 24 Aug 2019 20:48:46: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:48:46: #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 20:48:46: #1 tags after filtering in treatment: 9168277 INFO @ Sat, 24 Aug 2019 20:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:48:46: #1 finished! INFO @ Sat, 24 Aug 2019 20:48:46: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:48:46: 5000000 INFO @ Sat, 24 Aug 2019 20:48:47: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:48:47: 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 20:48:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.05_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/SRX5257218/SRX5257218.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:48:49: 1000000 INFO @ Sat, 24 Aug 2019 20:48:53: 6000000 INFO @ Sat, 24 Aug 2019 20:48:57: 2000000 INFO @ Sat, 24 Aug 2019 20:49:00: 7000000 INFO @ Sat, 24 Aug 2019 20:49:05: 3000000 INFO @ Sat, 24 Aug 2019 20:49:07: 8000000 INFO @ Sat, 24 Aug 2019 20:49:13: 4000000 INFO @ Sat, 24 Aug 2019 20:49:14: 9000000 INFO @ Sat, 24 Aug 2019 20:49:16: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 20:49:16: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 20:49:16: #1 total tags in treatment: 9168277 INFO @ Sat, 24 Aug 2019 20:49:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:49:16: #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 20:49:16: #1 tags after filtering in treatment: 9168277 INFO @ Sat, 24 Aug 2019 20:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:49:16: #1 finished! INFO @ Sat, 24 Aug 2019 20:49:16: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:49:16: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:49:16: 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 @ Sat, 24 Aug 2019 20:49:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.10_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/SRX5257218/SRX5257218.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:49:21: 5000000 INFO @ Sat, 24 Aug 2019 20:49:28: 6000000 INFO @ Sat, 24 Aug 2019 20:49:36: 7000000 INFO @ Sat, 24 Aug 2019 20:49:44: 8000000 INFO @ Sat, 24 Aug 2019 20:49:51: 9000000 INFO @ Sat, 24 Aug 2019 20:49:53: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 20:49:53: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 20:49:53: #1 total tags in treatment: 9168277 INFO @ Sat, 24 Aug 2019 20:49:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:49:53: #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 20:49:53: #1 tags after filtering in treatment: 9168277 INFO @ Sat, 24 Aug 2019 20:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:49:53: #1 finished! INFO @ Sat, 24 Aug 2019 20:49:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:49:54: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:49:54: 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 20:49:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.20_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/SRX5257218/SRX5257218.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257218/SRX5257218.20_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。