Job ID = 4289257 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:58:18 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 ) 2019-12-10T04:58:18 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 ) 2019-12-10T04:58:18 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 : 36,549,408 reads read : 73,098,816 reads written : 36,549,408 reads 0-length : 36,549,408 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: 00:06:39 36549408 reads; of these: 36549408 (100.00%) were unpaired; of these: 1804470 (4.94%) aligned 0 times 27475850 (75.17%) aligned exactly 1 time 7269088 (19.89%) aligned >1 times 95.06% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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 16 files... [bam_rmdupse_core] 19991227 / 34744938 = 0.5754 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:20:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.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 14:20:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:20:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:20:10: 1000000 INFO @ Tue, 10 Dec 2019 14:20:18: 2000000 INFO @ Tue, 10 Dec 2019 14:20:26: 3000000 INFO @ Tue, 10 Dec 2019 14:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.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 14:20:32: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:20:32: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:20:32: 4000000 INFO @ Tue, 10 Dec 2019 14:20:39: 5000000 INFO @ Tue, 10 Dec 2019 14:20:40: 1000000 INFO @ Tue, 10 Dec 2019 14:20:46: 6000000 INFO @ Tue, 10 Dec 2019 14:20:47: 2000000 INFO @ Tue, 10 Dec 2019 14:20:53: 7000000 INFO @ Tue, 10 Dec 2019 14:20:55: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:21:00: 8000000 INFO @ Tue, 10 Dec 2019 14:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.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 14:21:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:21:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:21:02: 4000000 INFO @ Tue, 10 Dec 2019 14:21:07: 9000000 INFO @ Tue, 10 Dec 2019 14:21:09: 5000000 INFO @ Tue, 10 Dec 2019 14:21:11: 1000000 INFO @ Tue, 10 Dec 2019 14:21:13: 10000000 INFO @ Tue, 10 Dec 2019 14:21:17: 6000000 INFO @ Tue, 10 Dec 2019 14:21:20: 11000000 INFO @ Tue, 10 Dec 2019 14:21:21: 2000000 INFO @ Tue, 10 Dec 2019 14:21:25: 7000000 INFO @ Tue, 10 Dec 2019 14:21:27: 12000000 INFO @ Tue, 10 Dec 2019 14:21:31: 3000000 INFO @ Tue, 10 Dec 2019 14:21:32: 8000000 INFO @ Tue, 10 Dec 2019 14:21:34: 13000000 INFO @ Tue, 10 Dec 2019 14:21:40: 9000000 INFO @ Tue, 10 Dec 2019 14:21:41: 4000000 INFO @ Tue, 10 Dec 2019 14:21:42: 14000000 INFO @ Tue, 10 Dec 2019 14:21:47: 10000000 INFO @ Tue, 10 Dec 2019 14:21:47: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:21:47: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:21:47: #1 total tags in treatment: 14753711 INFO @ Tue, 10 Dec 2019 14:21:47: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:21:47: #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 14:21:47: #1 tags after filtering in treatment: 14753711 INFO @ Tue, 10 Dec 2019 14:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:21:47: #1 finished! INFO @ Tue, 10 Dec 2019 14:21:47: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:21:49: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:21:49: 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 14:21:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.05_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/SRX6635430/SRX6635430.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:21:50: 5000000 INFO @ Tue, 10 Dec 2019 14:21:54: 11000000 INFO @ Tue, 10 Dec 2019 14:22:00: 6000000 INFO @ Tue, 10 Dec 2019 14:22:01: 12000000 INFO @ Tue, 10 Dec 2019 14:22:09: 13000000 INFO @ Tue, 10 Dec 2019 14:22:10: 7000000 INFO @ Tue, 10 Dec 2019 14:22:16: 14000000 INFO @ Tue, 10 Dec 2019 14:22:19: 8000000 INFO @ Tue, 10 Dec 2019 14:22:22: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:22:22: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:22:22: #1 total tags in treatment: 14753711 INFO @ Tue, 10 Dec 2019 14:22:22: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:22:22: #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 14:22:22: #1 tags after filtering in treatment: 14753711 INFO @ Tue, 10 Dec 2019 14:22:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:22:22: #1 finished! INFO @ Tue, 10 Dec 2019 14:22:22: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:22:23: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:22:23: 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 14:22:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.10_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/SRX6635430/SRX6635430.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:22:28: 9000000 INFO @ Tue, 10 Dec 2019 14:22:36: 10000000 INFO @ Tue, 10 Dec 2019 14:22:45: 11000000 INFO @ Tue, 10 Dec 2019 14:22:53: 12000000 INFO @ Tue, 10 Dec 2019 14:23:02: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:23:10: 14000000 INFO @ Tue, 10 Dec 2019 14:23:17: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:23:17: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:23:17: #1 total tags in treatment: 14753711 INFO @ Tue, 10 Dec 2019 14:23:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:23:17: #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 14:23:17: #1 tags after filtering in treatment: 14753711 INFO @ Tue, 10 Dec 2019 14:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:23:17: #1 finished! INFO @ Tue, 10 Dec 2019 14:23:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:23:17: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:23:18: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:23:18: 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 14:23:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.20_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/SRX6635430/SRX6635430.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635430/SRX6635430.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling