Job ID = 4289293 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:03:54 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 ) 2019-12-10T05:05:49 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 ) 2019-12-10T05:10:29 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 : 36,251,976 reads read : 72,503,952 reads written : 36,251,976 reads 0-length : 36,251,976 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: 00:06:47 36251976 reads; of these: 36251976 (100.00%) were unpaired; of these: 943217 (2.60%) aligned 0 times 30739459 (84.79%) aligned exactly 1 time 4569300 (12.60%) aligned >1 times 97.40% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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] 19484221 / 35308759 = 0.5518 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.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 14:28:06: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:28:06: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:28:13: 1000000 INFO @ Tue, 10 Dec 2019 14:28:20: 2000000 INFO @ Tue, 10 Dec 2019 14:28:27: 3000000 INFO @ Tue, 10 Dec 2019 14:28:33: 4000000 INFO @ Tue, 10 Dec 2019 14:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.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 14:28:36: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:28:36: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:28:40: 5000000 INFO @ Tue, 10 Dec 2019 14:28:43: 1000000 INFO @ Tue, 10 Dec 2019 14:28:47: 6000000 INFO @ Tue, 10 Dec 2019 14:28:50: 2000000 INFO @ Tue, 10 Dec 2019 14:28:54: 7000000 INFO @ Tue, 10 Dec 2019 14:28:57: 3000000 INFO @ Tue, 10 Dec 2019 14:29:01: 8000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:29:04: 4000000 INFO @ Tue, 10 Dec 2019 14:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.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 14:29:06: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:29:06: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:29:08: 9000000 INFO @ Tue, 10 Dec 2019 14:29:11: 5000000 INFO @ Tue, 10 Dec 2019 14:29:15: 1000000 INFO @ Tue, 10 Dec 2019 14:29:16: 10000000 INFO @ Tue, 10 Dec 2019 14:29:18: 6000000 INFO @ Tue, 10 Dec 2019 14:29:23: 11000000 INFO @ Tue, 10 Dec 2019 14:29:24: 2000000 INFO @ Tue, 10 Dec 2019 14:29:26: 7000000 INFO @ Tue, 10 Dec 2019 14:29:30: 12000000 INFO @ Tue, 10 Dec 2019 14:29:33: 8000000 INFO @ Tue, 10 Dec 2019 14:29:33: 3000000 INFO @ Tue, 10 Dec 2019 14:29:38: 13000000 INFO @ Tue, 10 Dec 2019 14:29:40: 9000000 INFO @ Tue, 10 Dec 2019 14:29:42: 4000000 INFO @ Tue, 10 Dec 2019 14:29:45: 14000000 INFO @ Tue, 10 Dec 2019 14:29:48: 10000000 INFO @ Tue, 10 Dec 2019 14:29:51: 5000000 INFO @ Tue, 10 Dec 2019 14:29:52: 15000000 INFO @ Tue, 10 Dec 2019 14:29:55: 11000000 INFO @ Tue, 10 Dec 2019 14:29:58: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:29:58: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:29:58: #1 total tags in treatment: 15824538 INFO @ Tue, 10 Dec 2019 14:29:58: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:29:58: #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 14:29:59: #1 tags after filtering in treatment: 15824538 INFO @ Tue, 10 Dec 2019 14:29:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:29:59: #1 finished! INFO @ Tue, 10 Dec 2019 14:29:59: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:29:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:29:59: 6000000 INFO @ Tue, 10 Dec 2019 14:30:00: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:30:00: 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 14:30:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.05_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/SRX6635441/SRX6635441.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:30:02: 12000000 INFO @ Tue, 10 Dec 2019 14:30:08: 7000000 INFO @ Tue, 10 Dec 2019 14:30:09: 13000000 INFO @ Tue, 10 Dec 2019 14:30:17: 14000000 INFO @ Tue, 10 Dec 2019 14:30:17: 8000000 INFO @ Tue, 10 Dec 2019 14:30:24: 15000000 INFO @ Tue, 10 Dec 2019 14:30:26: 9000000 INFO @ Tue, 10 Dec 2019 14:30:30: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:30:30: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:30:30: #1 total tags in treatment: 15824538 INFO @ Tue, 10 Dec 2019 14:30:30: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:30:30: #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 14:30:30: #1 tags after filtering in treatment: 15824538 INFO @ Tue, 10 Dec 2019 14:30:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:30:30: #1 finished! INFO @ Tue, 10 Dec 2019 14:30:30: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:30:31: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:30:31: 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 14:30:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.10_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/SRX6635441/SRX6635441.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:30:35: 10000000 INFO @ Tue, 10 Dec 2019 14:30:44: 11000000 INFO @ Tue, 10 Dec 2019 14:30:53: 12000000 INFO @ Tue, 10 Dec 2019 14:31:01: 13000000 INFO @ Tue, 10 Dec 2019 14:31:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:31:19: 15000000 INFO @ Tue, 10 Dec 2019 14:31:27: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:31:27: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:31:27: #1 total tags in treatment: 15824538 INFO @ Tue, 10 Dec 2019 14:31:27: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:31:27: #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 14:31:27: #1 tags after filtering in treatment: 15824538 INFO @ Tue, 10 Dec 2019 14:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:31:27: #1 finished! INFO @ Tue, 10 Dec 2019 14:31:27: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:31:28: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:31:28: 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 14:31:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.20_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/SRX6635441/SRX6635441.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635441/SRX6635441.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。