Job ID = 4289342 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 ) 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 ) 2019-12-10T05:16:16 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 ) 2019-12-10T05:16:22 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 ) 2019-12-10T05:16:58 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 ) 2019-12-10T05:21:34 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 ) spots read : 24,970,493 reads read : 24,970,493 reads written : 24,970,493 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: 00:05:13 24970493 reads; of these: 24970493 (100.00%) were unpaired; of these: 888294 (3.56%) aligned 0 times 21733625 (87.04%) aligned exactly 1 time 2348574 (9.41%) aligned >1 times 96.44% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 12027275 / 24082199 = 0.4994 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:33:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.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 14:33:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:33:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:34:05: 1000000 INFO @ Tue, 10 Dec 2019 14:34:12: 2000000 INFO @ Tue, 10 Dec 2019 14:34:18: 3000000 INFO @ Tue, 10 Dec 2019 14:34:25: 4000000 INFO @ Tue, 10 Dec 2019 14:34:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.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 14:34:29: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:34:29: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:34:32: 5000000 INFO @ Tue, 10 Dec 2019 14:34:35: 1000000 INFO @ Tue, 10 Dec 2019 14:34:38: 6000000 INFO @ Tue, 10 Dec 2019 14:34:42: 2000000 INFO @ Tue, 10 Dec 2019 14:34:45: 7000000 INFO @ Tue, 10 Dec 2019 14:34:48: 3000000 INFO @ Tue, 10 Dec 2019 14:34:51: 8000000 INFO @ Tue, 10 Dec 2019 14:34:55: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:34:58: 9000000 INFO @ Tue, 10 Dec 2019 14:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.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 14:34:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:34:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:35:01: 5000000 INFO @ Tue, 10 Dec 2019 14:35:05: 10000000 INFO @ Tue, 10 Dec 2019 14:35:06: 1000000 INFO @ Tue, 10 Dec 2019 14:35:08: 6000000 INFO @ Tue, 10 Dec 2019 14:35:11: 11000000 INFO @ Tue, 10 Dec 2019 14:35:14: 2000000 INFO @ Tue, 10 Dec 2019 14:35:15: 7000000 INFO @ Tue, 10 Dec 2019 14:35:18: 12000000 INFO @ Tue, 10 Dec 2019 14:35:18: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:35:18: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:35:18: #1 total tags in treatment: 12054924 INFO @ Tue, 10 Dec 2019 14:35:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:35:18: #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 14:35:19: #1 tags after filtering in treatment: 12054924 INFO @ Tue, 10 Dec 2019 14:35:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:35:19: #1 finished! INFO @ Tue, 10 Dec 2019 14:35:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:35:20: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:35:20: 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 14:35:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.05_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/SRX6678245/SRX6678245.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:35:21: 8000000 INFO @ Tue, 10 Dec 2019 14:35:21: 3000000 INFO @ Tue, 10 Dec 2019 14:35:28: 9000000 INFO @ Tue, 10 Dec 2019 14:35:28: 4000000 INFO @ Tue, 10 Dec 2019 14:35:34: 10000000 INFO @ Tue, 10 Dec 2019 14:35:36: 5000000 INFO @ Tue, 10 Dec 2019 14:35:41: 11000000 INFO @ Tue, 10 Dec 2019 14:35:43: 6000000 INFO @ Tue, 10 Dec 2019 14:35:47: 12000000 INFO @ Tue, 10 Dec 2019 14:35:48: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:35:48: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:35:48: #1 total tags in treatment: 12054924 INFO @ Tue, 10 Dec 2019 14:35:48: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:35:48: #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 14:35:48: #1 tags after filtering in treatment: 12054924 INFO @ Tue, 10 Dec 2019 14:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:35:48: #1 finished! INFO @ Tue, 10 Dec 2019 14:35:48: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:35:49: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:35:49: 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 14:35:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.10_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/SRX6678245/SRX6678245.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:35:50: 7000000 INFO @ Tue, 10 Dec 2019 14:35:57: 8000000 INFO @ Tue, 10 Dec 2019 14:36:05: 9000000 INFO @ Tue, 10 Dec 2019 14:36:12: 10000000 INFO @ Tue, 10 Dec 2019 14:36:19: 11000000 INFO @ Tue, 10 Dec 2019 14:36:26: 12000000 INFO @ Tue, 10 Dec 2019 14:36:27: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:36:27: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:36:27: #1 total tags in treatment: 12054924 INFO @ Tue, 10 Dec 2019 14:36:27: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:36:27: #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 14:36:27: #1 tags after filtering in treatment: 12054924 INFO @ Tue, 10 Dec 2019 14:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:36:27: #1 finished! INFO @ Tue, 10 Dec 2019 14:36:27: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:36:28: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:36:28: 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 14:36:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.20_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/SRX6678245/SRX6678245.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678245/SRX6678245.20_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。