Job ID = 4289256 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:57:04 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 ) 2019-12-10T04:57:04 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 ) 2019-12-10T04:57:04 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 ) 2019-12-10T05:04:24 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 ) spots read : 41,975,509 reads read : 83,951,018 reads written : 41,975,509 reads 0-length : 41,975,509 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: 00:07:12 41975509 reads; of these: 41975509 (100.00%) were unpaired; of these: 1289371 (3.07%) aligned 0 times 32453293 (77.31%) aligned exactly 1 time 8232845 (19.61%) aligned >1 times 96.93% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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 20 files... [bam_rmdupse_core] 24740701 / 40686138 = 0.6081 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:22:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.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 14:22:17: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:22:17: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:22:26: 1000000 INFO @ Tue, 10 Dec 2019 14:22:34: 2000000 INFO @ Tue, 10 Dec 2019 14:22:42: 3000000 INFO @ Tue, 10 Dec 2019 14:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.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 14:22:48: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:22:48: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:22:50: 4000000 INFO @ Tue, 10 Dec 2019 14:22:56: 1000000 INFO @ Tue, 10 Dec 2019 14:22:59: 5000000 INFO @ Tue, 10 Dec 2019 14:23:06: 2000000 INFO @ Tue, 10 Dec 2019 14:23:07: 6000000 INFO @ Tue, 10 Dec 2019 14:23:14: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:23:15: 7000000 INFO @ Tue, 10 Dec 2019 14:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.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 14:23:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:23:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:23:23: 4000000 INFO @ Tue, 10 Dec 2019 14:23:24: 8000000 INFO @ Tue, 10 Dec 2019 14:23:25: 1000000 INFO @ Tue, 10 Dec 2019 14:23:32: 5000000 INFO @ Tue, 10 Dec 2019 14:23:33: 9000000 INFO @ Tue, 10 Dec 2019 14:23:34: 2000000 INFO @ Tue, 10 Dec 2019 14:23:40: 6000000 INFO @ Tue, 10 Dec 2019 14:23:42: 10000000 INFO @ Tue, 10 Dec 2019 14:23:42: 3000000 INFO @ Tue, 10 Dec 2019 14:23:49: 7000000 INFO @ Tue, 10 Dec 2019 14:23:50: 4000000 INFO @ Tue, 10 Dec 2019 14:23:51: 11000000 INFO @ Tue, 10 Dec 2019 14:23:58: 8000000 INFO @ Tue, 10 Dec 2019 14:23:58: 5000000 INFO @ Tue, 10 Dec 2019 14:24:00: 12000000 INFO @ Tue, 10 Dec 2019 14:24:06: 6000000 INFO @ Tue, 10 Dec 2019 14:24:07: 9000000 INFO @ Tue, 10 Dec 2019 14:24:09: 13000000 INFO @ Tue, 10 Dec 2019 14:24:15: 7000000 INFO @ Tue, 10 Dec 2019 14:24:16: 10000000 INFO @ Tue, 10 Dec 2019 14:24:18: 14000000 INFO @ Tue, 10 Dec 2019 14:24:23: 8000000 INFO @ Tue, 10 Dec 2019 14:24:26: 11000000 INFO @ Tue, 10 Dec 2019 14:24:27: 15000000 INFO @ Tue, 10 Dec 2019 14:24:32: 9000000 INFO @ Tue, 10 Dec 2019 14:24:35: 12000000 INFO @ Tue, 10 Dec 2019 14:24:35: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:24:35: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:24:35: #1 total tags in treatment: 15945437 INFO @ Tue, 10 Dec 2019 14:24:35: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:24:35: #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 14:24:36: #1 tags after filtering in treatment: 15945437 INFO @ Tue, 10 Dec 2019 14:24:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:24:36: #1 finished! INFO @ Tue, 10 Dec 2019 14:24:36: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:24:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:24:37: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:24:37: 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 14:24:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.05_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/SRX6635429/SRX6635429.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:24:40: 10000000 INFO @ Tue, 10 Dec 2019 14:24:44: 13000000 INFO @ Tue, 10 Dec 2019 14:24:49: 11000000 INFO @ Tue, 10 Dec 2019 14:24:53: 14000000 INFO @ Tue, 10 Dec 2019 14:24:58: 12000000 INFO @ Tue, 10 Dec 2019 14:25:02: 15000000 INFO @ Tue, 10 Dec 2019 14:25:06: 13000000 INFO @ Tue, 10 Dec 2019 14:25:11: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:25:11: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:25:11: #1 total tags in treatment: 15945437 INFO @ Tue, 10 Dec 2019 14:25:11: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:25:11: #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 14:25:11: #1 tags after filtering in treatment: 15945437 INFO @ Tue, 10 Dec 2019 14:25:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:25:11: #1 finished! INFO @ Tue, 10 Dec 2019 14:25:11: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:25:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:25:13: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:25:13: 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 14:25:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.10_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/SRX6635429/SRX6635429.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:25:15: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:25:24: 15000000 INFO @ Tue, 10 Dec 2019 14:25:32: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:25:32: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:25:32: #1 total tags in treatment: 15945437 INFO @ Tue, 10 Dec 2019 14:25:32: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:25:32: #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 14:25:32: #1 tags after filtering in treatment: 15945437 INFO @ Tue, 10 Dec 2019 14:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:25:32: #1 finished! INFO @ Tue, 10 Dec 2019 14:25:32: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:25:33: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:25:33: 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 14:25:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.20_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/SRX6635429/SRX6635429.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635429/SRX6635429.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。