Job ID = 4289493 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:34:38 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 ) 2019-12-10T05:34:38 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 ) 2019-12-10T05:38:10 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 ) 2019-12-10T05:38:11 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 : 29,031,726 reads read : 29,031,726 reads written : 29,031,726 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: 00:06:40 29031726 reads; of these: 29031726 (100.00%) were unpaired; of these: 2357347 (8.12%) aligned 0 times 24345039 (83.86%) aligned exactly 1 time 2329340 (8.02%) aligned >1 times 91.88% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 15296958 / 26674379 = 0.5735 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:56:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.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 14:56:08: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:56:08: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:56:19: 1000000 INFO @ Tue, 10 Dec 2019 14:56:30: 2000000 INFO @ Tue, 10 Dec 2019 14:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.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 14:56:38: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:56:38: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:56:40: 3000000 INFO @ Tue, 10 Dec 2019 14:56:49: 1000000 INFO @ Tue, 10 Dec 2019 14:56:51: 4000000 INFO @ Tue, 10 Dec 2019 14:57:00: 2000000 INFO @ Tue, 10 Dec 2019 14:57:03: 5000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.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 14:57:08: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:57:08: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:57:10: 3000000 INFO @ Tue, 10 Dec 2019 14:57:14: 6000000 INFO @ Tue, 10 Dec 2019 14:57:20: 1000000 INFO @ Tue, 10 Dec 2019 14:57:22: 4000000 INFO @ Tue, 10 Dec 2019 14:57:25: 7000000 INFO @ Tue, 10 Dec 2019 14:57:30: 2000000 INFO @ Tue, 10 Dec 2019 14:57:33: 5000000 INFO @ Tue, 10 Dec 2019 14:57:37: 8000000 INFO @ Tue, 10 Dec 2019 14:57:40: 3000000 INFO @ Tue, 10 Dec 2019 14:57:43: 6000000 INFO @ Tue, 10 Dec 2019 14:57:48: 9000000 INFO @ Tue, 10 Dec 2019 14:57:49: 4000000 INFO @ Tue, 10 Dec 2019 14:57:52: 7000000 INFO @ Tue, 10 Dec 2019 14:57:59: 10000000 INFO @ Tue, 10 Dec 2019 14:58:00: 5000000 INFO @ Tue, 10 Dec 2019 14:58:02: 8000000 INFO @ Tue, 10 Dec 2019 14:58:11: 11000000 INFO @ Tue, 10 Dec 2019 14:58:11: 6000000 INFO @ Tue, 10 Dec 2019 14:58:12: 9000000 INFO @ Tue, 10 Dec 2019 14:58:14: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:58:14: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:58:14: #1 total tags in treatment: 11377421 INFO @ Tue, 10 Dec 2019 14:58:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:58:14: #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 14:58:15: #1 tags after filtering in treatment: 11377421 INFO @ Tue, 10 Dec 2019 14:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:58:15: #1 finished! INFO @ Tue, 10 Dec 2019 14:58:15: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:58:16: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:58:16: 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 @ Tue, 10 Dec 2019 14:58:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.05_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/SRX6678273/SRX6678273.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:58:22: 10000000 INFO @ Tue, 10 Dec 2019 14:58:23: 7000000 INFO @ Tue, 10 Dec 2019 14:58:32: 11000000 INFO @ Tue, 10 Dec 2019 14:58:34: 8000000 INFO @ Tue, 10 Dec 2019 14:58:35: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:58:35: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:58:35: #1 total tags in treatment: 11377421 INFO @ Tue, 10 Dec 2019 14:58:35: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:58:35: #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 14:58:36: #1 tags after filtering in treatment: 11377421 INFO @ Tue, 10 Dec 2019 14:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:58:36: #1 finished! INFO @ Tue, 10 Dec 2019 14:58:36: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:58:36: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:58:36: 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 14:58:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.10_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/SRX6678273/SRX6678273.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:58:45: 9000000 INFO @ Tue, 10 Dec 2019 14:58:56: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:59:08: 11000000 INFO @ Tue, 10 Dec 2019 14:59:12: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:59:12: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:59:12: #1 total tags in treatment: 11377421 INFO @ Tue, 10 Dec 2019 14:59:12: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:59:12: #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 14:59:13: #1 tags after filtering in treatment: 11377421 INFO @ Tue, 10 Dec 2019 14:59:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:59:13: #1 finished! INFO @ Tue, 10 Dec 2019 14:59:13: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:59:14: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:59:14: 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 14:59:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.20_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/SRX6678273/SRX6678273.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678273/SRX6678273.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。