Job ID = 4289453 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:27:47 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 ) 2019-12-10T05:27:47 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 ) 2019-12-10T05:32:16 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 ) 2019-12-10T05:47:42 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 ) 2019-12-10T06:00:43 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 ) 2019-12-10T06:04:54 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 ) spots read : 98,563,648 reads read : 98,563,648 reads written : 98,563,648 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: 00:18:58 98563648 reads; of these: 98563648 (100.00%) were unpaired; of these: 11947107 (12.12%) aligned 0 times 78909308 (80.06%) aligned exactly 1 time 7707233 (7.82%) aligned >1 times 87.88% overall alignment rate Time searching: 00:18:58 Overall time: 00:18:58 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 36 files... [bam_rmdupse_core] 68424858 / 86616541 = 0.7900 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 15:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.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 15:45:00: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:45:00: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:45:08: 1000000 INFO @ Tue, 10 Dec 2019 15:45:16: 2000000 INFO @ Tue, 10 Dec 2019 15:45:24: 3000000 INFO @ Tue, 10 Dec 2019 15:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.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 15:45:29: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:45:29: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:45:31: 4000000 INFO @ Tue, 10 Dec 2019 15:45:36: 1000000 INFO @ Tue, 10 Dec 2019 15:45:39: 5000000 INFO @ Tue, 10 Dec 2019 15:45:43: 2000000 INFO @ Tue, 10 Dec 2019 15:45:47: 6000000 INFO @ Tue, 10 Dec 2019 15:45:50: 3000000 INFO @ Tue, 10 Dec 2019 15:45:54: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 15:45:57: 4000000 INFO @ Tue, 10 Dec 2019 15:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.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 15:45:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:45:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:46:02: 8000000 INFO @ Tue, 10 Dec 2019 15:46:04: 5000000 INFO @ Tue, 10 Dec 2019 15:46:06: 1000000 INFO @ Tue, 10 Dec 2019 15:46:10: 9000000 INFO @ Tue, 10 Dec 2019 15:46:11: 6000000 INFO @ Tue, 10 Dec 2019 15:46:13: 2000000 INFO @ Tue, 10 Dec 2019 15:46:18: 7000000 INFO @ Tue, 10 Dec 2019 15:46:18: 10000000 INFO @ Tue, 10 Dec 2019 15:46:20: 3000000 INFO @ Tue, 10 Dec 2019 15:46:25: 8000000 INFO @ Tue, 10 Dec 2019 15:46:26: 11000000 INFO @ Tue, 10 Dec 2019 15:46:27: 4000000 INFO @ Tue, 10 Dec 2019 15:46:32: 9000000 INFO @ Tue, 10 Dec 2019 15:46:34: 12000000 INFO @ Tue, 10 Dec 2019 15:46:34: 5000000 INFO @ Tue, 10 Dec 2019 15:46:39: 10000000 INFO @ Tue, 10 Dec 2019 15:46:41: 13000000 INFO @ Tue, 10 Dec 2019 15:46:41: 6000000 INFO @ Tue, 10 Dec 2019 15:46:46: 11000000 INFO @ Tue, 10 Dec 2019 15:46:48: 7000000 INFO @ Tue, 10 Dec 2019 15:46:49: 14000000 INFO @ Tue, 10 Dec 2019 15:46:53: 12000000 INFO @ Tue, 10 Dec 2019 15:46:55: 8000000 INFO @ Tue, 10 Dec 2019 15:46:57: 15000000 INFO @ Tue, 10 Dec 2019 15:47:00: 13000000 INFO @ Tue, 10 Dec 2019 15:47:02: 9000000 INFO @ Tue, 10 Dec 2019 15:47:05: 16000000 INFO @ Tue, 10 Dec 2019 15:47:07: 14000000 INFO @ Tue, 10 Dec 2019 15:47:09: 10000000 INFO @ Tue, 10 Dec 2019 15:47:13: 17000000 INFO @ Tue, 10 Dec 2019 15:47:14: 15000000 INFO @ Tue, 10 Dec 2019 15:47:17: 11000000 INFO @ Tue, 10 Dec 2019 15:47:21: 18000000 INFO @ Tue, 10 Dec 2019 15:47:21: 16000000 INFO @ Tue, 10 Dec 2019 15:47:22: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 15:47:22: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 15:47:22: #1 total tags in treatment: 18191683 INFO @ Tue, 10 Dec 2019 15:47:22: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:47:22: #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 15:47:23: #1 tags after filtering in treatment: 18191683 INFO @ Tue, 10 Dec 2019 15:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:47:23: #1 finished! INFO @ Tue, 10 Dec 2019 15:47:23: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:47:24: 12000000 INFO @ Tue, 10 Dec 2019 15:47:24: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:47:24: 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 15:47:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.05_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/SRX6678264/SRX6678264.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:47:28: 17000000 INFO @ Tue, 10 Dec 2019 15:47:31: 13000000 INFO @ Tue, 10 Dec 2019 15:47:35: 18000000 INFO @ Tue, 10 Dec 2019 15:47:36: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 15:47:36: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 15:47:36: #1 total tags in treatment: 18191683 INFO @ Tue, 10 Dec 2019 15:47:36: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:47:36: #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 15:47:36: #1 tags after filtering in treatment: 18191683 INFO @ Tue, 10 Dec 2019 15:47:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:47:36: #1 finished! INFO @ Tue, 10 Dec 2019 15:47:36: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:47:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:47:37: 14000000 INFO @ Tue, 10 Dec 2019 15:47:38: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:47:38: 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 15:47:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.10_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/SRX6678264/SRX6678264.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:47:44: 15000000 INFO @ Tue, 10 Dec 2019 15:47:51: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 15:47:58: 17000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 15:48:05: 18000000 INFO @ Tue, 10 Dec 2019 15:48:06: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 15:48:06: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 15:48:06: #1 total tags in treatment: 18191683 INFO @ Tue, 10 Dec 2019 15:48:06: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:48:06: #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 15:48:07: #1 tags after filtering in treatment: 18191683 INFO @ Tue, 10 Dec 2019 15:48:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:48:07: #1 finished! INFO @ Tue, 10 Dec 2019 15:48:07: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:48:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:48:08: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:48:08: 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 15:48:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.20_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/SRX6678264/SRX6678264.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678264/SRX6678264.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling