Job ID = 4289477 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:34:37 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 ) 2019-12-10T05:36:09 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 ) 2019-12-10T05:38:14 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 ) 2019-12-10T05:38:14 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 ) 2019-12-10T05:38:14 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 ) 2019-12-10T05:38:14 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 : 30,040,736 reads read : 30,040,736 reads written : 30,040,736 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: 00:05:15 30040736 reads; of these: 30040736 (100.00%) were unpaired; of these: 2532545 (8.43%) aligned 0 times 24784796 (82.50%) aligned exactly 1 time 2723395 (9.07%) aligned >1 times 91.57% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 19688335 / 27508191 = 0.7157 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:52:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.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 14:52:15: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:52:15: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:52:22: 1000000 INFO @ Tue, 10 Dec 2019 14:52:30: 2000000 INFO @ Tue, 10 Dec 2019 14:52:38: 3000000 INFO @ Tue, 10 Dec 2019 14:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.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 14:52:44: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:52:44: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:52:46: 4000000 INFO @ Tue, 10 Dec 2019 14:52:54: 5000000 INFO @ Tue, 10 Dec 2019 14:52:54: 1000000 INFO @ Tue, 10 Dec 2019 14:53:02: 6000000 INFO @ Tue, 10 Dec 2019 14:53:04: 2000000 INFO @ Tue, 10 Dec 2019 14:53:10: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:53:14: 3000000 INFO @ Tue, 10 Dec 2019 14:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.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 14:53:14: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:53:14: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:53:17: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:53:17: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:53:17: #1 total tags in treatment: 7819856 INFO @ Tue, 10 Dec 2019 14:53:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:53:17: #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 14:53:17: #1 tags after filtering in treatment: 7819856 INFO @ Tue, 10 Dec 2019 14:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:53:17: #1 finished! INFO @ Tue, 10 Dec 2019 14:53:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:53:17: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:53:17: 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 14:53:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.05_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/SRX6678271/SRX6678271.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:53:23: 4000000 INFO @ Tue, 10 Dec 2019 14:53:24: 1000000 INFO @ Tue, 10 Dec 2019 14:53:33: 5000000 INFO @ Tue, 10 Dec 2019 14:53:35: 2000000 INFO @ Tue, 10 Dec 2019 14:53:43: 6000000 INFO @ Tue, 10 Dec 2019 14:53:45: 3000000 INFO @ Tue, 10 Dec 2019 14:53:53: 7000000 INFO @ Tue, 10 Dec 2019 14:53:55: 4000000 INFO @ Tue, 10 Dec 2019 14:54:01: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:54:01: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:54:01: #1 total tags in treatment: 7819856 INFO @ Tue, 10 Dec 2019 14:54:01: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:54:01: #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 14:54:01: #1 tags after filtering in treatment: 7819856 INFO @ Tue, 10 Dec 2019 14:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:54:01: #1 finished! INFO @ Tue, 10 Dec 2019 14:54:01: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:54:02: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:54:02: 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 14:54:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.10_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/SRX6678271/SRX6678271.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:54:05: 5000000 INFO @ Tue, 10 Dec 2019 14:54:14: 6000000 INFO @ Tue, 10 Dec 2019 14:54:23: 7000000 INFO @ Tue, 10 Dec 2019 14:54:30: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:54:30: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:54:30: #1 total tags in treatment: 7819856 INFO @ Tue, 10 Dec 2019 14:54:30: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:54:30: #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 14:54:30: #1 tags after filtering in treatment: 7819856 INFO @ Tue, 10 Dec 2019 14:54:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:54:30: #1 finished! INFO @ Tue, 10 Dec 2019 14:54:30: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:54:31: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:54:31: 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 14:54:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.20_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/SRX6678271/SRX6678271.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678271/SRX6678271.20_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。