Job ID = 2641085 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:15:49 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 ) 2019-08-24T12:27:00 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 : 68,830,502 reads read : 68,830,502 reads written : 68,830,502 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: 00:00:01 Multiseed full-index search: 00:11:16 68830502 reads; of these: 68830502 (100.00%) were unpaired; of these: 16169918 (23.49%) aligned 0 times 47367113 (68.82%) aligned exactly 1 time 5293471 (7.69%) aligned >1 times 76.51% overall alignment rate Time searching: 00:11:17 Overall time: 00:11:17 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 24 files... [bam_rmdupse_core] 40842601 / 52660584 = 0.7756 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.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 @ Sat, 24 Aug 2019 22:00:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:00:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:00:21: 1000000 INFO @ Sat, 24 Aug 2019 22:00:30: 2000000 INFO @ Sat, 24 Aug 2019 22:00:38: 3000000 INFO @ Sat, 24 Aug 2019 22:00:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.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 @ Sat, 24 Aug 2019 22:00:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:00:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:00:46: 4000000 INFO @ Sat, 24 Aug 2019 22:00:51: 1000000 INFO @ Sat, 24 Aug 2019 22:00:55: 5000000 INFO @ Sat, 24 Aug 2019 22:00:59: 2000000 INFO @ Sat, 24 Aug 2019 22:01:03: 6000000 INFO @ Sat, 24 Aug 2019 22:01:08: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:01:11: 7000000 INFO @ Sat, 24 Aug 2019 22:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.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 @ Sat, 24 Aug 2019 22:01:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:01:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:01:16: 4000000 INFO @ Sat, 24 Aug 2019 22:01:20: 8000000 INFO @ Sat, 24 Aug 2019 22:01:22: 1000000 INFO @ Sat, 24 Aug 2019 22:01:26: 5000000 INFO @ Sat, 24 Aug 2019 22:01:29: 9000000 INFO @ Sat, 24 Aug 2019 22:01:30: 2000000 INFO @ Sat, 24 Aug 2019 22:01:34: 6000000 INFO @ Sat, 24 Aug 2019 22:01:37: 10000000 INFO @ Sat, 24 Aug 2019 22:01:38: 3000000 INFO @ Sat, 24 Aug 2019 22:01:42: 7000000 INFO @ Sat, 24 Aug 2019 22:01:46: 11000000 INFO @ Sat, 24 Aug 2019 22:01:46: 4000000 INFO @ Sat, 24 Aug 2019 22:01:51: 8000000 INFO @ Sat, 24 Aug 2019 22:01:52: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:01:52: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:01:52: #1 total tags in treatment: 11817983 INFO @ Sat, 24 Aug 2019 22:01:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:01:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:01:52: #1 tags after filtering in treatment: 11817983 INFO @ Sat, 24 Aug 2019 22:01:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:01:52: #1 finished! INFO @ Sat, 24 Aug 2019 22:01:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:01:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:01:53: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:01:53: 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 @ Sat, 24 Aug 2019 22:01:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.05_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/SRX5431188/SRX5431188.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:01:54: 5000000 INFO @ Sat, 24 Aug 2019 22:01:59: 9000000 INFO @ Sat, 24 Aug 2019 22:02:02: 6000000 INFO @ Sat, 24 Aug 2019 22:02:07: 10000000 INFO @ Sat, 24 Aug 2019 22:02:09: 7000000 INFO @ Sat, 24 Aug 2019 22:02:15: 11000000 INFO @ Sat, 24 Aug 2019 22:02:16: 8000000 INFO @ Sat, 24 Aug 2019 22:02:22: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:02:22: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:02:22: #1 total tags in treatment: 11817983 INFO @ Sat, 24 Aug 2019 22:02:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:02:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:02:22: #1 tags after filtering in treatment: 11817983 INFO @ Sat, 24 Aug 2019 22:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:02:22: #1 finished! INFO @ Sat, 24 Aug 2019 22:02:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:02:23: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:02:23: 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 @ Sat, 24 Aug 2019 22:02:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.10_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/SRX5431188/SRX5431188.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:02:23: 9000000 INFO @ Sat, 24 Aug 2019 22:02:30: 10000000 INFO @ Sat, 24 Aug 2019 22:02:37: 11000000 INFO @ Sat, 24 Aug 2019 22:02:43: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:02:43: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:02:43: #1 total tags in treatment: 11817983 INFO @ Sat, 24 Aug 2019 22:02:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:02:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:02:43: #1 tags after filtering in treatment: 11817983 INFO @ Sat, 24 Aug 2019 22:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:02:43: #1 finished! INFO @ Sat, 24 Aug 2019 22:02:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:02:44: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:02:44: 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 @ Sat, 24 Aug 2019 22:02:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.20_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/SRX5431188/SRX5431188.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431188/SRX5431188.20_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。