Job ID = 4289336 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:07:55 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 ) 2019-12-10T05:15:50 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 : 28,144,993 reads read : 28,144,993 reads written : 28,144,993 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: 00:05:13 28144993 reads; of these: 28144993 (100.00%) were unpaired; of these: 791234 (2.81%) aligned 0 times 24407517 (86.72%) aligned exactly 1 time 2946242 (10.47%) aligned >1 times 97.19% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 14461246 / 27353759 = 0.5287 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.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 14:32:22: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:32:22: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:32:31: 1000000 INFO @ Tue, 10 Dec 2019 14:32:40: 2000000 INFO @ Tue, 10 Dec 2019 14:32:48: 3000000 INFO @ Tue, 10 Dec 2019 14:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.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 14:32:52: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:32:52: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:32:57: 4000000 INFO @ Tue, 10 Dec 2019 14:33:03: 1000000 INFO @ Tue, 10 Dec 2019 14:33:06: 5000000 INFO @ Tue, 10 Dec 2019 14:33:14: 2000000 INFO @ Tue, 10 Dec 2019 14:33:15: 6000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.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 14:33:22: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:33:22: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:33:24: 7000000 INFO @ Tue, 10 Dec 2019 14:33:24: 3000000 INFO @ Tue, 10 Dec 2019 14:33:32: 1000000 INFO @ Tue, 10 Dec 2019 14:33:33: 8000000 INFO @ Tue, 10 Dec 2019 14:33:36: 4000000 INFO @ Tue, 10 Dec 2019 14:33:41: 2000000 INFO @ Tue, 10 Dec 2019 14:33:42: 9000000 INFO @ Tue, 10 Dec 2019 14:33:48: 5000000 INFO @ Tue, 10 Dec 2019 14:33:50: 10000000 INFO @ Tue, 10 Dec 2019 14:33:51: 3000000 INFO @ Tue, 10 Dec 2019 14:33:59: 11000000 INFO @ Tue, 10 Dec 2019 14:34:00: 6000000 INFO @ Tue, 10 Dec 2019 14:34:00: 4000000 INFO @ Tue, 10 Dec 2019 14:34:08: 12000000 INFO @ Tue, 10 Dec 2019 14:34:09: 5000000 INFO @ Tue, 10 Dec 2019 14:34:11: 7000000 INFO @ Tue, 10 Dec 2019 14:34:16: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:34:16: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:34:16: #1 total tags in treatment: 12892513 INFO @ Tue, 10 Dec 2019 14:34:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:34:16: #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 14:34:16: #1 tags after filtering in treatment: 12892513 INFO @ Tue, 10 Dec 2019 14:34:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:34:16: #1 finished! INFO @ Tue, 10 Dec 2019 14:34:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:34:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:34:17: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:34:17: 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 14:34:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.05_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/SRX6678243/SRX6678243.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:34:18: 6000000 INFO @ Tue, 10 Dec 2019 14:34:23: 8000000 INFO @ Tue, 10 Dec 2019 14:34:27: 7000000 INFO @ Tue, 10 Dec 2019 14:34:35: 9000000 INFO @ Tue, 10 Dec 2019 14:34:36: 8000000 INFO @ Tue, 10 Dec 2019 14:34:45: 9000000 INFO @ Tue, 10 Dec 2019 14:34:46: 10000000 INFO @ Tue, 10 Dec 2019 14:34:54: 10000000 INFO @ Tue, 10 Dec 2019 14:34:58: 11000000 INFO @ Tue, 10 Dec 2019 14:35:03: 11000000 INFO @ Tue, 10 Dec 2019 14:35:09: 12000000 INFO @ Tue, 10 Dec 2019 14:35:12: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:35:19: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:35:19: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:35:19: #1 total tags in treatment: 12892513 INFO @ Tue, 10 Dec 2019 14:35:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:35:19: #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 14:35:19: #1 tags after filtering in treatment: 12892513 INFO @ Tue, 10 Dec 2019 14:35:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:35:19: #1 finished! INFO @ Tue, 10 Dec 2019 14:35:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:35:19: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:35:19: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:35:19: #1 total tags in treatment: 12892513 INFO @ Tue, 10 Dec 2019 14:35:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:35:19: #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 14:35:20: #1 tags after filtering in treatment: 12892513 INFO @ Tue, 10 Dec 2019 14:35:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:35:20: #1 finished! INFO @ Tue, 10 Dec 2019 14:35:20: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:35:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:35:20: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:35:20: 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 14:35:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.10_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/SRX6678243/SRX6678243.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:35:20: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:35:20: 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 14:35:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678243/SRX6678243.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。