Job ID = 4289321 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:01:45 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 ) 2019-12-10T05:02:54 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 : 25,272,067 reads read : 25,272,067 reads written : 25,272,067 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: 00:04:56 25272067 reads; of these: 25272067 (100.00%) were unpaired; of these: 847496 (3.35%) aligned 0 times 21725011 (85.96%) aligned exactly 1 time 2699560 (10.68%) aligned >1 times 96.65% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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] 12800800 / 24424571 = 0.5241 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:21:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.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 14:21:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:21:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:21:33: 1000000 INFO @ Tue, 10 Dec 2019 14:21:42: 2000000 INFO @ Tue, 10 Dec 2019 14:21:50: 3000000 INFO @ Tue, 10 Dec 2019 14:21:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.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 14:21:55: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:21:55: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:21:59: 4000000 INFO @ Tue, 10 Dec 2019 14:22:04: 1000000 INFO @ Tue, 10 Dec 2019 14:22:08: 5000000 INFO @ Tue, 10 Dec 2019 14:22:13: 2000000 INFO @ Tue, 10 Dec 2019 14:22:18: 6000000 INFO @ Tue, 10 Dec 2019 14:22:22: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.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 14:22:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:22:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:22:27: 7000000 INFO @ Tue, 10 Dec 2019 14:22:32: 4000000 INFO @ Tue, 10 Dec 2019 14:22:36: 1000000 INFO @ Tue, 10 Dec 2019 14:22:36: 8000000 INFO @ Tue, 10 Dec 2019 14:22:42: 5000000 INFO @ Tue, 10 Dec 2019 14:22:46: 9000000 INFO @ Tue, 10 Dec 2019 14:22:46: 2000000 INFO @ Tue, 10 Dec 2019 14:22:52: 6000000 INFO @ Tue, 10 Dec 2019 14:22:56: 10000000 INFO @ Tue, 10 Dec 2019 14:22:57: 3000000 INFO @ Tue, 10 Dec 2019 14:23:02: 7000000 INFO @ Tue, 10 Dec 2019 14:23:05: 11000000 INFO @ Tue, 10 Dec 2019 14:23:08: 4000000 INFO @ Tue, 10 Dec 2019 14:23:11: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:23:11: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:23:11: #1 total tags in treatment: 11623771 INFO @ Tue, 10 Dec 2019 14:23:11: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:23:11: #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 14:23:11: #1 tags after filtering in treatment: 11623771 INFO @ Tue, 10 Dec 2019 14:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:23:11: #1 finished! INFO @ Tue, 10 Dec 2019 14:23:11: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:23:12: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:23:12: 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 14:23:12: Process for pairing-model is terminated! INFO @ Tue, 10 Dec 2019 14:23:12: 8000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.05_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/SRX6678237/SRX6678237.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:23:18: 5000000 INFO @ Tue, 10 Dec 2019 14:23:22: 9000000 INFO @ Tue, 10 Dec 2019 14:23:28: 6000000 INFO @ Tue, 10 Dec 2019 14:23:31: 10000000 INFO @ Tue, 10 Dec 2019 14:23:39: 7000000 INFO @ Tue, 10 Dec 2019 14:23:41: 11000000 INFO @ Tue, 10 Dec 2019 14:23:47: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:23:47: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:23:47: #1 total tags in treatment: 11623771 INFO @ Tue, 10 Dec 2019 14:23:47: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:23:47: #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 14:23:47: #1 tags after filtering in treatment: 11623771 INFO @ Tue, 10 Dec 2019 14:23:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:23:47: #1 finished! INFO @ Tue, 10 Dec 2019 14:23:47: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:23:48: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:23:48: 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 14:23:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.10_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/SRX6678237/SRX6678237.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:23:49: 8000000 INFO @ Tue, 10 Dec 2019 14:23:59: 9000000 INFO @ Tue, 10 Dec 2019 14:24:09: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:24:17: 11000000 INFO @ Tue, 10 Dec 2019 14:24:21: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:24:21: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:24:21: #1 total tags in treatment: 11623771 INFO @ Tue, 10 Dec 2019 14:24:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:24:21: #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 14:24:22: #1 tags after filtering in treatment: 11623771 INFO @ Tue, 10 Dec 2019 14:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:24:22: #1 finished! INFO @ Tue, 10 Dec 2019 14:24:22: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:24:22: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:24:22: 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 14:24:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.20_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/SRX6678237/SRX6678237.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678237/SRX6678237.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。