Job ID = 4289324 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:10:02 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 ) 2019-12-10T05:10:02 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 : 24,146,315 reads read : 24,146,315 reads written : 24,146,315 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: 00:04:01 24146315 reads; of these: 24146315 (100.00%) were unpaired; of these: 4051330 (16.78%) aligned 0 times 18215999 (75.44%) aligned exactly 1 time 1878986 (7.78%) aligned >1 times 83.22% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 12188498 / 20094985 = 0.6065 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:22:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.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 14:22:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:22:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:22:42: 1000000 INFO @ Tue, 10 Dec 2019 14:22:51: 2000000 INFO @ Tue, 10 Dec 2019 14:22:59: 3000000 INFO @ Tue, 10 Dec 2019 14:23:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.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 14:23:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:23:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:23:08: 4000000 INFO @ Tue, 10 Dec 2019 14:23:13: 1000000 INFO @ Tue, 10 Dec 2019 14:23:16: 5000000 INFO @ Tue, 10 Dec 2019 14:23:22: 2000000 INFO @ Tue, 10 Dec 2019 14:23:25: 6000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:23:31: 3000000 INFO @ Tue, 10 Dec 2019 14:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.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 14:23:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:23:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:23:34: 7000000 INFO @ Tue, 10 Dec 2019 14:23:41: 4000000 INFO @ Tue, 10 Dec 2019 14:23:42: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:23:42: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:23:42: #1 total tags in treatment: 7906487 INFO @ Tue, 10 Dec 2019 14:23:42: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:23:42: #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 14:23:42: #1 tags after filtering in treatment: 7906487 INFO @ Tue, 10 Dec 2019 14:23:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:23:42: #1 finished! INFO @ Tue, 10 Dec 2019 14:23:42: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:23:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:23:43: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:23:43: 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 14:23:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.05_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/SRX6678240/SRX6678240.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:23:45: 1000000 INFO @ Tue, 10 Dec 2019 14:23:51: 5000000 INFO @ Tue, 10 Dec 2019 14:23:56: 2000000 INFO @ Tue, 10 Dec 2019 14:24:00: 6000000 INFO @ Tue, 10 Dec 2019 14:24:08: 3000000 INFO @ Tue, 10 Dec 2019 14:24:09: 7000000 INFO @ Tue, 10 Dec 2019 14:24:18: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:24:18: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:24:18: #1 total tags in treatment: 7906487 INFO @ Tue, 10 Dec 2019 14:24:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:24:18: #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 14:24:18: #1 tags after filtering in treatment: 7906487 INFO @ Tue, 10 Dec 2019 14:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:24:18: #1 finished! INFO @ Tue, 10 Dec 2019 14:24:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:24:18: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:24:18: 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 14:24:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.10_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/SRX6678240/SRX6678240.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:24:19: 4000000 INFO @ Tue, 10 Dec 2019 14:24:30: 5000000 INFO @ Tue, 10 Dec 2019 14:24:40: 6000000 INFO @ Tue, 10 Dec 2019 14:24:51: 7000000 INFO @ Tue, 10 Dec 2019 14:25:00: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:25:00: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:25:00: #1 total tags in treatment: 7906487 INFO @ Tue, 10 Dec 2019 14:25:00: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:25:00: #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 14:25:01: #1 tags after filtering in treatment: 7906487 INFO @ Tue, 10 Dec 2019 14:25:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:25:01: #1 finished! INFO @ Tue, 10 Dec 2019 14:25:01: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:25:01: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:25:01: 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 14:25:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.20_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/SRX6678240/SRX6678240.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678240/SRX6678240.20_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。