Job ID = 4289456 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 ) spots read : 27,918,505 reads read : 27,918,505 reads written : 27,918,505 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: 00:03:46 27918505 reads; of these: 27918505 (100.00%) were unpaired; of these: 4304378 (15.42%) aligned 0 times 21311229 (76.33%) aligned exactly 1 time 2302898 (8.25%) aligned >1 times 84.58% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 13464939 / 23614127 = 0.5702 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.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 14:50:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:50:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:50:08: 1000000 INFO @ Tue, 10 Dec 2019 14:50:13: 2000000 INFO @ Tue, 10 Dec 2019 14:50:18: 3000000 INFO @ Tue, 10 Dec 2019 14:50:24: 4000000 INFO @ Tue, 10 Dec 2019 14:50:29: 5000000 INFO @ Tue, 10 Dec 2019 14:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.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 14:50:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:50:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:50:35: 6000000 INFO @ Tue, 10 Dec 2019 14:50:37: 1000000 INFO @ Tue, 10 Dec 2019 14:50:41: 7000000 INFO @ Tue, 10 Dec 2019 14:50:43: 2000000 INFO @ Tue, 10 Dec 2019 14:50:47: 8000000 INFO @ Tue, 10 Dec 2019 14:50:48: 3000000 INFO @ Tue, 10 Dec 2019 14:50:52: 9000000 INFO @ Tue, 10 Dec 2019 14:50:54: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:50:59: 10000000 INFO @ Tue, 10 Dec 2019 14:51:00: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:51:00: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:51:00: #1 total tags in treatment: 10149188 INFO @ Tue, 10 Dec 2019 14:51:00: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:51:00: #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 14:51:00: #1 tags after filtering in treatment: 10149188 INFO @ Tue, 10 Dec 2019 14:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:51:00: #1 finished! INFO @ Tue, 10 Dec 2019 14:51:00: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:51:01: 5000000 INFO @ Tue, 10 Dec 2019 14:51:01: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:51:01: 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 14:51:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.05_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/SRX6678265/SRX6678265.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:51:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.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 14:51:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:51:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:51:08: 6000000 INFO @ Tue, 10 Dec 2019 14:51:09: 1000000 INFO @ Tue, 10 Dec 2019 14:51:15: 7000000 INFO @ Tue, 10 Dec 2019 14:51:17: 2000000 INFO @ Tue, 10 Dec 2019 14:51:21: 8000000 INFO @ Tue, 10 Dec 2019 14:51:24: 3000000 INFO @ Tue, 10 Dec 2019 14:51:28: 9000000 INFO @ Tue, 10 Dec 2019 14:51:33: 4000000 INFO @ Tue, 10 Dec 2019 14:51:35: 10000000 INFO @ Tue, 10 Dec 2019 14:51:36: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:51:36: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:51:36: #1 total tags in treatment: 10149188 INFO @ Tue, 10 Dec 2019 14:51:36: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:51:36: #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 14:51:36: #1 tags after filtering in treatment: 10149188 INFO @ Tue, 10 Dec 2019 14:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:51:36: #1 finished! INFO @ Tue, 10 Dec 2019 14:51:36: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:51:37: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:51:37: 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 14:51:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.10_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/SRX6678265/SRX6678265.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:51:41: 5000000 INFO @ Tue, 10 Dec 2019 14:51:47: 6000000 INFO @ Tue, 10 Dec 2019 14:51:54: 7000000 INFO @ Tue, 10 Dec 2019 14:51:59: 8000000 INFO @ Tue, 10 Dec 2019 14:52:04: 9000000 INFO @ Tue, 10 Dec 2019 14:52:10: 10000000 INFO @ Tue, 10 Dec 2019 14:52:10: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:52:10: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:52:10: #1 total tags in treatment: 10149188 INFO @ Tue, 10 Dec 2019 14:52:10: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:52:10: #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 14:52:11: #1 tags after filtering in treatment: 10149188 INFO @ Tue, 10 Dec 2019 14:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:52:11: #1 finished! INFO @ Tue, 10 Dec 2019 14:52:11: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:52:11: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:52:11: 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 14:52:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678265/SRX6678265.20_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。