Job ID = 4289355 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:34:21 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 : 22,431,504 reads read : 22,431,504 reads written : 22,431,504 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: 00:03:55 22431504 reads; of these: 22431504 (100.00%) were unpaired; of these: 971223 (4.33%) aligned 0 times 19229947 (85.73%) aligned exactly 1 time 2230334 (9.94%) aligned >1 times 95.67% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 14208926 / 21460281 = 0.6621 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.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 14:45:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:45:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:45:57: 1000000 INFO @ Tue, 10 Dec 2019 14:46:06: 2000000 INFO @ Tue, 10 Dec 2019 14:46:14: 3000000 INFO @ Tue, 10 Dec 2019 14:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.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 14:46:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:46:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:46:22: 4000000 INFO @ Tue, 10 Dec 2019 14:46:31: 1000000 INFO @ Tue, 10 Dec 2019 14:46:31: 5000000 INFO @ Tue, 10 Dec 2019 14:46:40: 6000000 INFO @ Tue, 10 Dec 2019 14:46:42: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:46:49: 7000000 INFO @ Tue, 10 Dec 2019 14:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.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 14:46:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:46:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:46:51: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:46:51: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:46:51: #1 total tags in treatment: 7251355 INFO @ Tue, 10 Dec 2019 14:46:51: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:46:51: #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 14:46:51: #1 tags after filtering in treatment: 7251355 INFO @ Tue, 10 Dec 2019 14:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:46:51: #1 finished! INFO @ Tue, 10 Dec 2019 14:46:51: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:46:51: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:46:51: 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 14:46:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.05_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/SRX6678251/SRX6678251.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:46:54: 3000000 INFO @ Tue, 10 Dec 2019 14:46:58: 1000000 INFO @ Tue, 10 Dec 2019 14:47:04: 4000000 INFO @ Tue, 10 Dec 2019 14:47:07: 2000000 INFO @ Tue, 10 Dec 2019 14:47:16: 5000000 INFO @ Tue, 10 Dec 2019 14:47:17: 3000000 INFO @ Tue, 10 Dec 2019 14:47:25: 4000000 INFO @ Tue, 10 Dec 2019 14:47:28: 6000000 INFO @ Tue, 10 Dec 2019 14:47:35: 5000000 INFO @ Tue, 10 Dec 2019 14:47:40: 7000000 INFO @ Tue, 10 Dec 2019 14:47:42: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:47:42: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:47:42: #1 total tags in treatment: 7251355 INFO @ Tue, 10 Dec 2019 14:47:42: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:47:42: #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 14:47:42: #1 tags after filtering in treatment: 7251355 INFO @ Tue, 10 Dec 2019 14:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:47:42: #1 finished! INFO @ Tue, 10 Dec 2019 14:47:42: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:47:43: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:47:43: 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 14:47:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.10_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/SRX6678251/SRX6678251.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:47:44: 6000000 INFO @ Tue, 10 Dec 2019 14:47:53: 7000000 INFO @ Tue, 10 Dec 2019 14:47:55: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:47:55: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:47:55: #1 total tags in treatment: 7251355 INFO @ Tue, 10 Dec 2019 14:47:55: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:47:55: #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 14:47:55: #1 tags after filtering in treatment: 7251355 INFO @ Tue, 10 Dec 2019 14:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:47:55: #1 finished! INFO @ Tue, 10 Dec 2019 14:47:55: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:47:56: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:47:56: 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 14:47:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.20_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/SRX6678251/SRX6678251.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678251/SRX6678251.20_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。