Job ID = 2641066 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:03:50 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 : 26,252,416 reads read : 52,504,832 reads written : 26,252,416 reads 0-length : 26,252,416 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: 00:04:45 26252416 reads; of these: 26252416 (100.00%) were unpaired; of these: 1200686 (4.57%) aligned 0 times 22480341 (85.63%) aligned exactly 1 time 2571389 (9.79%) aligned >1 times 95.43% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 13840259 / 25051730 = 0.5525 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.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 @ Sat, 24 Aug 2019 21:22:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:22:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:22:44: 1000000 INFO @ Sat, 24 Aug 2019 21:22:53: 2000000 INFO @ Sat, 24 Aug 2019 21:23:02: 3000000 INFO @ Sat, 24 Aug 2019 21:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.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 @ Sat, 24 Aug 2019 21:23:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:23:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:23:11: 4000000 INFO @ Sat, 24 Aug 2019 21:23:14: 1000000 INFO @ Sat, 24 Aug 2019 21:23:19: 5000000 INFO @ Sat, 24 Aug 2019 21:23:21: 2000000 INFO @ Sat, 24 Aug 2019 21:23:27: 6000000 INFO @ Sat, 24 Aug 2019 21:23:29: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.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 @ Sat, 24 Aug 2019 21:23:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:23:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:23:36: 7000000 INFO @ Sat, 24 Aug 2019 21:23:37: 4000000 INFO @ Sat, 24 Aug 2019 21:23:44: 5000000 INFO @ Sat, 24 Aug 2019 21:23:44: 1000000 INFO @ Sat, 24 Aug 2019 21:23:45: 8000000 INFO @ Sat, 24 Aug 2019 21:23:52: 6000000 INFO @ Sat, 24 Aug 2019 21:23:53: 2000000 INFO @ Sat, 24 Aug 2019 21:23:54: 9000000 INFO @ Sat, 24 Aug 2019 21:23:59: 7000000 INFO @ Sat, 24 Aug 2019 21:24:02: 10000000 INFO @ Sat, 24 Aug 2019 21:24:02: 3000000 INFO @ Sat, 24 Aug 2019 21:24:07: 8000000 INFO @ Sat, 24 Aug 2019 21:24:11: 11000000 INFO @ Sat, 24 Aug 2019 21:24:11: 4000000 INFO @ Sat, 24 Aug 2019 21:24:12: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:24:12: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:24:12: #1 total tags in treatment: 11211471 INFO @ Sat, 24 Aug 2019 21:24:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:24:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:24:13: #1 tags after filtering in treatment: 11211471 INFO @ Sat, 24 Aug 2019 21:24:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:24:13: #1 finished! INFO @ Sat, 24 Aug 2019 21:24:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:24:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:24:13: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:24:13: 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 @ Sat, 24 Aug 2019 21:24:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.05_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/SRX5257260/SRX5257260.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:24:15: 9000000 INFO @ Sat, 24 Aug 2019 21:24:20: 5000000 INFO @ Sat, 24 Aug 2019 21:24:22: 10000000 INFO @ Sat, 24 Aug 2019 21:24:28: 6000000 INFO @ Sat, 24 Aug 2019 21:24:30: 11000000 INFO @ Sat, 24 Aug 2019 21:24:31: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:24:31: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:24:31: #1 total tags in treatment: 11211471 INFO @ Sat, 24 Aug 2019 21:24:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:24:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:24:31: #1 tags after filtering in treatment: 11211471 INFO @ Sat, 24 Aug 2019 21:24:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:24:31: #1 finished! INFO @ Sat, 24 Aug 2019 21:24:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:24:32: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:24:32: 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 @ Sat, 24 Aug 2019 21:24:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.10_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/SRX5257260/SRX5257260.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:24:37: 7000000 INFO @ Sat, 24 Aug 2019 21:24:45: 8000000 INFO @ Sat, 24 Aug 2019 21:24:54: 9000000 INFO @ Sat, 24 Aug 2019 21:25:02: 10000000 INFO @ Sat, 24 Aug 2019 21:25:11: 11000000 INFO @ Sat, 24 Aug 2019 21:25:12: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:25:12: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:25:12: #1 total tags in treatment: 11211471 INFO @ Sat, 24 Aug 2019 21:25:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:25:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:25:12: #1 tags after filtering in treatment: 11211471 INFO @ Sat, 24 Aug 2019 21:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:25:12: #1 finished! INFO @ Sat, 24 Aug 2019 21:25:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:25:12: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:25:13: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:25:13: 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 @ Sat, 24 Aug 2019 21:25:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.20_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/SRX5257260/SRX5257260.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257260/SRX5257260.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。