Job ID = 2009648 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 439,965 reads read : 439,965 reads written : 439,965 2019-07-05T10:26:19 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 : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-07-05T10:30:33 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 : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-07-05T10:36:37 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 : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778511.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778526.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778537.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778571.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778631.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778636.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778644.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778648.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778662.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR778718.sra.cache’: 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: 00:07:26 40439965 reads; of these: 40439965 (100.00%) were unpaired; of these: 7985726 (19.75%) aligned 0 times 30483792 (75.38%) aligned exactly 1 time 1970447 (4.87%) aligned >1 times 80.25% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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 16 files... [bam_rmdupse_core] 23852175 / 32454239 = 0.7349 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 20:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.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 @ Fri, 05 Jul 2019 20:04:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:04:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:04:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.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 @ Fri, 05 Jul 2019 20:04:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:04:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:04:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.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 @ Fri, 05 Jul 2019 20:04:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:04:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:05:02: 1000000 INFO @ Fri, 05 Jul 2019 20:05:03: 1000000 INFO @ Fri, 05 Jul 2019 20:05:04: 1000000 INFO @ Fri, 05 Jul 2019 20:05:12: 2000000 INFO @ Fri, 05 Jul 2019 20:05:14: 2000000 INFO @ Fri, 05 Jul 2019 20:05:14: 2000000 INFO @ Fri, 05 Jul 2019 20:05:22: 3000000 INFO @ Fri, 05 Jul 2019 20:05:24: 3000000 INFO @ Fri, 05 Jul 2019 20:05:24: 3000000 INFO @ Fri, 05 Jul 2019 20:05:33: 4000000 INFO @ Fri, 05 Jul 2019 20:05:34: 4000000 INFO @ Fri, 05 Jul 2019 20:05:34: 4000000 INFO @ Fri, 05 Jul 2019 20:05:43: 5000000 INFO @ Fri, 05 Jul 2019 20:05:43: 5000000 INFO @ Fri, 05 Jul 2019 20:05:44: 5000000 INFO @ Fri, 05 Jul 2019 20:05:52: 6000000 INFO @ Fri, 05 Jul 2019 20:05:53: 6000000 INFO @ Fri, 05 Jul 2019 20:05:54: 6000000 INFO @ Fri, 05 Jul 2019 20:06:03: 7000000 INFO @ Fri, 05 Jul 2019 20:06:04: 7000000 INFO @ Fri, 05 Jul 2019 20:06:05: 7000000 INFO @ Fri, 05 Jul 2019 20:06:12: 8000000 INFO @ Fri, 05 Jul 2019 20:06:14: 8000000 INFO @ Fri, 05 Jul 2019 20:06:15: 8000000 INFO @ Fri, 05 Jul 2019 20:06:18: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:06:18: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:06:18: #1 total tags in treatment: 8602064 INFO @ Fri, 05 Jul 2019 20:06:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:06:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 20:06:18: #1 tags after filtering in treatment: 8602064 INFO @ Fri, 05 Jul 2019 20:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:06:18: #1 finished! INFO @ Fri, 05 Jul 2019 20:06:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:06:19: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:06:19: 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 @ Fri, 05 Jul 2019 20:06:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.20_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/ERX769136/ERX769136.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:06:20: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:06:20: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:06:20: #1 total tags in treatment: 8602064 INFO @ Fri, 05 Jul 2019 20:06:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:06:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 20:06:20: #1 tags after filtering in treatment: 8602064 INFO @ Fri, 05 Jul 2019 20:06:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:06:20: #1 finished! INFO @ Fri, 05 Jul 2019 20:06:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:06:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:06:21: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:06:21: 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 @ Fri, 05 Jul 2019 20:06:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.05_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 20:06:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:06:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:06:21: #1 total tags in treatment: 8602064 INFO @ Fri, 05 Jul 2019 20:06:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:06:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:06:21: #1 tags after filtering in treatment: 8602064 INFO @ Fri, 05 Jul 2019 20:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:06:21: #1 finished! INFO @ Fri, 05 Jul 2019 20:06:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:06:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:06:22: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:06:22: 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 @ Fri, 05 Jul 2019 20:06:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.10_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/ERX769136/ERX769136.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX769136/ERX769136.10_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。