Job ID = 2010782 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:43:46 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 ) 2019-07-05T15:46:38 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 : 16,960,096 reads read : 16,960,096 reads written : 16,960,096 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: 00:02:50 16960096 reads; of these: 16960096 (100.00%) were unpaired; of these: 2686388 (15.84%) aligned 0 times 11356214 (66.96%) aligned exactly 1 time 2917494 (17.20%) aligned >1 times 84.16% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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 8 files... [bam_rmdupse_core] 8385803 / 14273708 = 0.5875 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 @ Sat, 06 Jul 2019 00:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.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, 06 Jul 2019 00:53:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:53:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:53:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.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, 06 Jul 2019 00:53:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:53:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.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, 06 Jul 2019 00:53:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:53:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:53:47: 1000000 INFO @ Sat, 06 Jul 2019 00:53:51: 1000000 INFO @ Sat, 06 Jul 2019 00:53:51: 1000000 INFO @ Sat, 06 Jul 2019 00:53:55: 2000000 INFO @ Sat, 06 Jul 2019 00:54:00: 2000000 INFO @ Sat, 06 Jul 2019 00:54:01: 2000000 INFO @ Sat, 06 Jul 2019 00:54:02: 3000000 INFO @ Sat, 06 Jul 2019 00:54:09: 4000000 INFO @ Sat, 06 Jul 2019 00:54:10: 3000000 INFO @ Sat, 06 Jul 2019 00:54:10: 3000000 INFO @ Sat, 06 Jul 2019 00:54:16: 5000000 INFO @ Sat, 06 Jul 2019 00:54:19: 4000000 INFO @ Sat, 06 Jul 2019 00:54:19: 4000000 INFO @ Sat, 06 Jul 2019 00:54:22: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:54:22: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:54:22: #1 total tags in treatment: 5887905 INFO @ Sat, 06 Jul 2019 00:54:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:54:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:54:22: #1 tags after filtering in treatment: 5887905 INFO @ Sat, 06 Jul 2019 00:54:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:54:22: #1 finished! INFO @ Sat, 06 Jul 2019 00:54:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:54:23: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:54:23: 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, 06 Jul 2019 00:54:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.05_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/SRX399187/SRX399187.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:54:27: 5000000 INFO @ Sat, 06 Jul 2019 00:54:28: 5000000 INFO @ Sat, 06 Jul 2019 00:54:35: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:54:35: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:54:35: #1 total tags in treatment: 5887905 INFO @ Sat, 06 Jul 2019 00:54:35: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:54:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:54:35: #1 tags after filtering in treatment: 5887905 INFO @ Sat, 06 Jul 2019 00:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:54:35: #1 finished! INFO @ Sat, 06 Jul 2019 00:54:35: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:54:35: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:54:35: 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, 06 Jul 2019 00:54:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.20_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/SRX399187/SRX399187.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:54:36: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:54:36: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:54:36: #1 total tags in treatment: 5887905 INFO @ Sat, 06 Jul 2019 00:54:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:54:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:54:36: #1 tags after filtering in treatment: 5887905 INFO @ Sat, 06 Jul 2019 00:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:54:36: #1 finished! INFO @ Sat, 06 Jul 2019 00:54:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:54:37: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:54:37: 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 @ Sat, 06 Jul 2019 00:54:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.10_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/SRX399187/SRX399187.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX399187/SRX399187.10_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。