Job ID = 2010765 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:28:00 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 ) 2019-07-05T15:28:00 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 ) 2019-07-05T15:34:53 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 : 28,645,216 reads read : 28,645,216 reads written : 28,645,216 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: 00:04:58 28645216 reads; of these: 28645216 (100.00%) were unpaired; of these: 6877043 (24.01%) aligned 0 times 19553793 (68.26%) aligned exactly 1 time 2214380 (7.73%) aligned >1 times 75.99% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 18080030 / 21768173 = 0.8306 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 00:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.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 00:51:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:51:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.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 00:51:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:51:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:51:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.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 00:51:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:51:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:51:48: 1000000 INFO @ Sat, 06 Jul 2019 00:51:51: 1000000 INFO @ Sat, 06 Jul 2019 00:51:52: 1000000 INFO @ Sat, 06 Jul 2019 00:51:57: 2000000 INFO @ Sat, 06 Jul 2019 00:52:00: 2000000 INFO @ Sat, 06 Jul 2019 00:52:00: 2000000 INFO @ Sat, 06 Jul 2019 00:52:06: 3000000 INFO @ Sat, 06 Jul 2019 00:52:09: 3000000 INFO @ Sat, 06 Jul 2019 00:52:09: 3000000 INFO @ Sat, 06 Jul 2019 00:52:12: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:52:12: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:52:12: #1 total tags in treatment: 3688143 INFO @ Sat, 06 Jul 2019 00:52:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:12: #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 00:52:12: #1 tags after filtering in treatment: 3688143 INFO @ Sat, 06 Jul 2019 00:52:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:12: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:12: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 00:52:12: Too few paired peaks (35) 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 00:52:12: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:52:14: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:52:14: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:52:14: #1 total tags in treatment: 3688143 INFO @ Sat, 06 Jul 2019 00:52:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:14: #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 00:52:14: #1 tags after filtering in treatment: 3688143 INFO @ Sat, 06 Jul 2019 00:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:14: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:14: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 00:52:14: Too few paired peaks (35) 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 00:52:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:52:16: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 00:52:16: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 00:52:16: #1 total tags in treatment: 3688143 INFO @ Sat, 06 Jul 2019 00:52:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:16: #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 00:52:16: #1 tags after filtering in treatment: 3688143 INFO @ Sat, 06 Jul 2019 00:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:52:16: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:16: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 00:52:16: Too few paired peaks (35) 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 00:52:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.10_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/SRX387223/SRX387223.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387223/SRX387223.10_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。