Job ID = 2010364 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T13:15:44 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 ) 2019-07-05T13:15:58 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 : 11,810,219 reads read : 11,810,219 reads written : 11,810,219 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: 00:02:23 11810219 reads; of these: 11810219 (100.00%) were unpaired; of these: 1258526 (10.66%) aligned 0 times 9099842 (77.05%) aligned exactly 1 time 1451851 (12.29%) aligned >1 times 89.34% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 3934709 / 10551693 = 0.3729 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 22:28:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.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 22:28:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:28:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:28:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.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 22:28:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:28:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:28:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.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 22:28:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:28:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:28:35: 1000000 INFO @ Fri, 05 Jul 2019 22:28:36: 1000000 INFO @ Fri, 05 Jul 2019 22:28:39: 1000000 INFO @ Fri, 05 Jul 2019 22:28:43: 2000000 INFO @ Fri, 05 Jul 2019 22:28:44: 2000000 INFO @ Fri, 05 Jul 2019 22:28:48: 2000000 INFO @ Fri, 05 Jul 2019 22:28:51: 3000000 INFO @ Fri, 05 Jul 2019 22:28:52: 3000000 INFO @ Fri, 05 Jul 2019 22:28:57: 3000000 INFO @ Fri, 05 Jul 2019 22:28:58: 4000000 INFO @ Fri, 05 Jul 2019 22:29:00: 4000000 INFO @ Fri, 05 Jul 2019 22:29:05: 5000000 INFO @ Fri, 05 Jul 2019 22:29:07: 4000000 INFO @ Fri, 05 Jul 2019 22:29:08: 5000000 INFO @ Fri, 05 Jul 2019 22:29:12: 6000000 INFO @ Fri, 05 Jul 2019 22:29:16: 6000000 INFO @ Fri, 05 Jul 2019 22:29:16: 5000000 INFO @ Fri, 05 Jul 2019 22:29:16: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:29:16: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:29:16: #1 total tags in treatment: 6616984 INFO @ Fri, 05 Jul 2019 22:29:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:29:16: #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 22:29:17: #1 tags after filtering in treatment: 6616984 INFO @ Fri, 05 Jul 2019 22:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:29:17: #1 finished! INFO @ Fri, 05 Jul 2019 22:29:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:29:17: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:29:17: 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 22:29:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.10_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/SRX377017/SRX377017.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:29:20: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:29:20: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:29:20: #1 total tags in treatment: 6616984 INFO @ Fri, 05 Jul 2019 22:29:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:29:20: #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 22:29:20: #1 tags after filtering in treatment: 6616984 INFO @ Fri, 05 Jul 2019 22:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:29:20: #1 finished! INFO @ Fri, 05 Jul 2019 22:29:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:29:21: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:29:21: 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 22:29:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.05_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/SRX377017/SRX377017.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:29:24: 6000000 INFO @ Fri, 05 Jul 2019 22:29:28: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:29:28: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:29:28: #1 total tags in treatment: 6616984 INFO @ Fri, 05 Jul 2019 22:29:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:29:28: #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 22:29:29: #1 tags after filtering in treatment: 6616984 INFO @ Fri, 05 Jul 2019 22:29:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:29:29: #1 finished! INFO @ Fri, 05 Jul 2019 22:29:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:29:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:29:29: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:29:29: 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 22:29:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.20_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/SRX377017/SRX377017.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX377017/SRX377017.20_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。