Job ID = 2009747 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T10:41:29 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 : 14,977,685 reads read : 14,977,685 reads written : 14,977,685 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR497924.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: 00:02:27 14977685 reads; of these: 14977685 (100.00%) were unpaired; of these: 7537795 (50.33%) aligned 0 times 5036090 (33.62%) aligned exactly 1 time 2403800 (16.05%) aligned >1 times 49.67% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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_rmdupse_core] 4064031 / 7439890 = 0.5462 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 19:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.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 19:47:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:47:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.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 19:47:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:47:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.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 19:47:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:47:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:47:13: 1000000 INFO @ Fri, 05 Jul 2019 19:47:15: 1000000 INFO @ Fri, 05 Jul 2019 19:47:15: 1000000 INFO @ Fri, 05 Jul 2019 19:47:22: 2000000 INFO @ Fri, 05 Jul 2019 19:47:25: 2000000 INFO @ Fri, 05 Jul 2019 19:47:25: 2000000 INFO @ Fri, 05 Jul 2019 19:47:31: 3000000 INFO @ Fri, 05 Jul 2019 19:47:35: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:47:35: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:47:35: #1 total tags in treatment: 3375859 INFO @ Fri, 05 Jul 2019 19:47:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:35: #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 19:47:35: #1 tags after filtering in treatment: 3375859 INFO @ Fri, 05 Jul 2019 19:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:35: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:47:35: #2 number of paired peaks: 52 WARNING @ Fri, 05 Jul 2019 19:47:35: Too few paired peaks (52) 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 19:47:35: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:47:35: 3000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.05_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 19:47:35: 3000000 pass1 - making usageList (0 chroms): 204 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:47:38: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:47:38: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:47:38: #1 total tags in treatment: 3375859 INFO @ Fri, 05 Jul 2019 19:47:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:38: #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 19:47:38: #1 tags after filtering in treatment: 3375859 INFO @ Fri, 05 Jul 2019 19:47:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:38: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:47:39: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:47:39: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:47:39: #1 total tags in treatment: 3375859 INFO @ Fri, 05 Jul 2019 19:47:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:39: #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 19:47:39: #2 number of paired peaks: 52 WARNING @ Fri, 05 Jul 2019 19:47:39: Too few paired peaks (52) 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 19:47:39: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:47:39: #1 tags after filtering in treatment: 3375859 INFO @ Fri, 05 Jul 2019 19:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:39: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:39: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:47:39: #2 number of paired peaks: 52 WARNING @ Fri, 05 Jul 2019 19:47:39: Too few paired peaks (52) 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 19:47:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.10_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/SRX148603/SRX148603.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX148603/SRX148603.10_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。