Job ID = 2001641 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:53:43 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 ) 2019-07-04T21:53:43 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 : 31,625,526 reads read : 31,625,526 reads written : 31,625,526 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: 00:00:01 Multiseed full-index search: 00:02:28 31625526 reads; of these: 31625526 (100.00%) were unpaired; of these: 31624022 (100.00%) aligned 0 times 193 (0.00%) aligned exactly 1 time 1311 (0.00%) aligned >1 times 0.00% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 334 / 1504 = 0.2221 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 07:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:01:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:01:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:01:52: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:01:52: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:01:52: #1 total tags in treatment: 1170 INFO @ Fri, 05 Jul 2019 07:01:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:01:52: #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 07:01:52: #1 tags after filtering in treatment: 1153 INFO @ Fri, 05 Jul 2019 07:01:52: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 07:01:52: #1 finished! INFO @ Fri, 05 Jul 2019 07:01:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:01:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:01:52: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 07:01:52: 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 07:01:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.05_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/rn6/ERX101956/ERX101956.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:01:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:01:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:01:53: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:01:53: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:01:53: #1 total tags in treatment: 1170 INFO @ Fri, 05 Jul 2019 07:01:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:01:53: #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 07:01:53: #1 tags after filtering in treatment: 1153 INFO @ Fri, 05 Jul 2019 07:01:53: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 07:01:53: #1 finished! INFO @ Fri, 05 Jul 2019 07:01:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:01:53: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 07:01:53: 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 07:01:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.10_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/rn6/ERX101956/ERX101956.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:01:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:01:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:01:54: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:01:54: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:01:54: #1 total tags in treatment: 1170 INFO @ Fri, 05 Jul 2019 07:01:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:01:54: #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 07:01:54: #1 tags after filtering in treatment: 1153 INFO @ Fri, 05 Jul 2019 07:01:54: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 07:01:54: #1 finished! INFO @ Fri, 05 Jul 2019 07:01:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:01:54: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 07:01:54: 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 07:01:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.20_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/rn6/ERX101956/ERX101956.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/rn6/ERX101956/ERX101956.20_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。