Job ID = 2010268 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T13:00:34 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 ) 2019-07-05T13:00:34 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 ) 2019-07-05T13:03:13 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 ) 2019-07-05T13:04:34 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 ) 2019-07-05T13:04:34 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 ) 2019-07-05T13:04:34 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 : 21,186,955 reads read : 42,373,910 reads written : 21,186,955 reads 0-length : 21,186,955 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: 00:03:37 21186955 reads; of these: 21186955 (100.00%) were unpaired; of these: 1735867 (8.19%) aligned 0 times 17318644 (81.74%) aligned exactly 1 time 2132444 (10.06%) aligned >1 times 91.81% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 7749375 / 19451088 = 0.3984 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 22:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.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 22:15:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:15:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.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 22:15:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:15:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.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 22:15:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:15:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:15:25: 1000000 INFO @ Fri, 05 Jul 2019 22:15:26: 1000000 INFO @ Fri, 05 Jul 2019 22:15:26: 1000000 INFO @ Fri, 05 Jul 2019 22:15:34: 2000000 INFO @ Fri, 05 Jul 2019 22:15:34: 2000000 INFO @ Fri, 05 Jul 2019 22:15:35: 2000000 INFO @ Fri, 05 Jul 2019 22:15:42: 3000000 INFO @ Fri, 05 Jul 2019 22:15:42: 3000000 INFO @ Fri, 05 Jul 2019 22:15:43: 3000000 INFO @ Fri, 05 Jul 2019 22:15:49: 4000000 INFO @ Fri, 05 Jul 2019 22:15:50: 4000000 INFO @ Fri, 05 Jul 2019 22:15:51: 4000000 INFO @ Fri, 05 Jul 2019 22:15:56: 5000000 INFO @ Fri, 05 Jul 2019 22:15:58: 5000000 INFO @ Fri, 05 Jul 2019 22:15:59: 5000000 INFO @ Fri, 05 Jul 2019 22:16:03: 6000000 INFO @ Fri, 05 Jul 2019 22:16:06: 6000000 INFO @ Fri, 05 Jul 2019 22:16:07: 6000000 INFO @ Fri, 05 Jul 2019 22:16:11: 7000000 INFO @ Fri, 05 Jul 2019 22:16:14: 7000000 INFO @ Fri, 05 Jul 2019 22:16:16: 7000000 INFO @ Fri, 05 Jul 2019 22:16:18: 8000000 INFO @ Fri, 05 Jul 2019 22:16:22: 8000000 INFO @ Fri, 05 Jul 2019 22:16:23: 8000000 INFO @ Fri, 05 Jul 2019 22:16:25: 9000000 INFO @ Fri, 05 Jul 2019 22:16:30: 9000000 INFO @ Fri, 05 Jul 2019 22:16:31: 9000000 INFO @ Fri, 05 Jul 2019 22:16:32: 10000000 INFO @ Fri, 05 Jul 2019 22:16:37: 10000000 INFO @ Fri, 05 Jul 2019 22:16:39: 11000000 INFO @ Fri, 05 Jul 2019 22:16:39: 10000000 INFO @ Fri, 05 Jul 2019 22:16:44: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:16:44: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:16:44: #1 total tags in treatment: 11701713 INFO @ Fri, 05 Jul 2019 22:16:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:16:44: #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 22:16:44: #1 tags after filtering in treatment: 11701713 INFO @ Fri, 05 Jul 2019 22:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:16:44: #1 finished! INFO @ Fri, 05 Jul 2019 22:16:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:16:45: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:16:45: 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 22:16:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.20_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/SRX3316857/SRX3316857.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:16:45: 11000000 INFO @ Fri, 05 Jul 2019 22:16:47: 11000000 INFO @ Fri, 05 Jul 2019 22:16:51: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:16:51: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:16:51: #1 total tags in treatment: 11701713 INFO @ Fri, 05 Jul 2019 22:16:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:16:51: #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 22:16:51: #1 tags after filtering in treatment: 11701713 INFO @ Fri, 05 Jul 2019 22:16:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:16:51: #1 finished! INFO @ Fri, 05 Jul 2019 22:16:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:16:52: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:16:52: 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 22:16:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.05_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/SRX3316857/SRX3316857.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:16:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:16:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:16:53: #1 total tags in treatment: 11701713 INFO @ Fri, 05 Jul 2019 22:16:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:16:53: #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 22:16:53: #1 tags after filtering in treatment: 11701713 INFO @ Fri, 05 Jul 2019 22:16:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:16:53: #1 finished! INFO @ Fri, 05 Jul 2019 22:16:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:16:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:16:54: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:16:54: 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 22:16:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.10_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/SRX3316857/SRX3316857.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3316857/SRX3316857.10_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。