Job ID = 2641090 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T12:15:22 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 ) 2019-08-24T12:15:22 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 ) 2019-08-24T12:15:22 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 ) 2019-08-24T12:15:22 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 ) 2019-08-24T12:17:38 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 : 66,398,609 reads read : 66,398,609 reads written : 66,398,609 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: 00:13:14 66398609 reads; of these: 66398609 (100.00%) were unpaired; of these: 3712650 (5.59%) aligned 0 times 51842306 (78.08%) aligned exactly 1 time 10843653 (16.33%) aligned >1 times 94.41% overall alignment rate Time searching: 00:13:14 Overall time: 00:13:14 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 28 files... [bam_rmdupse_core] 49943400 / 62685959 = 0.7967 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:04:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.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, 24 Aug 2019 22:04:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:04:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:04:53: 1000000 INFO @ Sat, 24 Aug 2019 22:05:01: 2000000 INFO @ Sat, 24 Aug 2019 22:05:09: 3000000 INFO @ Sat, 24 Aug 2019 22:05:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.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, 24 Aug 2019 22:05:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:05:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:05:17: 4000000 INFO @ Sat, 24 Aug 2019 22:05:23: 1000000 INFO @ Sat, 24 Aug 2019 22:05:25: 5000000 INFO @ Sat, 24 Aug 2019 22:05:32: 2000000 INFO @ Sat, 24 Aug 2019 22:05:33: 6000000 INFO @ Sat, 24 Aug 2019 22:05:41: 3000000 INFO @ Sat, 24 Aug 2019 22:05:41: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:05:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.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, 24 Aug 2019 22:05:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:05:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:05:49: 4000000 INFO @ Sat, 24 Aug 2019 22:05:49: 8000000 INFO @ Sat, 24 Aug 2019 22:05:53: 1000000 INFO @ Sat, 24 Aug 2019 22:05:57: 5000000 INFO @ Sat, 24 Aug 2019 22:05:58: 9000000 INFO @ Sat, 24 Aug 2019 22:06:01: 2000000 INFO @ Sat, 24 Aug 2019 22:06:05: 6000000 INFO @ Sat, 24 Aug 2019 22:06:06: 10000000 INFO @ Sat, 24 Aug 2019 22:06:09: 3000000 INFO @ Sat, 24 Aug 2019 22:06:13: 7000000 INFO @ Sat, 24 Aug 2019 22:06:15: 11000000 INFO @ Sat, 24 Aug 2019 22:06:17: 4000000 INFO @ Sat, 24 Aug 2019 22:06:21: 8000000 INFO @ Sat, 24 Aug 2019 22:06:23: 12000000 INFO @ Sat, 24 Aug 2019 22:06:25: 5000000 INFO @ Sat, 24 Aug 2019 22:06:28: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:06:28: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:06:28: #1 total tags in treatment: 12742559 INFO @ Sat, 24 Aug 2019 22:06:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:06:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:06:29: #1 tags after filtering in treatment: 12742559 INFO @ Sat, 24 Aug 2019 22:06:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:06:29: #1 finished! INFO @ Sat, 24 Aug 2019 22:06:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:06:30: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:06:30: 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 @ Sat, 24 Aug 2019 22:06:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.05_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/SRX5431193/SRX5431193.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:06:30: 9000000 INFO @ Sat, 24 Aug 2019 22:06:32: 6000000 INFO @ Sat, 24 Aug 2019 22:06:38: 10000000 INFO @ Sat, 24 Aug 2019 22:06:40: 7000000 INFO @ Sat, 24 Aug 2019 22:06:46: 11000000 INFO @ Sat, 24 Aug 2019 22:06:48: 8000000 INFO @ Sat, 24 Aug 2019 22:06:53: 12000000 INFO @ Sat, 24 Aug 2019 22:06:56: 9000000 INFO @ Sat, 24 Aug 2019 22:06:59: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:06:59: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:06:59: #1 total tags in treatment: 12742559 INFO @ Sat, 24 Aug 2019 22:06:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:06:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:06:59: #1 tags after filtering in treatment: 12742559 INFO @ Sat, 24 Aug 2019 22:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:06:59: #1 finished! INFO @ Sat, 24 Aug 2019 22:06:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:07:00: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:07:00: 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 @ Sat, 24 Aug 2019 22:07:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.10_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/SRX5431193/SRX5431193.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:07:04: 10000000 INFO @ Sat, 24 Aug 2019 22:07:11: 11000000 INFO @ Sat, 24 Aug 2019 22:07:19: 12000000 INFO @ Sat, 24 Aug 2019 22:07:24: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:07:24: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:07:24: #1 total tags in treatment: 12742559 INFO @ Sat, 24 Aug 2019 22:07:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:07:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:07:25: #1 tags after filtering in treatment: 12742559 INFO @ Sat, 24 Aug 2019 22:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 22:07:25: #1 finished! INFO @ Sat, 24 Aug 2019 22:07:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:07:26: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:07:26: 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 @ Sat, 24 Aug 2019 22:07:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.20_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/SRX5431193/SRX5431193.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5431193/SRX5431193.20_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。