Job ID = 2009714 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T10:35:18 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T10:45:03 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 : 53,063,874 reads read : 53,063,874 reads written : 53,063,874 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: 00:08:44 53063874 reads; of these: 53063874 (100.00%) were unpaired; of these: 4886428 (9.21%) aligned 0 times 35028384 (66.01%) aligned exactly 1 time 13149062 (24.78%) aligned >1 times 90.79% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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 20 files... [bam_rmdupse_core] 32379915 / 48177446 = 0.6721 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 20:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.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 20:32:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:32:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:32:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.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 20:32:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:32:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:32:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.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 20:32:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:32:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:32:43: 1000000 INFO @ Fri, 05 Jul 2019 20:32:46: 1000000 INFO @ Fri, 05 Jul 2019 20:32:46: 1000000 INFO @ Fri, 05 Jul 2019 20:32:50: 2000000 INFO @ Fri, 05 Jul 2019 20:32:54: 2000000 INFO @ Fri, 05 Jul 2019 20:32:55: 2000000 INFO @ Fri, 05 Jul 2019 20:32:57: 3000000 INFO @ Fri, 05 Jul 2019 20:33:02: 3000000 INFO @ Fri, 05 Jul 2019 20:33:03: 4000000 INFO @ Fri, 05 Jul 2019 20:33:04: 3000000 INFO @ Fri, 05 Jul 2019 20:33:10: 4000000 INFO @ Fri, 05 Jul 2019 20:33:10: 5000000 INFO @ Fri, 05 Jul 2019 20:33:12: 4000000 INFO @ Fri, 05 Jul 2019 20:33:18: 6000000 INFO @ Fri, 05 Jul 2019 20:33:19: 5000000 INFO @ Fri, 05 Jul 2019 20:33:20: 5000000 INFO @ Fri, 05 Jul 2019 20:33:25: 7000000 INFO @ Fri, 05 Jul 2019 20:33:26: 6000000 INFO @ Fri, 05 Jul 2019 20:33:29: 6000000 INFO @ Fri, 05 Jul 2019 20:33:32: 8000000 INFO @ Fri, 05 Jul 2019 20:33:34: 7000000 INFO @ Fri, 05 Jul 2019 20:33:37: 7000000 INFO @ Fri, 05 Jul 2019 20:33:38: 9000000 INFO @ Fri, 05 Jul 2019 20:33:41: 8000000 INFO @ Fri, 05 Jul 2019 20:33:45: 10000000 INFO @ Fri, 05 Jul 2019 20:33:45: 8000000 INFO @ Fri, 05 Jul 2019 20:33:49: 9000000 INFO @ Fri, 05 Jul 2019 20:33:53: 11000000 INFO @ Fri, 05 Jul 2019 20:33:55: 9000000 INFO @ Fri, 05 Jul 2019 20:33:56: 10000000 INFO @ Fri, 05 Jul 2019 20:34:00: 12000000 INFO @ Fri, 05 Jul 2019 20:34:03: 10000000 INFO @ Fri, 05 Jul 2019 20:34:04: 11000000 INFO @ Fri, 05 Jul 2019 20:34:06: 13000000 INFO @ Fri, 05 Jul 2019 20:34:11: 12000000 INFO @ Fri, 05 Jul 2019 20:34:11: 11000000 INFO @ Fri, 05 Jul 2019 20:34:13: 14000000 INFO @ Fri, 05 Jul 2019 20:34:18: 13000000 INFO @ Fri, 05 Jul 2019 20:34:20: 12000000 INFO @ Fri, 05 Jul 2019 20:34:20: 15000000 INFO @ Fri, 05 Jul 2019 20:34:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:34:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:34:25: #1 total tags in treatment: 15797531 INFO @ Fri, 05 Jul 2019 20:34:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:34:25: #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 20:34:26: #1 tags after filtering in treatment: 15797531 INFO @ Fri, 05 Jul 2019 20:34:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:34:26: #1 finished! INFO @ Fri, 05 Jul 2019 20:34:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:34:26: 14000000 INFO @ Fri, 05 Jul 2019 20:34:27: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:34:27: 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 20:34:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.05_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/SRX1135894/SRX1135894.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:34:28: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 20:34:33: 15000000 INFO @ Fri, 05 Jul 2019 20:34:36: 14000000 INFO @ Fri, 05 Jul 2019 20:34:39: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:34:39: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:34:39: #1 total tags in treatment: 15797531 INFO @ Fri, 05 Jul 2019 20:34:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:34:39: #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 20:34:39: #1 tags after filtering in treatment: 15797531 INFO @ Fri, 05 Jul 2019 20:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:34:39: #1 finished! INFO @ Fri, 05 Jul 2019 20:34:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:34:41: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:34:41: 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 20:34:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.20_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/SRX1135894/SRX1135894.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:34:45: 15000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 20:34:51: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:34:51: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:34:51: #1 total tags in treatment: 15797531 INFO @ Fri, 05 Jul 2019 20:34:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:34:51: #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 20:34:51: #1 tags after filtering in treatment: 15797531 INFO @ Fri, 05 Jul 2019 20:34:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:34:51: #1 finished! INFO @ Fri, 05 Jul 2019 20:34:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:34:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:34:52: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:34:52: 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 20:34:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.10_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/SRX1135894/SRX1135894.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1135894/SRX1135894.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling