Job ID = 2640926 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:58:18 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 ) 2019-08-24T10:58:18 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 ) 2019-08-24T10:58:18 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 : 36,274,499 reads read : 36,274,499 reads written : 36,274,499 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: 00:06:37 36274499 reads; of these: 36274499 (100.00%) were unpaired; of these: 1485063 (4.09%) aligned 0 times 29253212 (80.64%) aligned exactly 1 time 5536224 (15.26%) aligned >1 times 95.91% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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 16 files... [bam_rmdupse_core] 18971244 / 34789436 = 0.5453 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.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 20:29:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:29:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:29:53: 1000000 INFO @ Sat, 24 Aug 2019 20:30:03: 2000000 INFO @ Sat, 24 Aug 2019 20:30:12: 3000000 INFO @ Sat, 24 Aug 2019 20:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.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 20:30:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:30:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:30:22: 4000000 INFO @ Sat, 24 Aug 2019 20:30:25: 1000000 INFO @ Sat, 24 Aug 2019 20:30:32: 5000000 INFO @ Sat, 24 Aug 2019 20:30:36: 2000000 INFO @ Sat, 24 Aug 2019 20:30:41: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:30:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.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 20:30:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:30:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:30:47: 3000000 INFO @ Sat, 24 Aug 2019 20:30:51: 7000000 INFO @ Sat, 24 Aug 2019 20:30:52: 1000000 INFO @ Sat, 24 Aug 2019 20:30:57: 4000000 INFO @ Sat, 24 Aug 2019 20:31:00: 2000000 INFO @ Sat, 24 Aug 2019 20:31:01: 8000000 INFO @ Sat, 24 Aug 2019 20:31:07: 5000000 INFO @ Sat, 24 Aug 2019 20:31:08: 3000000 INFO @ Sat, 24 Aug 2019 20:31:10: 9000000 INFO @ Sat, 24 Aug 2019 20:31:16: 4000000 INFO @ Sat, 24 Aug 2019 20:31:17: 6000000 INFO @ Sat, 24 Aug 2019 20:31:19: 10000000 INFO @ Sat, 24 Aug 2019 20:31:24: 5000000 INFO @ Sat, 24 Aug 2019 20:31:26: 7000000 INFO @ Sat, 24 Aug 2019 20:31:28: 11000000 INFO @ Sat, 24 Aug 2019 20:31:32: 6000000 INFO @ Sat, 24 Aug 2019 20:31:36: 8000000 INFO @ Sat, 24 Aug 2019 20:31:38: 12000000 INFO @ Sat, 24 Aug 2019 20:31:40: 7000000 INFO @ Sat, 24 Aug 2019 20:31:46: 9000000 INFO @ Sat, 24 Aug 2019 20:31:47: 13000000 INFO @ Sat, 24 Aug 2019 20:31:49: 8000000 INFO @ Sat, 24 Aug 2019 20:31:55: 10000000 INFO @ Sat, 24 Aug 2019 20:31:57: 14000000 INFO @ Sat, 24 Aug 2019 20:31:58: 9000000 INFO @ Sat, 24 Aug 2019 20:32:05: 11000000 INFO @ Sat, 24 Aug 2019 20:32:08: 10000000 INFO @ Sat, 24 Aug 2019 20:32:08: 15000000 INFO @ Sat, 24 Aug 2019 20:32:15: 12000000 INFO @ Sat, 24 Aug 2019 20:32:17: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:32:17: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:32:17: #1 total tags in treatment: 15818192 INFO @ Sat, 24 Aug 2019 20:32:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:32:17: #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 20:32:17: 11000000 INFO @ Sat, 24 Aug 2019 20:32:17: #1 tags after filtering in treatment: 15818192 INFO @ Sat, 24 Aug 2019 20:32:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:32:17: #1 finished! INFO @ Sat, 24 Aug 2019 20:32:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:32:18: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:32:18: 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 20:32:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.05_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/SRX4703449/SRX4703449.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:32:24: 13000000 INFO @ Sat, 24 Aug 2019 20:32:27: 12000000 INFO @ Sat, 24 Aug 2019 20:32:33: 14000000 INFO @ Sat, 24 Aug 2019 20:32:36: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:32:42: 15000000 INFO @ Sat, 24 Aug 2019 20:32:45: 14000000 INFO @ Sat, 24 Aug 2019 20:32:50: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:32:50: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:32:50: #1 total tags in treatment: 15818192 INFO @ Sat, 24 Aug 2019 20:32:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:32:50: #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 20:32:51: #1 tags after filtering in treatment: 15818192 INFO @ Sat, 24 Aug 2019 20:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:32:51: #1 finished! INFO @ Sat, 24 Aug 2019 20:32:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:32:52: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:32:52: 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 @ Sat, 24 Aug 2019 20:32:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.10_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/SRX4703449/SRX4703449.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:32:55: 15000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 20:33:03: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:33:03: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:33:03: #1 total tags in treatment: 15818192 INFO @ Sat, 24 Aug 2019 20:33:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:33:03: #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 20:33:03: #1 tags after filtering in treatment: 15818192 INFO @ Sat, 24 Aug 2019 20:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:33:03: #1 finished! INFO @ Sat, 24 Aug 2019 20:33:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:33:04: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:33:04: 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 20:33:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.20_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/SRX4703449/SRX4703449.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703449/SRX4703449.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling