Job ID = 2009854 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T11:10:16 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 ) 2019-07-05T11:10:16 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 : 56,707,000 reads read : 56,707,000 reads written : 56,707,000 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR585734.sra.cache’: 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: 00:17:44 56707000 reads; of these: 56707000 (100.00%) were unpaired; of these: 12551338 (22.13%) aligned 0 times 38949552 (68.69%) aligned exactly 1 time 5206110 (9.18%) aligned >1 times 77.87% overall alignment rate Time searching: 00:17:44 Overall time: 00:17:44 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 12 files... [bam_rmdupse_core] 29054616 / 44155662 = 0.6580 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 20:38:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.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 20:38:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:38:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.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 20:38:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:38:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:38:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.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 20:38:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:38:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:39:02: 1000000 INFO @ Fri, 05 Jul 2019 20:39:03: 1000000 INFO @ Fri, 05 Jul 2019 20:39:04: 1000000 INFO @ Fri, 05 Jul 2019 20:39:10: 2000000 INFO @ Fri, 05 Jul 2019 20:39:10: 2000000 INFO @ Fri, 05 Jul 2019 20:39:12: 2000000 INFO @ Fri, 05 Jul 2019 20:39:16: 3000000 INFO @ Fri, 05 Jul 2019 20:39:17: 3000000 INFO @ Fri, 05 Jul 2019 20:39:19: 3000000 INFO @ Fri, 05 Jul 2019 20:39:23: 4000000 INFO @ Fri, 05 Jul 2019 20:39:25: 4000000 INFO @ Fri, 05 Jul 2019 20:39:27: 4000000 INFO @ Fri, 05 Jul 2019 20:39:30: 5000000 INFO @ Fri, 05 Jul 2019 20:39:32: 5000000 INFO @ Fri, 05 Jul 2019 20:39:34: 5000000 INFO @ Fri, 05 Jul 2019 20:39:36: 6000000 INFO @ Fri, 05 Jul 2019 20:39:40: 6000000 INFO @ Fri, 05 Jul 2019 20:39:42: 6000000 INFO @ Fri, 05 Jul 2019 20:39:43: 7000000 INFO @ Fri, 05 Jul 2019 20:39:47: 7000000 INFO @ Fri, 05 Jul 2019 20:39:49: 7000000 INFO @ Fri, 05 Jul 2019 20:39:50: 8000000 INFO @ Fri, 05 Jul 2019 20:39:54: 8000000 INFO @ Fri, 05 Jul 2019 20:39:57: 8000000 INFO @ Fri, 05 Jul 2019 20:39:57: 9000000 INFO @ Fri, 05 Jul 2019 20:40:02: 9000000 INFO @ Fri, 05 Jul 2019 20:40:04: 10000000 INFO @ Fri, 05 Jul 2019 20:40:04: 9000000 INFO @ Fri, 05 Jul 2019 20:40:09: 10000000 INFO @ Fri, 05 Jul 2019 20:40:10: 11000000 INFO @ Fri, 05 Jul 2019 20:40:11: 10000000 INFO @ Fri, 05 Jul 2019 20:40:17: 11000000 INFO @ Fri, 05 Jul 2019 20:40:17: 12000000 INFO @ Fri, 05 Jul 2019 20:40:19: 11000000 INFO @ Fri, 05 Jul 2019 20:40:24: 13000000 INFO @ Fri, 05 Jul 2019 20:40:24: 12000000 INFO @ Fri, 05 Jul 2019 20:40:26: 12000000 INFO @ Fri, 05 Jul 2019 20:40:30: 14000000 INFO @ Fri, 05 Jul 2019 20:40:31: 13000000 INFO @ Fri, 05 Jul 2019 20:40:34: 13000000 INFO @ Fri, 05 Jul 2019 20:40:37: 15000000 INFO @ Fri, 05 Jul 2019 20:40:38: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:40:38: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:40:38: #1 total tags in treatment: 15101046 INFO @ Fri, 05 Jul 2019 20:40:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:40:38: #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 20:40:38: #1 tags after filtering in treatment: 15101046 INFO @ Fri, 05 Jul 2019 20:40:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:40:38: #1 finished! INFO @ Fri, 05 Jul 2019 20:40:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:40:38: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 20:40:39: 14000000 INFO @ Fri, 05 Jul 2019 20:40:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:40:39: 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 20:40:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.10_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/SRX193513/SRX193513.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:40:41: 14000000 INFO @ Fri, 05 Jul 2019 20:40:46: 15000000 INFO @ Fri, 05 Jul 2019 20:40:47: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:40:47: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:40:47: #1 total tags in treatment: 15101046 INFO @ Fri, 05 Jul 2019 20:40:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:40:47: #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 20:40:47: #1 tags after filtering in treatment: 15101046 INFO @ Fri, 05 Jul 2019 20:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:40:47: #1 finished! INFO @ Fri, 05 Jul 2019 20:40:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:40:48: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:40:48: 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 20:40:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.05_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/SRX193513/SRX193513.05_model.r’: No such file or directory rm: INFO @ Fri, 05 Jul 2019 20:40:48: 15000000 cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:40:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:40:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:40:49: #1 total tags in treatment: 15101046 INFO @ Fri, 05 Jul 2019 20:40:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:40:49: #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 20:40:50: #1 tags after filtering in treatment: 15101046 INFO @ Fri, 05 Jul 2019 20:40:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:40:50: #1 finished! INFO @ Fri, 05 Jul 2019 20:40:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:40:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:40:51: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:40:51: 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 20:40:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.20_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/SRX193513/SRX193513.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193513/SRX193513.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。