Job ID = 2009852 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T11:08:43 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 ) 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 : 48,106,811 reads read : 48,106,811 reads written : 48,106,811 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR585732.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: 00:05:54 48106811 reads; of these: 48106811 (100.00%) were unpaired; of these: 11521596 (23.95%) aligned 0 times 32592379 (67.75%) aligned exactly 1 time 3992836 (8.30%) aligned >1 times 76.05% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 24138301 / 36585215 = 0.6598 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 20:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.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 20:25:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:25:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:25:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.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 20:25:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:25:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:25:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.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 20:25:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:25:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:25:26: 1000000 INFO @ Fri, 05 Jul 2019 20:25:26: 1000000 INFO @ Fri, 05 Jul 2019 20:25:27: 1000000 INFO @ Fri, 05 Jul 2019 20:25:33: 2000000 INFO @ Fri, 05 Jul 2019 20:25:35: 2000000 INFO @ Fri, 05 Jul 2019 20:25:36: 2000000 INFO @ Fri, 05 Jul 2019 20:25:40: 3000000 INFO @ Fri, 05 Jul 2019 20:25:43: 3000000 INFO @ Fri, 05 Jul 2019 20:25:45: 3000000 INFO @ Fri, 05 Jul 2019 20:25:46: 4000000 INFO @ Fri, 05 Jul 2019 20:25:51: 4000000 INFO @ Fri, 05 Jul 2019 20:25:52: 4000000 INFO @ Fri, 05 Jul 2019 20:25:53: 5000000 INFO @ Fri, 05 Jul 2019 20:25:59: 5000000 INFO @ Fri, 05 Jul 2019 20:26:00: 6000000 INFO @ Fri, 05 Jul 2019 20:26:00: 5000000 INFO @ Fri, 05 Jul 2019 20:26:07: 7000000 INFO @ Fri, 05 Jul 2019 20:26:08: 6000000 INFO @ Fri, 05 Jul 2019 20:26:09: 6000000 INFO @ Fri, 05 Jul 2019 20:26:13: 8000000 INFO @ Fri, 05 Jul 2019 20:26:16: 7000000 INFO @ Fri, 05 Jul 2019 20:26:17: 7000000 INFO @ Fri, 05 Jul 2019 20:26:20: 9000000 INFO @ Fri, 05 Jul 2019 20:26:25: 8000000 INFO @ Fri, 05 Jul 2019 20:26:25: 8000000 INFO @ Fri, 05 Jul 2019 20:26:27: 10000000 INFO @ Fri, 05 Jul 2019 20:26:33: 9000000 INFO @ Fri, 05 Jul 2019 20:26:33: 9000000 INFO @ Fri, 05 Jul 2019 20:26:34: 11000000 INFO @ Fri, 05 Jul 2019 20:26:41: 12000000 INFO @ Fri, 05 Jul 2019 20:26:41: 10000000 INFO @ Fri, 05 Jul 2019 20:26:42: 10000000 INFO @ Fri, 05 Jul 2019 20:26:44: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:26:44: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:26:44: #1 total tags in treatment: 12446914 INFO @ Fri, 05 Jul 2019 20:26:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:26:44: #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 20:26:44: #1 tags after filtering in treatment: 12446914 INFO @ Fri, 05 Jul 2019 20:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:26:44: #1 finished! INFO @ Fri, 05 Jul 2019 20:26:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:26:45: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:26:45: 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 20:26:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.20_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/SRX193511/SRX193511.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:26:49: 11000000 INFO @ Fri, 05 Jul 2019 20:26:50: 11000000 INFO @ Fri, 05 Jul 2019 20:26:58: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 20:26:59: 12000000 INFO @ Fri, 05 Jul 2019 20:27:01: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:27:01: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:27:01: #1 total tags in treatment: 12446914 INFO @ Fri, 05 Jul 2019 20:27:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:27:01: #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 20:27:01: #1 tags after filtering in treatment: 12446914 INFO @ Fri, 05 Jul 2019 20:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:27:01: #1 finished! INFO @ Fri, 05 Jul 2019 20:27:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:27:02: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:27:02: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:27:02: #1 total tags in treatment: 12446914 INFO @ Fri, 05 Jul 2019 20:27:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:27:02: #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 20:27:02: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:27:02: 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 20:27:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.10_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/SRX193511/SRX193511.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:27:03: #1 tags after filtering in treatment: 12446914 INFO @ Fri, 05 Jul 2019 20:27:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:27:03: #1 finished! INFO @ Fri, 05 Jul 2019 20:27:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:27:04: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:27:04: 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 @ Fri, 05 Jul 2019 20:27:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.05_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/SRX193511/SRX193511.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193511/SRX193511.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。