Job ID = 2010055 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T12:21:44 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 ) 2019-07-05T12:24:36 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 ) 2019-07-05T12:31:10 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 : 45,346,306 reads read : 45,346,306 reads written : 45,346,306 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: 00:08:14 45346306 reads; of these: 45346306 (100.00%) were unpaired; of these: 2460777 (5.43%) aligned 0 times 31651463 (69.80%) aligned exactly 1 time 11234066 (24.77%) aligned >1 times 94.57% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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 20 files... [bam_rmdupse_core] 29676292 / 42885529 = 0.6920 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 21:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.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 21:50:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:50:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:50:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.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 21:50:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:50:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.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 21:50:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:50:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:50:20: 1000000 INFO @ Fri, 05 Jul 2019 21:50:22: 1000000 INFO @ Fri, 05 Jul 2019 21:50:23: 1000000 INFO @ Fri, 05 Jul 2019 21:50:30: 2000000 INFO @ Fri, 05 Jul 2019 21:50:31: 2000000 INFO @ Fri, 05 Jul 2019 21:50:34: 2000000 INFO @ Fri, 05 Jul 2019 21:50:39: 3000000 INFO @ Fri, 05 Jul 2019 21:50:40: 3000000 INFO @ Fri, 05 Jul 2019 21:50:44: 3000000 INFO @ Fri, 05 Jul 2019 21:50:48: 4000000 INFO @ Fri, 05 Jul 2019 21:50:50: 4000000 INFO @ Fri, 05 Jul 2019 21:50:54: 4000000 INFO @ Fri, 05 Jul 2019 21:50:57: 5000000 INFO @ Fri, 05 Jul 2019 21:50:58: 5000000 INFO @ Fri, 05 Jul 2019 21:51:04: 5000000 INFO @ Fri, 05 Jul 2019 21:51:06: 6000000 INFO @ Fri, 05 Jul 2019 21:51:07: 6000000 INFO @ Fri, 05 Jul 2019 21:51:13: 6000000 INFO @ Fri, 05 Jul 2019 21:51:15: 7000000 INFO @ Fri, 05 Jul 2019 21:51:16: 7000000 INFO @ Fri, 05 Jul 2019 21:51:23: 7000000 INFO @ Fri, 05 Jul 2019 21:51:24: 8000000 INFO @ Fri, 05 Jul 2019 21:51:25: 8000000 INFO @ Fri, 05 Jul 2019 21:51:32: 9000000 INFO @ Fri, 05 Jul 2019 21:51:33: 8000000 INFO @ Fri, 05 Jul 2019 21:51:33: 9000000 INFO @ Fri, 05 Jul 2019 21:51:41: 10000000 INFO @ Fri, 05 Jul 2019 21:51:43: 10000000 INFO @ Fri, 05 Jul 2019 21:51:43: 9000000 INFO @ Fri, 05 Jul 2019 21:51:52: 11000000 INFO @ Fri, 05 Jul 2019 21:51:53: 11000000 INFO @ Fri, 05 Jul 2019 21:51:53: 10000000 INFO @ Fri, 05 Jul 2019 21:52:02: 12000000 INFO @ Fri, 05 Jul 2019 21:52:02: 11000000 INFO @ Fri, 05 Jul 2019 21:52:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:52:11: 12000000 INFO @ Fri, 05 Jul 2019 21:52:12: 13000000 INFO @ Fri, 05 Jul 2019 21:52:13: 13000000 INFO @ Fri, 05 Jul 2019 21:52:13: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:52:13: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:52:13: #1 total tags in treatment: 13209237 INFO @ Fri, 05 Jul 2019 21:52:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:52:13: #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 21:52:14: #1 tags after filtering in treatment: 13209237 INFO @ Fri, 05 Jul 2019 21:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:52:14: #1 finished! INFO @ Fri, 05 Jul 2019 21:52:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:52:14: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:52:14: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:52:14: #1 total tags in treatment: 13209237 INFO @ Fri, 05 Jul 2019 21:52:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:52:14: #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 21:52:15: #1 tags after filtering in treatment: 13209237 INFO @ Fri, 05 Jul 2019 21:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:52:15: #1 finished! INFO @ Fri, 05 Jul 2019 21:52:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:52:15: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:52:15: 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 21:52:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.05_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 21:52:16: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:52:16: 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 21:52:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.10_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/SRX2609718/SRX2609718.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 pass1 - making usageList (0 chroms): 3819 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:52:21: 13000000 INFO @ Fri, 05 Jul 2019 21:52:23: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:52:23: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:52:23: #1 total tags in treatment: 13209237 INFO @ Fri, 05 Jul 2019 21:52:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:52:23: #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 21:52:23: #1 tags after filtering in treatment: 13209237 INFO @ Fri, 05 Jul 2019 21:52:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:52:23: #1 finished! INFO @ Fri, 05 Jul 2019 21:52:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:52:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:52:24: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:52:24: 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 21:52:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.20_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/SRX2609718/SRX2609718.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2609718/SRX2609718.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling