Job ID = 2640741 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T10:04:34 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 : 46,323,127 reads read : 46,323,127 reads written : 46,323,127 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: 00:12:10 46323127 reads; of these: 46323127 (100.00%) were unpaired; of these: 948711 (2.05%) aligned 0 times 39638731 (85.57%) aligned exactly 1 time 5735685 (12.38%) aligned >1 times 97.95% overall alignment rate Time searching: 00:12:10 Overall time: 00:12:10 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] 27514537 / 45374416 = 0.6064 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.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 19:36:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:36:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:36:27: 1000000 INFO @ Sat, 24 Aug 2019 19:36:38: 2000000 INFO @ Sat, 24 Aug 2019 19:36:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.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 19:36:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:36:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:36:50: 3000000 INFO @ Sat, 24 Aug 2019 19:36:55: 1000000 INFO @ Sat, 24 Aug 2019 19:37:01: 4000000 INFO @ Sat, 24 Aug 2019 19:37:04: 2000000 INFO @ Sat, 24 Aug 2019 19:37:12: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:37:14: 3000000 INFO @ Sat, 24 Aug 2019 19:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.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 19:37:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:37:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:37:23: 4000000 INFO @ Sat, 24 Aug 2019 19:37:24: 6000000 INFO @ Sat, 24 Aug 2019 19:37:25: 1000000 INFO @ Sat, 24 Aug 2019 19:37:32: 5000000 INFO @ Sat, 24 Aug 2019 19:37:34: 2000000 INFO @ Sat, 24 Aug 2019 19:37:35: 7000000 INFO @ Sat, 24 Aug 2019 19:37:42: 6000000 INFO @ Sat, 24 Aug 2019 19:37:44: 3000000 INFO @ Sat, 24 Aug 2019 19:37:47: 8000000 INFO @ Sat, 24 Aug 2019 19:37:51: 7000000 INFO @ Sat, 24 Aug 2019 19:37:53: 4000000 INFO @ Sat, 24 Aug 2019 19:37:58: 9000000 INFO @ Sat, 24 Aug 2019 19:38:01: 8000000 INFO @ Sat, 24 Aug 2019 19:38:02: 5000000 INFO @ Sat, 24 Aug 2019 19:38:10: 10000000 INFO @ Sat, 24 Aug 2019 19:38:10: 9000000 INFO @ Sat, 24 Aug 2019 19:38:11: 6000000 INFO @ Sat, 24 Aug 2019 19:38:20: 10000000 INFO @ Sat, 24 Aug 2019 19:38:21: 7000000 INFO @ Sat, 24 Aug 2019 19:38:21: 11000000 INFO @ Sat, 24 Aug 2019 19:38:29: 11000000 INFO @ Sat, 24 Aug 2019 19:38:30: 8000000 INFO @ Sat, 24 Aug 2019 19:38:33: 12000000 INFO @ Sat, 24 Aug 2019 19:38:38: 12000000 INFO @ Sat, 24 Aug 2019 19:38:39: 9000000 INFO @ Sat, 24 Aug 2019 19:38:44: 13000000 INFO @ Sat, 24 Aug 2019 19:38:48: 13000000 INFO @ Sat, 24 Aug 2019 19:38:49: 10000000 INFO @ Sat, 24 Aug 2019 19:38:56: 14000000 INFO @ Sat, 24 Aug 2019 19:38:57: 14000000 INFO @ Sat, 24 Aug 2019 19:38:58: 11000000 INFO @ Sat, 24 Aug 2019 19:39:07: 15000000 INFO @ Sat, 24 Aug 2019 19:39:07: 15000000 INFO @ Sat, 24 Aug 2019 19:39:07: 12000000 INFO @ Sat, 24 Aug 2019 19:39:16: 16000000 INFO @ Sat, 24 Aug 2019 19:39:17: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 19:39:19: 16000000 INFO @ Sat, 24 Aug 2019 19:39:26: 17000000 INFO @ Sat, 24 Aug 2019 19:39:26: 14000000 INFO @ Sat, 24 Aug 2019 19:39:30: 17000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 19:39:34: #1 tag size is determined as 31 bps INFO @ Sat, 24 Aug 2019 19:39:34: #1 tag size = 31 INFO @ Sat, 24 Aug 2019 19:39:34: #1 total tags in treatment: 17859879 INFO @ Sat, 24 Aug 2019 19:39:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:39:34: #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 19:39:34: #1 tags after filtering in treatment: 17859879 INFO @ Sat, 24 Aug 2019 19:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:39:34: #1 finished! INFO @ Sat, 24 Aug 2019 19:39:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:39:35: 15000000 INFO @ Sat, 24 Aug 2019 19:39:35: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:39:35: 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 19:39:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.10_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/ERX2732432/ERX2732432.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:39:40: #1 tag size is determined as 31 bps INFO @ Sat, 24 Aug 2019 19:39:40: #1 tag size = 31 INFO @ Sat, 24 Aug 2019 19:39:40: #1 total tags in treatment: 17859879 INFO @ Sat, 24 Aug 2019 19:39:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:39:40: #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 19:39:40: #1 tags after filtering in treatment: 17859879 INFO @ Sat, 24 Aug 2019 19:39:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:39:40: #1 finished! INFO @ Sat, 24 Aug 2019 19:39:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:39:41: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:39:41: 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 @ Sat, 24 Aug 2019 19:39:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.05_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/ERX2732432/ERX2732432.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:39:44: 16000000 INFO @ Sat, 24 Aug 2019 19:39:53: 17000000 INFO @ Sat, 24 Aug 2019 19:40:00: #1 tag size is determined as 31 bps INFO @ Sat, 24 Aug 2019 19:40:00: #1 tag size = 31 INFO @ Sat, 24 Aug 2019 19:40:00: #1 total tags in treatment: 17859879 INFO @ Sat, 24 Aug 2019 19:40:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:40:00: #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 19:40:01: #1 tags after filtering in treatment: 17859879 INFO @ Sat, 24 Aug 2019 19:40:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:40:01: #1 finished! INFO @ Sat, 24 Aug 2019 19:40:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:40:02: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:40:02: 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 @ Sat, 24 Aug 2019 19:40:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.20_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/ERX2732432/ERX2732432.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732432/ERX2732432.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling