Job ID = 2008302 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T09:29:01 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 : 9,301,918 reads read : 18,603,836 reads written : 18,603,836 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: 00:11:40 9301918 reads; of these: 9301918 (100.00%) were paired; of these: 750696 (8.07%) aligned concordantly 0 times 7432666 (79.90%) aligned concordantly exactly 1 time 1118556 (12.03%) aligned concordantly >1 times ---- 750696 pairs aligned concordantly 0 times; of these: 306291 (40.80%) aligned discordantly 1 time ---- 444405 pairs aligned 0 times concordantly or discordantly; of these: 888810 mates make up the pairs; of these: 643306 (72.38%) aligned 0 times 106369 (11.97%) aligned exactly 1 time 139135 (15.65%) aligned >1 times 96.54% overall alignment rate Time searching: 00:11:40 Overall time: 00:11:44 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 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1186220 / 8826461 = 0.1344 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 19:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.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 19:08:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.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 19:08:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.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 19:08:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:08:50: 1000000 INFO @ Fri, 05 Jul 2019 19:08:53: 1000000 INFO @ Fri, 05 Jul 2019 19:08:56: 1000000 INFO @ Fri, 05 Jul 2019 19:08:58: 2000000 INFO @ Fri, 05 Jul 2019 19:09:04: 2000000 INFO @ Fri, 05 Jul 2019 19:09:07: 3000000 INFO @ Fri, 05 Jul 2019 19:09:07: 2000000 INFO @ Fri, 05 Jul 2019 19:09:15: 4000000 INFO @ Fri, 05 Jul 2019 19:09:16: 3000000 INFO @ Fri, 05 Jul 2019 19:09:19: 3000000 INFO @ Fri, 05 Jul 2019 19:09:24: 5000000 INFO @ Fri, 05 Jul 2019 19:09:28: 4000000 INFO @ Fri, 05 Jul 2019 19:09:31: 4000000 INFO @ Fri, 05 Jul 2019 19:09:32: 6000000 INFO @ Fri, 05 Jul 2019 19:09:39: 5000000 INFO @ Fri, 05 Jul 2019 19:09:41: 7000000 INFO @ Fri, 05 Jul 2019 19:09:42: 5000000 INFO @ Fri, 05 Jul 2019 19:09:49: 8000000 INFO @ Fri, 05 Jul 2019 19:09:51: 6000000 INFO @ Fri, 05 Jul 2019 19:09:53: 6000000 INFO @ Fri, 05 Jul 2019 19:09:57: 9000000 INFO @ Fri, 05 Jul 2019 19:10:02: 7000000 INFO @ Fri, 05 Jul 2019 19:10:05: 7000000 INFO @ Fri, 05 Jul 2019 19:10:06: 10000000 INFO @ Fri, 05 Jul 2019 19:10:14: 8000000 INFO @ Fri, 05 Jul 2019 19:10:14: 11000000 INFO @ Fri, 05 Jul 2019 19:10:16: 8000000 INFO @ Fri, 05 Jul 2019 19:10:24: 12000000 INFO @ Fri, 05 Jul 2019 19:10:25: 9000000 INFO @ Fri, 05 Jul 2019 19:10:28: 9000000 INFO @ Fri, 05 Jul 2019 19:10:33: 13000000 INFO @ Fri, 05 Jul 2019 19:10:36: 10000000 INFO @ Fri, 05 Jul 2019 19:10:39: 10000000 INFO @ Fri, 05 Jul 2019 19:10:43: 14000000 INFO @ Fri, 05 Jul 2019 19:10:48: 11000000 INFO @ Fri, 05 Jul 2019 19:10:50: 11000000 INFO @ Fri, 05 Jul 2019 19:10:51: 15000000 INFO @ Fri, 05 Jul 2019 19:10:56: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:10:56: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:10:56: #1 total tags in treatment: 7378166 INFO @ Fri, 05 Jul 2019 19:10:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:10:56: #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 19:10:57: #1 tags after filtering in treatment: 4232584 INFO @ Fri, 05 Jul 2019 19:10:57: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 05 Jul 2019 19:10:57: #1 finished! INFO @ Fri, 05 Jul 2019 19:10:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:10:57: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:10:57: 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 19:10:57: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:10:59: 12000000 INFO @ Fri, 05 Jul 2019 19:11:01: 12000000 cut: /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.05_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/ERX585812/ERX585812.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:11:10: 13000000 INFO @ Fri, 05 Jul 2019 19:11:13: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:11:20: 14000000 INFO @ Fri, 05 Jul 2019 19:11:23: 14000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:11:32: 15000000 INFO @ Fri, 05 Jul 2019 19:11:35: 15000000 INFO @ Fri, 05 Jul 2019 19:11:38: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:11:38: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:11:38: #1 total tags in treatment: 7378166 INFO @ Fri, 05 Jul 2019 19:11:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:11:38: #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 19:11:39: #1 tags after filtering in treatment: 4232584 INFO @ Fri, 05 Jul 2019 19:11:39: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 05 Jul 2019 19:11:39: #1 finished! INFO @ Fri, 05 Jul 2019 19:11:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:11:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:11:39: 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 19:11:39: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:11:41: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:11:41: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:11:41: #1 total tags in treatment: 7378166 INFO @ Fri, 05 Jul 2019 19:11:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:11:41: #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 19:11:42: #1 tags after filtering in treatment: 4232584 INFO @ Fri, 05 Jul 2019 19:11:42: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 05 Jul 2019 19:11:42: #1 finished! INFO @ Fri, 05 Jul 2019 19:11:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:11:42: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:11:42: 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 19:11:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.20_model.r’rm: : No such file or directorycannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.10_model.r’ : No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.20_*.xls’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.10_*.xls’: No such file or directory: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.20_peaks.narrowPeak’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585812/ERX585812.10_peaks.narrowPeak’: No such file or directory: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling