Job ID = 2011827 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:50:39 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 ) 2019-07-05T17:53:37 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 ) 2019-07-05T17:53:37 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 : 15,828,117 reads read : 31,656,234 reads written : 31,656,234 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: 00:14:54 15828117 reads; of these: 15828117 (100.00%) were paired; of these: 2625236 (16.59%) aligned concordantly 0 times 6816770 (43.07%) aligned concordantly exactly 1 time 6386111 (40.35%) aligned concordantly >1 times ---- 2625236 pairs aligned concordantly 0 times; of these: 15683 (0.60%) aligned discordantly 1 time ---- 2609553 pairs aligned 0 times concordantly or discordantly; of these: 5219106 mates make up the pairs; of these: 4725837 (90.55%) aligned 0 times 246994 (4.73%) aligned exactly 1 time 246275 (4.72%) aligned >1 times 85.07% overall alignment rate Time searching: 00:14:54 Overall time: 00:14:54 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_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] 6433907 / 13213903 = 0.4869 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 @ Sat, 06 Jul 2019 03:19:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.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, 06 Jul 2019 03:19:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:19:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:19:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.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, 06 Jul 2019 03:19:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:19:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.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, 06 Jul 2019 03:19:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:19:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:19:48: 1000000 INFO @ Sat, 06 Jul 2019 03:19:50: 1000000 INFO @ Sat, 06 Jul 2019 03:19:51: 1000000 INFO @ Sat, 06 Jul 2019 03:19:55: 2000000 INFO @ Sat, 06 Jul 2019 03:19:58: 2000000 INFO @ Sat, 06 Jul 2019 03:19:59: 2000000 INFO @ Sat, 06 Jul 2019 03:20:02: 3000000 INFO @ Sat, 06 Jul 2019 03:20:05: 3000000 INFO @ Sat, 06 Jul 2019 03:20:07: 3000000 INFO @ Sat, 06 Jul 2019 03:20:09: 4000000 INFO @ Sat, 06 Jul 2019 03:20:13: 4000000 INFO @ Sat, 06 Jul 2019 03:20:15: 4000000 INFO @ Sat, 06 Jul 2019 03:20:16: 5000000 INFO @ Sat, 06 Jul 2019 03:20:21: 5000000 INFO @ Sat, 06 Jul 2019 03:20:22: 5000000 INFO @ Sat, 06 Jul 2019 03:20:23: 6000000 INFO @ Sat, 06 Jul 2019 03:20:29: 6000000 INFO @ Sat, 06 Jul 2019 03:20:29: 7000000 INFO @ Sat, 06 Jul 2019 03:20:30: 6000000 INFO @ Sat, 06 Jul 2019 03:20:36: 8000000 INFO @ Sat, 06 Jul 2019 03:20:37: 7000000 INFO @ Sat, 06 Jul 2019 03:20:38: 7000000 INFO @ Sat, 06 Jul 2019 03:20:42: 9000000 INFO @ Sat, 06 Jul 2019 03:20:45: 8000000 INFO @ Sat, 06 Jul 2019 03:20:46: 8000000 INFO @ Sat, 06 Jul 2019 03:20:49: 10000000 INFO @ Sat, 06 Jul 2019 03:20:53: 9000000 INFO @ Sat, 06 Jul 2019 03:20:53: 9000000 INFO @ Sat, 06 Jul 2019 03:20:56: 11000000 INFO @ Sat, 06 Jul 2019 03:21:00: 10000000 INFO @ Sat, 06 Jul 2019 03:21:01: 10000000 INFO @ Sat, 06 Jul 2019 03:21:03: 12000000 INFO @ Sat, 06 Jul 2019 03:21:08: 11000000 INFO @ Sat, 06 Jul 2019 03:21:08: 11000000 INFO @ Sat, 06 Jul 2019 03:21:09: 13000000 INFO @ Sat, 06 Jul 2019 03:21:15: 12000000 INFO @ Sat, 06 Jul 2019 03:21:16: 14000000 INFO @ Sat, 06 Jul 2019 03:21:16: 12000000 INFO @ Sat, 06 Jul 2019 03:21:16: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 03:21:16: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 03:21:16: #1 total tags in treatment: 6771645 INFO @ Sat, 06 Jul 2019 03:21:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:21:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:21:17: #1 tags after filtering in treatment: 3695724 INFO @ Sat, 06 Jul 2019 03:21:17: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 06 Jul 2019 03:21:17: #1 finished! INFO @ Sat, 06 Jul 2019 03:21:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:21:17: #2 number of paired peaks: 69 WARNING @ Sat, 06 Jul 2019 03:21:17: Too few paired peaks (69) 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, 06 Jul 2019 03:21:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.05_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/SRX5123299/SRX5123299.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:21:23: 13000000 INFO @ Sat, 06 Jul 2019 03:21:24: 13000000 INFO @ Sat, 06 Jul 2019 03:21:31: 14000000 INFO @ Sat, 06 Jul 2019 03:21:31: 14000000 INFO @ Sat, 06 Jul 2019 03:21:31: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 03:21:31: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 03:21:31: #1 total tags in treatment: 6771645 INFO @ Sat, 06 Jul 2019 03:21:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:21:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:21:32: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 03:21:32: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 03:21:32: #1 total tags in treatment: 6771645 INFO @ Sat, 06 Jul 2019 03:21:32: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:21:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:21:32: #1 tags after filtering in treatment: 3695724 INFO @ Sat, 06 Jul 2019 03:21:32: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 06 Jul 2019 03:21:32: #1 finished! INFO @ Sat, 06 Jul 2019 03:21:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:21:32: #1 tags after filtering in treatment: 3695724 INFO @ Sat, 06 Jul 2019 03:21:32: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 06 Jul 2019 03:21:32: #1 finished! INFO @ Sat, 06 Jul 2019 03:21:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:21:32: #2 number of paired peaks: 69 WARNING @ Sat, 06 Jul 2019 03:21:32: Too few paired peaks (69) 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, 06 Jul 2019 03:21:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.10_peaks.narrowPeak: No such file or directory INFO @ Sat, 06 Jul 2019 03:21:32: #2 number of paired peaks: 69 WARNING @ Sat, 06 Jul 2019 03:21:32: Too few paired peaks (69) 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, 06 Jul 2019 03:21:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.20_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/SRX5123299/SRX5123299.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5123299/SRX5123299.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。