Job ID = 2010571 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:14:20 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 : 12,278,914 reads read : 24,557,828 reads written : 24,557,828 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: 00:09:09 12278914 reads; of these: 12278914 (100.00%) were paired; of these: 3105599 (25.29%) aligned concordantly 0 times 6909571 (56.27%) aligned concordantly exactly 1 time 2263744 (18.44%) aligned concordantly >1 times ---- 3105599 pairs aligned concordantly 0 times; of these: 316639 (10.20%) aligned discordantly 1 time ---- 2788960 pairs aligned 0 times concordantly or discordantly; of these: 5577920 mates make up the pairs; of these: 5196209 (93.16%) aligned 0 times 173358 (3.11%) aligned exactly 1 time 208353 (3.74%) aligned >1 times 78.84% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 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] 1825505 / 9481997 = 0.1925 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 23:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.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 23:40:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:40:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:40:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.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 23:40:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:40:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.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 23:40:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:40:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:40:18: 1000000 INFO @ Fri, 05 Jul 2019 23:40:19: 1000000 INFO @ Fri, 05 Jul 2019 23:40:21: 1000000 INFO @ Fri, 05 Jul 2019 23:40:26: 2000000 INFO @ Fri, 05 Jul 2019 23:40:26: 2000000 INFO @ Fri, 05 Jul 2019 23:40:31: 2000000 INFO @ Fri, 05 Jul 2019 23:40:33: 3000000 INFO @ Fri, 05 Jul 2019 23:40:34: 3000000 INFO @ Fri, 05 Jul 2019 23:40:40: 4000000 INFO @ Fri, 05 Jul 2019 23:40:40: 3000000 INFO @ Fri, 05 Jul 2019 23:40:42: 4000000 INFO @ Fri, 05 Jul 2019 23:40:47: 5000000 INFO @ Fri, 05 Jul 2019 23:40:49: 5000000 INFO @ Fri, 05 Jul 2019 23:40:50: 4000000 INFO @ Fri, 05 Jul 2019 23:40:54: 6000000 INFO @ Fri, 05 Jul 2019 23:40:57: 6000000 INFO @ Fri, 05 Jul 2019 23:41:00: 5000000 INFO @ Fri, 05 Jul 2019 23:41:01: 7000000 INFO @ Fri, 05 Jul 2019 23:41:05: 7000000 INFO @ Fri, 05 Jul 2019 23:41:08: 8000000 INFO @ Fri, 05 Jul 2019 23:41:10: 6000000 INFO @ Fri, 05 Jul 2019 23:41:13: 8000000 INFO @ Fri, 05 Jul 2019 23:41:14: 9000000 INFO @ Fri, 05 Jul 2019 23:41:19: 7000000 INFO @ Fri, 05 Jul 2019 23:41:21: 9000000 INFO @ Fri, 05 Jul 2019 23:41:21: 10000000 INFO @ Fri, 05 Jul 2019 23:41:28: 11000000 INFO @ Fri, 05 Jul 2019 23:41:28: 10000000 INFO @ Fri, 05 Jul 2019 23:41:29: 8000000 INFO @ Fri, 05 Jul 2019 23:41:35: 12000000 INFO @ Fri, 05 Jul 2019 23:41:36: 11000000 INFO @ Fri, 05 Jul 2019 23:41:39: 9000000 INFO @ Fri, 05 Jul 2019 23:41:41: 13000000 INFO @ Fri, 05 Jul 2019 23:41:44: 12000000 INFO @ Fri, 05 Jul 2019 23:41:48: 10000000 INFO @ Fri, 05 Jul 2019 23:41:48: 14000000 INFO @ Fri, 05 Jul 2019 23:41:52: 13000000 INFO @ Fri, 05 Jul 2019 23:41:55: 15000000 INFO @ Fri, 05 Jul 2019 23:41:57: 11000000 INFO @ Fri, 05 Jul 2019 23:41:59: 14000000 INFO @ Fri, 05 Jul 2019 23:42:00: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:42:00: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:42:00: #1 total tags in treatment: 7395993 INFO @ Fri, 05 Jul 2019 23:42:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:42:00: #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 23:42:00: #1 tags after filtering in treatment: 5004637 INFO @ Fri, 05 Jul 2019 23:42:00: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:42:00: #1 finished! INFO @ Fri, 05 Jul 2019 23:42:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:42:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:42:01: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:42:01: 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 23:42:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.20_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/SRX381272/SRX381272.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:42:07: 12000000 INFO @ Fri, 05 Jul 2019 23:42:07: 15000000 INFO @ Fri, 05 Jul 2019 23:42:13: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:42:13: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:42:13: #1 total tags in treatment: 7395993 INFO @ Fri, 05 Jul 2019 23:42:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:42:13: #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 23:42:13: #1 tags after filtering in treatment: 5004637 INFO @ Fri, 05 Jul 2019 23:42:13: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:42:13: #1 finished! INFO @ Fri, 05 Jul 2019 23:42:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:42:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:42:13: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:42:13: 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 23:42:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.05_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/SRX381272/SRX381272.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:42:16: 13000000 INFO @ Fri, 05 Jul 2019 23:42:25: 14000000 INFO @ Fri, 05 Jul 2019 23:42:34: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:42:40: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:42:40: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:42:40: #1 total tags in treatment: 7395993 INFO @ Fri, 05 Jul 2019 23:42:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:42:40: #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 23:42:40: #1 tags after filtering in treatment: 5004637 INFO @ Fri, 05 Jul 2019 23:42:40: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 23:42:40: #1 finished! INFO @ Fri, 05 Jul 2019 23:42:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:42:41: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:42:41: 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 @ Fri, 05 Jul 2019 23:42:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.10_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/SRX381272/SRX381272.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381272/SRX381272.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。