Job ID = 2010578 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:25:45 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 ) 2019-07-05T14:25:45 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 : 10,998,430 reads read : 21,996,860 reads written : 21,996,860 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: 00:10:16 10998430 reads; of these: 10998430 (100.00%) were paired; of these: 1273257 (11.58%) aligned concordantly 0 times 8186381 (74.43%) aligned concordantly exactly 1 time 1538792 (13.99%) aligned concordantly >1 times ---- 1273257 pairs aligned concordantly 0 times; of these: 201099 (15.79%) aligned discordantly 1 time ---- 1072158 pairs aligned 0 times concordantly or discordantly; of these: 2144316 mates make up the pairs; of these: 1930511 (90.03%) aligned 0 times 106466 (4.97%) aligned exactly 1 time 107339 (5.01%) aligned >1 times 91.22% overall alignment rate Time searching: 00:10:16 Overall time: 00:10:16 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] 148869 / 9881833 = 0.0151 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 23:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.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 23:44:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.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 23:44:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:44:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.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 23:44:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:44:56: 1000000 INFO @ Fri, 05 Jul 2019 23:44:56: 1000000 INFO @ Fri, 05 Jul 2019 23:44:59: 1000000 INFO @ Fri, 05 Jul 2019 23:45:03: 2000000 INFO @ Fri, 05 Jul 2019 23:45:04: 2000000 INFO @ Fri, 05 Jul 2019 23:45:07: 2000000 INFO @ Fri, 05 Jul 2019 23:45:10: 3000000 INFO @ Fri, 05 Jul 2019 23:45:13: 3000000 INFO @ Fri, 05 Jul 2019 23:45:15: 3000000 INFO @ Fri, 05 Jul 2019 23:45:18: 4000000 INFO @ Fri, 05 Jul 2019 23:45:21: 4000000 INFO @ Fri, 05 Jul 2019 23:45:24: 4000000 INFO @ Fri, 05 Jul 2019 23:45:25: 5000000 INFO @ Fri, 05 Jul 2019 23:45:30: 5000000 INFO @ Fri, 05 Jul 2019 23:45:32: 6000000 INFO @ Fri, 05 Jul 2019 23:45:33: 5000000 INFO @ Fri, 05 Jul 2019 23:45:38: 6000000 INFO @ Fri, 05 Jul 2019 23:45:39: 7000000 INFO @ Fri, 05 Jul 2019 23:45:41: 6000000 INFO @ Fri, 05 Jul 2019 23:45:46: 7000000 INFO @ Fri, 05 Jul 2019 23:45:46: 8000000 INFO @ Fri, 05 Jul 2019 23:45:49: 7000000 INFO @ Fri, 05 Jul 2019 23:45:53: 9000000 INFO @ Fri, 05 Jul 2019 23:45:54: 8000000 INFO @ Fri, 05 Jul 2019 23:45:57: 8000000 INFO @ Fri, 05 Jul 2019 23:46:00: 10000000 INFO @ Fri, 05 Jul 2019 23:46:02: 9000000 INFO @ Fri, 05 Jul 2019 23:46:05: 9000000 INFO @ Fri, 05 Jul 2019 23:46:09: 11000000 INFO @ Fri, 05 Jul 2019 23:46:10: 10000000 INFO @ Fri, 05 Jul 2019 23:46:13: 10000000 INFO @ Fri, 05 Jul 2019 23:46:16: 12000000 INFO @ Fri, 05 Jul 2019 23:46:17: 11000000 INFO @ Fri, 05 Jul 2019 23:46:20: 11000000 INFO @ Fri, 05 Jul 2019 23:46:23: 13000000 INFO @ Fri, 05 Jul 2019 23:46:25: 12000000 INFO @ Fri, 05 Jul 2019 23:46:28: 12000000 INFO @ Fri, 05 Jul 2019 23:46:30: 14000000 INFO @ Fri, 05 Jul 2019 23:46:33: 13000000 INFO @ Fri, 05 Jul 2019 23:46:36: 13000000 INFO @ Fri, 05 Jul 2019 23:46:37: 15000000 INFO @ Fri, 05 Jul 2019 23:46:41: 14000000 INFO @ Fri, 05 Jul 2019 23:46:44: 14000000 INFO @ Fri, 05 Jul 2019 23:46:44: 16000000 INFO @ Fri, 05 Jul 2019 23:46:48: 15000000 INFO @ Fri, 05 Jul 2019 23:46:51: 17000000 INFO @ Fri, 05 Jul 2019 23:46:51: 15000000 INFO @ Fri, 05 Jul 2019 23:46:56: 16000000 INFO @ Fri, 05 Jul 2019 23:46:58: 18000000 INFO @ Fri, 05 Jul 2019 23:46:59: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:47:04: 17000000 INFO @ Fri, 05 Jul 2019 23:47:04: 19000000 INFO @ Fri, 05 Jul 2019 23:47:07: 17000000 INFO @ Fri, 05 Jul 2019 23:47:10: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:47:10: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:47:10: #1 total tags in treatment: 9576876 INFO @ Fri, 05 Jul 2019 23:47:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:47:10: #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 23:47:10: #1 tags after filtering in treatment: 5772579 INFO @ Fri, 05 Jul 2019 23:47:10: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:47:10: #1 finished! INFO @ Fri, 05 Jul 2019 23:47:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:47:10: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:47:10: 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 23:47:10: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:47:12: 18000000 INFO @ Fri, 05 Jul 2019 23:47:15: 18000000 INFO @ Fri, 05 Jul 2019 23:47:19: 19000000 INFO @ Fri, 05 Jul 2019 23:47:22: 19000000 INFO @ Fri, 05 Jul 2019 23:47:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:47:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:47:25: #1 total tags in treatment: 9576876 INFO @ Fri, 05 Jul 2019 23:47:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:47:25: #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 23:47:26: #1 tags after filtering in treatment: 5772579 INFO @ Fri, 05 Jul 2019 23:47:26: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:47:26: #1 finished! INFO @ Fri, 05 Jul 2019 23:47:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:47:26: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:47:26: 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 23:47:26: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:47:28: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:47:28: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:47:28: #1 total tags in treatment: 9576876 INFO @ Fri, 05 Jul 2019 23:47:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:47:28: #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 23:47:29: #1 tags after filtering in treatment: 5772579 INFO @ Fri, 05 Jul 2019 23:47:29: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:47:29: #1 finished! INFO @ Fri, 05 Jul 2019 23:47:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:47:29: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:47:29: 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 23:47:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.05_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/SRX381279/SRX381279.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.05_model.r’rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.10_*.xls’: No such file or directory: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.05_*.xls’: No such file or directoryrm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381279/SRX381279.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。