Job ID = 2010317 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:03:15 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 ) 2019-07-05T13:04:02 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 : 15,216,466 reads read : 30,432,932 reads written : 30,432,932 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1009109.sra.cache’: 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: 00:11:25 15216466 reads; of these: 15216466 (100.00%) were paired; of these: 4877296 (32.05%) aligned concordantly 0 times 6425293 (42.23%) aligned concordantly exactly 1 time 3913877 (25.72%) aligned concordantly >1 times ---- 4877296 pairs aligned concordantly 0 times; of these: 4743 (0.10%) aligned discordantly 1 time ---- 4872553 pairs aligned 0 times concordantly or discordantly; of these: 9745106 mates make up the pairs; of these: 9143916 (93.83%) aligned 0 times 161097 (1.65%) aligned exactly 1 time 440093 (4.52%) aligned >1 times 69.95% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 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] 2100279 / 10335023 = 0.2032 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 22:25:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.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 22:25:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:25:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.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 22:25:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:25:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.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 22:25:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:25:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:25:47: 1000000 INFO @ Fri, 05 Jul 2019 22:25:47: 1000000 INFO @ Fri, 05 Jul 2019 22:25:50: 1000000 INFO @ Fri, 05 Jul 2019 22:25:54: 2000000 INFO @ Fri, 05 Jul 2019 22:25:55: 2000000 INFO @ Fri, 05 Jul 2019 22:25:58: 2000000 INFO @ Fri, 05 Jul 2019 22:26:02: 3000000 INFO @ Fri, 05 Jul 2019 22:26:03: 3000000 INFO @ Fri, 05 Jul 2019 22:26:06: 3000000 INFO @ Fri, 05 Jul 2019 22:26:09: 4000000 INFO @ Fri, 05 Jul 2019 22:26:10: 4000000 INFO @ Fri, 05 Jul 2019 22:26:15: 4000000 INFO @ Fri, 05 Jul 2019 22:26:16: 5000000 INFO @ Fri, 05 Jul 2019 22:26:18: 5000000 INFO @ Fri, 05 Jul 2019 22:26:23: 5000000 INFO @ Fri, 05 Jul 2019 22:26:23: 6000000 INFO @ Fri, 05 Jul 2019 22:26:26: 6000000 INFO @ Fri, 05 Jul 2019 22:26:31: 7000000 INFO @ Fri, 05 Jul 2019 22:26:31: 6000000 INFO @ Fri, 05 Jul 2019 22:26:33: 7000000 INFO @ Fri, 05 Jul 2019 22:26:38: 8000000 INFO @ Fri, 05 Jul 2019 22:26:40: 7000000 INFO @ Fri, 05 Jul 2019 22:26:40: 8000000 INFO @ Fri, 05 Jul 2019 22:26:45: 9000000 INFO @ Fri, 05 Jul 2019 22:26:47: 9000000 INFO @ Fri, 05 Jul 2019 22:26:48: 8000000 INFO @ Fri, 05 Jul 2019 22:26:52: 10000000 INFO @ Fri, 05 Jul 2019 22:26:54: 10000000 INFO @ Fri, 05 Jul 2019 22:26:56: 9000000 INFO @ Fri, 05 Jul 2019 22:26:59: 11000000 INFO @ Fri, 05 Jul 2019 22:27:01: 11000000 INFO @ Fri, 05 Jul 2019 22:27:04: 10000000 INFO @ Fri, 05 Jul 2019 22:27:06: 12000000 INFO @ Fri, 05 Jul 2019 22:27:08: 12000000 INFO @ Fri, 05 Jul 2019 22:27:12: 11000000 INFO @ Fri, 05 Jul 2019 22:27:13: 13000000 INFO @ Fri, 05 Jul 2019 22:27:15: 13000000 INFO @ Fri, 05 Jul 2019 22:27:20: 12000000 INFO @ Fri, 05 Jul 2019 22:27:21: 14000000 INFO @ Fri, 05 Jul 2019 22:27:23: 14000000 INFO @ Fri, 05 Jul 2019 22:27:27: 13000000 INFO @ Fri, 05 Jul 2019 22:27:29: 15000000 INFO @ Fri, 05 Jul 2019 22:27:31: 15000000 INFO @ Fri, 05 Jul 2019 22:27:35: 14000000 INFO @ Fri, 05 Jul 2019 22:27:36: 16000000 INFO @ Fri, 05 Jul 2019 22:27:38: 16000000 INFO @ Fri, 05 Jul 2019 22:27:43: 15000000 INFO @ Fri, 05 Jul 2019 22:27:43: 17000000 INFO @ Fri, 05 Jul 2019 22:27:44: #1 tag size is determined as 45 bps INFO @ Fri, 05 Jul 2019 22:27:44: #1 tag size = 45 INFO @ Fri, 05 Jul 2019 22:27:44: #1 total tags in treatment: 8239395 INFO @ Fri, 05 Jul 2019 22:27:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:27:44: #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 22:27:44: #1 tags after filtering in treatment: 5072268 INFO @ Fri, 05 Jul 2019 22:27:44: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 22:27:44: #1 finished! INFO @ Fri, 05 Jul 2019 22:27:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:27:44: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:27:44: 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 22:27:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.05_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/SRX362219/SRX362219.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:27:45: 17000000 INFO @ Fri, 05 Jul 2019 22:27:46: #1 tag size is determined as 45 bps INFO @ Fri, 05 Jul 2019 22:27:46: #1 tag size = 45 INFO @ Fri, 05 Jul 2019 22:27:46: #1 total tags in treatment: 8239395 INFO @ Fri, 05 Jul 2019 22:27:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:27:46: #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 22:27:46: #1 tags after filtering in treatment: 5072268 INFO @ Fri, 05 Jul 2019 22:27:46: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 22:27:46: #1 finished! INFO @ Fri, 05 Jul 2019 22:27:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:27:46: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:27:46: 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 22:27:46: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 22:27:50: 16000000 INFO @ Fri, 05 Jul 2019 22:27:58: 17000000 INFO @ Fri, 05 Jul 2019 22:27:59: #1 tag size is determined as 45 bps INFO @ Fri, 05 Jul 2019 22:27:59: #1 tag size = 45 INFO @ Fri, 05 Jul 2019 22:27:59: #1 total tags in treatment: 8239395 INFO @ Fri, 05 Jul 2019 22:27:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:27:59: #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 22:27:59: #1 tags after filtering in treatment: 5072268 INFO @ Fri, 05 Jul 2019 22:27:59: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 22:27:59: #1 finished! INFO @ Fri, 05 Jul 2019 22:27:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:27:59: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:27:59: 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 22:27:59: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.20_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX362219/SRX362219.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。