Job ID = 2010525 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:50:23 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T13:50:23 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035329' 2019-07-05T13:50:23 fasterq-dump.2.9.6 err: invalid accession 'SRR1035329' spots read : 12,830,028 reads read : 25,660,056 reads written : 25,660,056 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: 00:10:23 12830028 reads; of these: 12830028 (100.00%) were paired; of these: 977386 (7.62%) aligned concordantly 0 times 9633010 (75.08%) aligned concordantly exactly 1 time 2219632 (17.30%) aligned concordantly >1 times ---- 977386 pairs aligned concordantly 0 times; of these: 242653 (24.83%) aligned discordantly 1 time ---- 734733 pairs aligned 0 times concordantly or discordantly; of these: 1469466 mates make up the pairs; of these: 1160932 (79.00%) aligned 0 times 157206 (10.70%) aligned exactly 1 time 151328 (10.30%) aligned >1 times 95.48% overall alignment rate Time searching: 00:10:25 Overall time: 00:10:25 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] 593221 / 12080713 = 0.0491 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 23:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.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 23:23:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.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 23:23:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.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 23:23:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:26: 1000000 INFO @ Fri, 05 Jul 2019 23:23:26: 1000000 INFO @ Fri, 05 Jul 2019 23:23:28: 1000000 INFO @ Fri, 05 Jul 2019 23:23:33: 2000000 INFO @ Fri, 05 Jul 2019 23:23:34: 2000000 INFO @ Fri, 05 Jul 2019 23:23:35: 2000000 INFO @ Fri, 05 Jul 2019 23:23:41: 3000000 INFO @ Fri, 05 Jul 2019 23:23:41: 3000000 INFO @ Fri, 05 Jul 2019 23:23:43: 3000000 INFO @ Fri, 05 Jul 2019 23:23:48: 4000000 INFO @ Fri, 05 Jul 2019 23:23:48: 4000000 INFO @ Fri, 05 Jul 2019 23:23:50: 4000000 INFO @ Fri, 05 Jul 2019 23:23:56: 5000000 INFO @ Fri, 05 Jul 2019 23:23:56: 5000000 INFO @ Fri, 05 Jul 2019 23:23:57: 5000000 INFO @ Fri, 05 Jul 2019 23:24:03: 6000000 INFO @ Fri, 05 Jul 2019 23:24:03: 6000000 INFO @ Fri, 05 Jul 2019 23:24:05: 6000000 INFO @ Fri, 05 Jul 2019 23:24:10: 7000000 INFO @ Fri, 05 Jul 2019 23:24:10: 7000000 INFO @ Fri, 05 Jul 2019 23:24:12: 7000000 INFO @ Fri, 05 Jul 2019 23:24:17: 8000000 INFO @ Fri, 05 Jul 2019 23:24:18: 8000000 INFO @ Fri, 05 Jul 2019 23:24:19: 8000000 INFO @ Fri, 05 Jul 2019 23:24:25: 9000000 INFO @ Fri, 05 Jul 2019 23:24:27: 9000000 INFO @ Fri, 05 Jul 2019 23:24:27: 9000000 INFO @ Fri, 05 Jul 2019 23:24:32: 10000000 INFO @ Fri, 05 Jul 2019 23:24:34: 10000000 INFO @ Fri, 05 Jul 2019 23:24:35: 10000000 INFO @ Fri, 05 Jul 2019 23:24:40: 11000000 INFO @ Fri, 05 Jul 2019 23:24:41: 11000000 INFO @ Fri, 05 Jul 2019 23:24:43: 11000000 INFO @ Fri, 05 Jul 2019 23:24:47: 12000000 INFO @ Fri, 05 Jul 2019 23:24:49: 12000000 INFO @ Fri, 05 Jul 2019 23:24:51: 12000000 INFO @ Fri, 05 Jul 2019 23:24:54: 13000000 INFO @ Fri, 05 Jul 2019 23:24:56: 13000000 INFO @ Fri, 05 Jul 2019 23:24:58: 13000000 INFO @ Fri, 05 Jul 2019 23:25:01: 14000000 INFO @ Fri, 05 Jul 2019 23:25:03: 14000000 INFO @ Fri, 05 Jul 2019 23:25:06: 14000000 INFO @ Fri, 05 Jul 2019 23:25:08: 15000000 INFO @ Fri, 05 Jul 2019 23:25:11: 15000000 INFO @ Fri, 05 Jul 2019 23:25:13: 15000000 INFO @ Fri, 05 Jul 2019 23:25:15: 16000000 INFO @ Fri, 05 Jul 2019 23:25:18: 16000000 INFO @ Fri, 05 Jul 2019 23:25:20: 16000000 INFO @ Fri, 05 Jul 2019 23:25:22: 17000000 INFO @ Fri, 05 Jul 2019 23:25:25: 17000000 INFO @ Fri, 05 Jul 2019 23:25:28: 17000000 INFO @ Fri, 05 Jul 2019 23:25:29: 18000000 INFO @ Fri, 05 Jul 2019 23:25:33: 18000000 INFO @ Fri, 05 Jul 2019 23:25:35: 18000000 INFO @ Fri, 05 Jul 2019 23:25:36: 19000000 INFO @ Fri, 05 Jul 2019 23:25:40: 19000000 INFO @ Fri, 05 Jul 2019 23:25:43: 20000000 INFO @ Fri, 05 Jul 2019 23:25:43: 19000000 INFO @ Fri, 05 Jul 2019 23:25:47: 20000000 INFO @ Fri, 05 Jul 2019 23:25:50: 21000000 INFO @ Fri, 05 Jul 2019 23:25:50: 20000000 INFO @ Fri, 05 Jul 2019 23:25:54: 21000000 INFO @ Fri, 05 Jul 2019 23:25:57: 22000000 INFO @ Fri, 05 Jul 2019 23:25:58: 21000000 INFO @ Fri, 05 Jul 2019 23:26:02: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:26:04: 23000000 INFO @ Fri, 05 Jul 2019 23:26:06: 22000000 INFO @ Fri, 05 Jul 2019 23:26:07: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:26:07: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:26:07: #1 total tags in treatment: 11262362 INFO @ Fri, 05 Jul 2019 23:26:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:26:07: #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 23:26:07: #1 tags after filtering in treatment: 7136273 INFO @ Fri, 05 Jul 2019 23:26:07: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:26:07: #1 finished! INFO @ Fri, 05 Jul 2019 23:26:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:26:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:26:07: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:26:07: 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 23:26:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.10_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/SRX381228/SRX381228.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:26:09: 23000000 INFO @ Fri, 05 Jul 2019 23:26:11: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:26:11: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:26:11: #1 total tags in treatment: 11262362 INFO @ Fri, 05 Jul 2019 23:26:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:26:11: #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 23:26:11: #1 tags after filtering in treatment: 7136273 INFO @ Fri, 05 Jul 2019 23:26:11: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:26:11: #1 finished! INFO @ Fri, 05 Jul 2019 23:26:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:26:12: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:26:12: 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 23:26:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.20_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/SRX381228/SRX381228.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:26:13: 23000000 INFO @ Fri, 05 Jul 2019 23:26:16: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:26:16: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:26:16: #1 total tags in treatment: 11262362 INFO @ Fri, 05 Jul 2019 23:26:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:26:16: #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 23:26:16: #1 tags after filtering in treatment: 7136273 INFO @ Fri, 05 Jul 2019 23:26:16: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:26:16: #1 finished! INFO @ Fri, 05 Jul 2019 23:26:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:26:16: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:26:16: 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 23:26:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.05_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/SRX381228/SRX381228.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381228/SRX381228.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。