Job ID = 2010518 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035323' (), 32768) from '172.19.7.82' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035323' (), 32768) from '172.19.7.82' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035323' (), 32768) from '172.19.7.82' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035323' (), 32768) from '172.19.7.82' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #5996545 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035323' (), 32768) from '172.19.7.82' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #7995393 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035323' (), 32768) from '172.19.7.82' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #16385 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T13:49:41 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' 2019-07-05T13:49:41 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' 2019-07-05T13:49:41 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035323' (), 32768) from '172.19.7.82' 2019-07-05T13:49:41 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' 2019-07-05T13:49:41 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' 2019-07-05T13:49:41 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' 2019-07-05T13:49:41 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035323' (), 32768) from '172.19.7.82' 2019-07-05T13:49:41 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #1998849 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) spots read : 11,975,962 reads read : 23,951,924 reads written : 23,951,924 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: 00:10:54 11975962 reads; of these: 11975962 (100.00%) were paired; of these: 987157 (8.24%) aligned concordantly 0 times 8810952 (73.57%) aligned concordantly exactly 1 time 2177853 (18.19%) aligned concordantly >1 times ---- 987157 pairs aligned concordantly 0 times; of these: 161949 (16.41%) aligned discordantly 1 time ---- 825208 pairs aligned 0 times concordantly or discordantly; of these: 1650416 mates make up the pairs; of these: 1269021 (76.89%) aligned 0 times 249712 (15.13%) aligned exactly 1 time 131683 (7.98%) aligned >1 times 94.70% overall alignment rate Time searching: 00:10:54 Overall time: 00:10:54 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] 829759 / 11131387 = 0.0745 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 23:39:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.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 23:39:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:39:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:39:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.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 23:39:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:39:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.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 23:39:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:39:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:39:50: 1000000 INFO @ Fri, 05 Jul 2019 23:39:50: 1000000 INFO @ Fri, 05 Jul 2019 23:39:52: 1000000 INFO @ Fri, 05 Jul 2019 23:39:58: 2000000 INFO @ Fri, 05 Jul 2019 23:40:00: 2000000 INFO @ Fri, 05 Jul 2019 23:40:00: 2000000 INFO @ Fri, 05 Jul 2019 23:40:05: 3000000 INFO @ Fri, 05 Jul 2019 23:40:09: 3000000 INFO @ Fri, 05 Jul 2019 23:40:09: 3000000 INFO @ Fri, 05 Jul 2019 23:40:13: 4000000 INFO @ Fri, 05 Jul 2019 23:40:18: 4000000 INFO @ Fri, 05 Jul 2019 23:40:18: 4000000 INFO @ Fri, 05 Jul 2019 23:40:20: 5000000 INFO @ Fri, 05 Jul 2019 23:40:27: 5000000 INFO @ Fri, 05 Jul 2019 23:40:27: 5000000 INFO @ Fri, 05 Jul 2019 23:40:28: 6000000 INFO @ Fri, 05 Jul 2019 23:40:35: 6000000 INFO @ Fri, 05 Jul 2019 23:40:35: 7000000 INFO @ Fri, 05 Jul 2019 23:40:36: 6000000 INFO @ Fri, 05 Jul 2019 23:40:43: 8000000 INFO @ Fri, 05 Jul 2019 23:40:44: 7000000 INFO @ Fri, 05 Jul 2019 23:40:46: 7000000 INFO @ Fri, 05 Jul 2019 23:40:50: 9000000 INFO @ Fri, 05 Jul 2019 23:40:52: 8000000 INFO @ Fri, 05 Jul 2019 23:40:55: 8000000 INFO @ Fri, 05 Jul 2019 23:40:58: 10000000 INFO @ Fri, 05 Jul 2019 23:41:01: 9000000 INFO @ Fri, 05 Jul 2019 23:41:04: 9000000 INFO @ Fri, 05 Jul 2019 23:41:05: 11000000 INFO @ Fri, 05 Jul 2019 23:41:09: 10000000 INFO @ Fri, 05 Jul 2019 23:41:13: 12000000 INFO @ Fri, 05 Jul 2019 23:41:13: 10000000 INFO @ Fri, 05 Jul 2019 23:41:18: 11000000 INFO @ Fri, 05 Jul 2019 23:41:20: 13000000 INFO @ Fri, 05 Jul 2019 23:41:22: 11000000 INFO @ Fri, 05 Jul 2019 23:41:26: 12000000 INFO @ Fri, 05 Jul 2019 23:41:28: 14000000 INFO @ Fri, 05 Jul 2019 23:41:31: 12000000 INFO @ Fri, 05 Jul 2019 23:41:35: 13000000 INFO @ Fri, 05 Jul 2019 23:41:35: 15000000 INFO @ Fri, 05 Jul 2019 23:41:40: 13000000 INFO @ Fri, 05 Jul 2019 23:41:42: 16000000 INFO @ Fri, 05 Jul 2019 23:41:43: 14000000 INFO @ Fri, 05 Jul 2019 23:41:49: 14000000 INFO @ Fri, 05 Jul 2019 23:41:50: 17000000 INFO @ Fri, 05 Jul 2019 23:41:51: 15000000 INFO @ Fri, 05 Jul 2019 23:41:57: 18000000 INFO @ Fri, 05 Jul 2019 23:41:57: 15000000 INFO @ Fri, 05 Jul 2019 23:42:00: 16000000 INFO @ Fri, 05 Jul 2019 23:42:04: 19000000 INFO @ Fri, 05 Jul 2019 23:42:05: 16000000 INFO @ Fri, 05 Jul 2019 23:42:08: 17000000 INFO @ Fri, 05 Jul 2019 23:42:12: 20000000 INFO @ Fri, 05 Jul 2019 23:42:14: 17000000 INFO @ Fri, 05 Jul 2019 23:42:16: 18000000 INFO @ Fri, 05 Jul 2019 23:42:19: 21000000 INFO @ Fri, 05 Jul 2019 23:42:19: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:42:19: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:42:19: #1 total tags in treatment: 10191921 INFO @ Fri, 05 Jul 2019 23:42:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:42:19: #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 23:42:20: #1 tags after filtering in treatment: 7155824 INFO @ Fri, 05 Jul 2019 23:42:20: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 23:42:20: #1 finished! INFO @ Fri, 05 Jul 2019 23:42:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:42:20: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:42:20: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:42:20: 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 23:42:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.10_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/SRX381222/SRX381222.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:42:22: 18000000 INFO @ Fri, 05 Jul 2019 23:42:25: 19000000 INFO @ Fri, 05 Jul 2019 23:42:30: 19000000 INFO @ Fri, 05 Jul 2019 23:42:33: 20000000 INFO @ Fri, 05 Jul 2019 23:42:38: 20000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:42:41: 21000000 INFO @ Fri, 05 Jul 2019 23:42:41: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:42:41: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:42:41: #1 total tags in treatment: 10191921 INFO @ Fri, 05 Jul 2019 23:42:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:42:41: #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 23:42:42: #1 tags after filtering in treatment: 7155824 INFO @ Fri, 05 Jul 2019 23:42:42: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 23:42:42: #1 finished! INFO @ Fri, 05 Jul 2019 23:42:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:42:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:42:42: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:42:42: 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 23:42:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.20_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/SRX381222/SRX381222.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:42:46: 21000000 INFO @ Fri, 05 Jul 2019 23:42:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:42:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:42:46: #1 total tags in treatment: 10191921 INFO @ Fri, 05 Jul 2019 23:42:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:42:46: #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 23:42:46: #1 tags after filtering in treatment: 7155824 INFO @ Fri, 05 Jul 2019 23:42:46: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 23:42:46: #1 finished! INFO @ Fri, 05 Jul 2019 23:42:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:42:47: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:42:47: 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 23:42:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.05_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/SRX381222/SRX381222.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381222/SRX381222.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling