Job ID = 2010520 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:49:53 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' 2019-07-05T13:49:53 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/SRR1035325' 2019-07-05T13:49:53 fasterq-dump.2.9.6 err: invalid accession 'SRR1035325' 2019-07-05T13:50:08 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' 2019-07-05T13:50:08 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/SRR1035325' 2019-07-05T13:50:08 fasterq-dump.2.9.6 err: invalid accession 'SRR1035325' 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/SRR1035325' 2019-07-05T13:50:23 fasterq-dump.2.9.6 err: invalid accession 'SRR1035325' 2019-07-05T14:02:36 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 ) 2019-07-05T14:05:02 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 : 13,560,437 reads read : 27,120,874 reads written : 27,120,874 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: 00:12:32 13560437 reads; of these: 13560437 (100.00%) were paired; of these: 1271973 (9.38%) aligned concordantly 0 times 10219385 (75.36%) aligned concordantly exactly 1 time 2069079 (15.26%) aligned concordantly >1 times ---- 1271973 pairs aligned concordantly 0 times; of these: 163184 (12.83%) aligned discordantly 1 time ---- 1108789 pairs aligned 0 times concordantly or discordantly; of these: 2217578 mates make up the pairs; of these: 1736892 (78.32%) aligned 0 times 334767 (15.10%) aligned exactly 1 time 145919 (6.58%) aligned >1 times 93.60% overall alignment rate Time searching: 00:12:32 Overall time: 00:12:32 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] 604834 / 12406482 = 0.0488 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 23:36:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.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 23:36:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.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 23:36:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.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 23:36:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:32: 1000000 INFO @ Fri, 05 Jul 2019 23:36:32: 1000000 INFO @ Fri, 05 Jul 2019 23:36:33: 1000000 INFO @ Fri, 05 Jul 2019 23:36:41: 2000000 INFO @ Fri, 05 Jul 2019 23:36:42: 2000000 INFO @ Fri, 05 Jul 2019 23:36:43: 2000000 INFO @ Fri, 05 Jul 2019 23:36:49: 3000000 INFO @ Fri, 05 Jul 2019 23:36:52: 3000000 INFO @ Fri, 05 Jul 2019 23:36:53: 3000000 INFO @ Fri, 05 Jul 2019 23:36:58: 4000000 INFO @ Fri, 05 Jul 2019 23:37:01: 4000000 INFO @ Fri, 05 Jul 2019 23:37:02: 4000000 INFO @ Fri, 05 Jul 2019 23:37:06: 5000000 INFO @ Fri, 05 Jul 2019 23:37:11: 5000000 INFO @ Fri, 05 Jul 2019 23:37:12: 5000000 INFO @ Fri, 05 Jul 2019 23:37:15: 6000000 INFO @ Fri, 05 Jul 2019 23:37:20: 6000000 INFO @ Fri, 05 Jul 2019 23:37:21: 6000000 INFO @ Fri, 05 Jul 2019 23:37:23: 7000000 INFO @ Fri, 05 Jul 2019 23:37:29: 7000000 INFO @ Fri, 05 Jul 2019 23:37:30: 7000000 INFO @ Fri, 05 Jul 2019 23:37:31: 8000000 INFO @ Fri, 05 Jul 2019 23:37:38: 8000000 INFO @ Fri, 05 Jul 2019 23:37:39: 8000000 INFO @ Fri, 05 Jul 2019 23:37:39: 9000000 INFO @ Fri, 05 Jul 2019 23:37:48: 10000000 INFO @ Fri, 05 Jul 2019 23:37:48: 9000000 INFO @ Fri, 05 Jul 2019 23:37:49: 9000000 INFO @ Fri, 05 Jul 2019 23:37:56: 11000000 INFO @ Fri, 05 Jul 2019 23:37:57: 10000000 INFO @ Fri, 05 Jul 2019 23:37:58: 10000000 INFO @ Fri, 05 Jul 2019 23:38:05: 12000000 INFO @ Fri, 05 Jul 2019 23:38:07: 11000000 INFO @ Fri, 05 Jul 2019 23:38:07: 11000000 INFO @ Fri, 05 Jul 2019 23:38:13: 13000000 INFO @ Fri, 05 Jul 2019 23:38:16: 12000000 INFO @ Fri, 05 Jul 2019 23:38:17: 12000000 INFO @ Fri, 05 Jul 2019 23:38:21: 14000000 INFO @ Fri, 05 Jul 2019 23:38:26: 13000000 INFO @ Fri, 05 Jul 2019 23:38:27: 13000000 INFO @ Fri, 05 Jul 2019 23:38:29: 15000000 INFO @ Fri, 05 Jul 2019 23:38:36: 14000000 INFO @ Fri, 05 Jul 2019 23:38:36: 14000000 INFO @ Fri, 05 Jul 2019 23:38:38: 16000000 INFO @ Fri, 05 Jul 2019 23:38:46: 15000000 INFO @ Fri, 05 Jul 2019 23:38:46: 17000000 INFO @ Fri, 05 Jul 2019 23:38:46: 15000000 INFO @ Fri, 05 Jul 2019 23:38:54: 18000000 INFO @ Fri, 05 Jul 2019 23:38:55: 16000000 INFO @ Fri, 05 Jul 2019 23:38:55: 16000000 INFO @ Fri, 05 Jul 2019 23:39:02: 19000000 INFO @ Fri, 05 Jul 2019 23:39:04: 17000000 INFO @ Fri, 05 Jul 2019 23:39:05: 17000000 INFO @ Fri, 05 Jul 2019 23:39:11: 20000000 INFO @ Fri, 05 Jul 2019 23:39:14: 18000000 INFO @ Fri, 05 Jul 2019 23:39:14: 18000000 INFO @ Fri, 05 Jul 2019 23:39:19: 21000000 INFO @ Fri, 05 Jul 2019 23:39:24: 19000000 INFO @ Fri, 05 Jul 2019 23:39:24: 19000000 INFO @ Fri, 05 Jul 2019 23:39:27: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:39:33: 20000000 INFO @ Fri, 05 Jul 2019 23:39:33: 20000000 INFO @ Fri, 05 Jul 2019 23:39:35: 23000000 INFO @ Fri, 05 Jul 2019 23:39:43: 21000000 INFO @ Fri, 05 Jul 2019 23:39:43: 21000000 INFO @ Fri, 05 Jul 2019 23:39:44: 24000000 INFO @ Fri, 05 Jul 2019 23:39:45: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:39:45: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:39:45: #1 total tags in treatment: 11685847 INFO @ Fri, 05 Jul 2019 23:39:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:39:45: #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 23:39:46: #1 tags after filtering in treatment: 7635921 INFO @ Fri, 05 Jul 2019 23:39:46: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:39:46: #1 finished! INFO @ Fri, 05 Jul 2019 23:39:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:39:46: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:39:46: 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 23:39:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.20_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/SRX381224/SRX381224.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:39:53: 22000000 INFO @ Fri, 05 Jul 2019 23:39:53: 22000000 INFO @ Fri, 05 Jul 2019 23:40:02: 23000000 INFO @ Fri, 05 Jul 2019 23:40:03: 23000000 INFO @ Fri, 05 Jul 2019 23:40:12: 24000000 INFO @ Fri, 05 Jul 2019 23:40:12: 24000000 INFO @ Fri, 05 Jul 2019 23:40:14: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:40:14: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:40:14: #1 total tags in treatment: 11685847 INFO @ Fri, 05 Jul 2019 23:40:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:40:14: #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 23:40:14: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:40:14: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:40:14: #1 total tags in treatment: 11685847 INFO @ Fri, 05 Jul 2019 23:40:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:40:14: #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 23:40:14: #1 tags after filtering in treatment: 7635921 INFO @ Fri, 05 Jul 2019 23:40:14: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:40:14: #1 finished! INFO @ Fri, 05 Jul 2019 23:40:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:40:14: #1 tags after filtering in treatment: 7635921 INFO @ Fri, 05 Jul 2019 23:40:14: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:40:14: #1 finished! INFO @ Fri, 05 Jul 2019 23:40:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:40:15: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:40:15: 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 23:40:15: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:40:15: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:40:15: 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 23:40:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.10_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/SRX381224/SRX381224.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.05_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/SRX381224/SRX381224.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381224/SRX381224.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling