Job ID = 2011678 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T16:56:04 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' 2019-07-05T16:56:04 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/sra52/SRR/007522/SRR7703237' 2019-07-05T16:56:04 fasterq-dump.2.9.6 err: invalid accession 'SRR7703237' 2019-07-05T16:56:19 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' 2019-07-05T16:56:19 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/sra52/SRR/007522/SRR7703237' 2019-07-05T16:56:19 fasterq-dump.2.9.6 err: invalid accession 'SRR7703237' 2019-07-05T16:56:34 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' 2019-07-05T16:56:34 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/sra52/SRR/007522/SRR7703237' 2019-07-05T16:56:34 fasterq-dump.2.9.6 err: invalid accession 'SRR7703237' 2019-07-05T16:56:49 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' 2019-07-05T16:56:49 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/sra52/SRR/007522/SRR7703237' 2019-07-05T16:56:49 fasterq-dump.2.9.6 err: invalid accession 'SRR7703237' 2019-07-05T17:16:47 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 ) 2019-07-05T17:16:47 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 ) 2019-07-05T17:16:47 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 ) 2019-07-05T17:23:07 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 ) 2019-07-05T17:23:07 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 ) 2019-07-05T17:27:22 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 : 22,586,751 reads read : 45,173,502 reads written : 45,173,502 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: 00:34:24 22586751 reads; of these: 22586751 (100.00%) were paired; of these: 4577713 (20.27%) aligned concordantly 0 times 14640800 (64.82%) aligned concordantly exactly 1 time 3368238 (14.91%) aligned concordantly >1 times ---- 4577713 pairs aligned concordantly 0 times; of these: 2164109 (47.27%) aligned discordantly 1 time ---- 2413604 pairs aligned 0 times concordantly or discordantly; of these: 4827208 mates make up the pairs; of these: 3417947 (70.81%) aligned 0 times 351318 (7.28%) aligned exactly 1 time 1057943 (21.92%) aligned >1 times 92.43% overall alignment rate Time searching: 00:34:24 Overall time: 00:34:24 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 28 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] 1207139 / 20043822 = 0.0602 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 @ Sat, 06 Jul 2019 03:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.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 @ Sat, 06 Jul 2019 03:40:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:40:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.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 @ Sat, 06 Jul 2019 03:40:47: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:40:47: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.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 @ Sat, 06 Jul 2019 03:40:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:40:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:40:56: 1000000 INFO @ Sat, 06 Jul 2019 03:40:57: 1000000 INFO @ Sat, 06 Jul 2019 03:40:58: 1000000 INFO @ Sat, 06 Jul 2019 03:41:06: 2000000 INFO @ Sat, 06 Jul 2019 03:41:08: 2000000 INFO @ Sat, 06 Jul 2019 03:41:08: 2000000 INFO @ Sat, 06 Jul 2019 03:41:17: 3000000 INFO @ Sat, 06 Jul 2019 03:41:18: 3000000 INFO @ Sat, 06 Jul 2019 03:41:19: 3000000 INFO @ Sat, 06 Jul 2019 03:41:27: 4000000 INFO @ Sat, 06 Jul 2019 03:41:28: 4000000 INFO @ Sat, 06 Jul 2019 03:41:29: 4000000 INFO @ Sat, 06 Jul 2019 03:41:37: 5000000 INFO @ Sat, 06 Jul 2019 03:41:39: 5000000 INFO @ Sat, 06 Jul 2019 03:41:40: 5000000 INFO @ Sat, 06 Jul 2019 03:41:48: 6000000 INFO @ Sat, 06 Jul 2019 03:41:49: 6000000 INFO @ Sat, 06 Jul 2019 03:41:50: 6000000 INFO @ Sat, 06 Jul 2019 03:41:58: 7000000 INFO @ Sat, 06 Jul 2019 03:42:00: 7000000 INFO @ Sat, 06 Jul 2019 03:42:00: 7000000 INFO @ Sat, 06 Jul 2019 03:42:08: 8000000 INFO @ Sat, 06 Jul 2019 03:42:10: 8000000 INFO @ Sat, 06 Jul 2019 03:42:11: 8000000 INFO @ Sat, 06 Jul 2019 03:42:19: 9000000 INFO @ Sat, 06 Jul 2019 03:42:21: 9000000 INFO @ Sat, 06 Jul 2019 03:42:21: 9000000 INFO @ Sat, 06 Jul 2019 03:42:29: 10000000 INFO @ Sat, 06 Jul 2019 03:42:31: 10000000 INFO @ Sat, 06 Jul 2019 03:42:32: 10000000 INFO @ Sat, 06 Jul 2019 03:42:39: 11000000 INFO @ Sat, 06 Jul 2019 03:42:42: 11000000 INFO @ Sat, 06 Jul 2019 03:42:42: 11000000 INFO @ Sat, 06 Jul 2019 03:42:49: 12000000 INFO @ Sat, 06 Jul 2019 03:42:53: 12000000 INFO @ Sat, 06 Jul 2019 03:42:53: 12000000 INFO @ Sat, 06 Jul 2019 03:43:00: 13000000 INFO @ Sat, 06 Jul 2019 03:43:03: 13000000 INFO @ Sat, 06 Jul 2019 03:43:03: 13000000 INFO @ Sat, 06 Jul 2019 03:43:10: 14000000 INFO @ Sat, 06 Jul 2019 03:43:14: 14000000 INFO @ Sat, 06 Jul 2019 03:43:14: 14000000 INFO @ Sat, 06 Jul 2019 03:43:20: 15000000 INFO @ Sat, 06 Jul 2019 03:43:25: 15000000 INFO @ Sat, 06 Jul 2019 03:43:25: 15000000 INFO @ Sat, 06 Jul 2019 03:43:30: 16000000 INFO @ Sat, 06 Jul 2019 03:43:35: 16000000 INFO @ Sat, 06 Jul 2019 03:43:35: 16000000 INFO @ Sat, 06 Jul 2019 03:43:41: 17000000 INFO @ Sat, 06 Jul 2019 03:43:46: 17000000 INFO @ Sat, 06 Jul 2019 03:43:46: 17000000 INFO @ Sat, 06 Jul 2019 03:43:51: 18000000 INFO @ Sat, 06 Jul 2019 03:43:57: 18000000 INFO @ Sat, 06 Jul 2019 03:43:57: 18000000 INFO @ Sat, 06 Jul 2019 03:44:01: 19000000 INFO @ Sat, 06 Jul 2019 03:44:08: 19000000 INFO @ Sat, 06 Jul 2019 03:44:08: 19000000 INFO @ Sat, 06 Jul 2019 03:44:12: 20000000 INFO @ Sat, 06 Jul 2019 03:44:18: 20000000 INFO @ Sat, 06 Jul 2019 03:44:19: 20000000 INFO @ Sat, 06 Jul 2019 03:44:22: 21000000 INFO @ Sat, 06 Jul 2019 03:44:29: 21000000 INFO @ Sat, 06 Jul 2019 03:44:29: 21000000 INFO @ Sat, 06 Jul 2019 03:44:32: 22000000 INFO @ Sat, 06 Jul 2019 03:44:40: 22000000 INFO @ Sat, 06 Jul 2019 03:44:40: 22000000 INFO @ Sat, 06 Jul 2019 03:44:42: 23000000 INFO @ Sat, 06 Jul 2019 03:44:50: 23000000 INFO @ Sat, 06 Jul 2019 03:44:50: 23000000 INFO @ Sat, 06 Jul 2019 03:44:52: 24000000 INFO @ Sat, 06 Jul 2019 03:45:01: 24000000 INFO @ Sat, 06 Jul 2019 03:45:01: 24000000 INFO @ Sat, 06 Jul 2019 03:45:03: 25000000 INFO @ Sat, 06 Jul 2019 03:45:11: 25000000 INFO @ Sat, 06 Jul 2019 03:45:11: 25000000 INFO @ Sat, 06 Jul 2019 03:45:13: 26000000 INFO @ Sat, 06 Jul 2019 03:45:22: 26000000 INFO @ Sat, 06 Jul 2019 03:45:22: 26000000 INFO @ Sat, 06 Jul 2019 03:45:23: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:45:32: 27000000 INFO @ Sat, 06 Jul 2019 03:45:32: 27000000 INFO @ Sat, 06 Jul 2019 03:45:33: 28000000 INFO @ Sat, 06 Jul 2019 03:45:42: 28000000 INFO @ Sat, 06 Jul 2019 03:45:43: 28000000 INFO @ Sat, 06 Jul 2019 03:45:43: 29000000 INFO @ Sat, 06 Jul 2019 03:45:53: 29000000 INFO @ Sat, 06 Jul 2019 03:45:53: 29000000 INFO @ Sat, 06 Jul 2019 03:45:53: 30000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:46:03: 30000000 INFO @ Sat, 06 Jul 2019 03:46:04: 31000000 INFO @ Sat, 06 Jul 2019 03:46:04: 30000000 INFO @ Sat, 06 Jul 2019 03:46:14: 31000000 INFO @ Sat, 06 Jul 2019 03:46:14: 32000000 INFO @ Sat, 06 Jul 2019 03:46:14: 31000000 INFO @ Sat, 06 Jul 2019 03:46:24: 33000000 INFO @ Sat, 06 Jul 2019 03:46:24: 32000000 INFO @ Sat, 06 Jul 2019 03:46:24: 32000000 INFO @ Sat, 06 Jul 2019 03:46:34: 34000000 INFO @ Sat, 06 Jul 2019 03:46:34: 33000000 INFO @ Sat, 06 Jul 2019 03:46:35: 33000000 INFO @ Sat, 06 Jul 2019 03:46:44: 35000000 INFO @ Sat, 06 Jul 2019 03:46:45: 34000000 INFO @ Sat, 06 Jul 2019 03:46:45: 34000000 INFO @ Sat, 06 Jul 2019 03:46:55: 36000000 INFO @ Sat, 06 Jul 2019 03:46:55: 35000000 INFO @ Sat, 06 Jul 2019 03:46:56: 35000000 INFO @ Sat, 06 Jul 2019 03:47:05: 37000000 INFO @ Sat, 06 Jul 2019 03:47:05: 36000000 INFO @ Sat, 06 Jul 2019 03:47:06: 36000000 INFO @ Sat, 06 Jul 2019 03:47:15: 38000000 INFO @ Sat, 06 Jul 2019 03:47:16: 37000000 INFO @ Sat, 06 Jul 2019 03:47:16: 37000000 INFO @ Sat, 06 Jul 2019 03:47:25: 39000000 INFO @ Sat, 06 Jul 2019 03:47:26: 38000000 INFO @ Sat, 06 Jul 2019 03:47:27: 38000000 INFO @ Sat, 06 Jul 2019 03:47:29: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:47:29: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:47:29: #1 total tags in treatment: 16878602 INFO @ Sat, 06 Jul 2019 03:47:29: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:47:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:47:29: #1 tags after filtering in treatment: 10610930 INFO @ Sat, 06 Jul 2019 03:47:29: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:47:29: #1 finished! INFO @ Sat, 06 Jul 2019 03:47:29: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:47:30: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:47:30: 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 @ Sat, 06 Jul 2019 03:47:30: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:47:36: 39000000 INFO @ Sat, 06 Jul 2019 03:47:37: 39000000 INFO @ Sat, 06 Jul 2019 03:47:40: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:47:40: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:47:40: #1 total tags in treatment: 16878602 INFO @ Sat, 06 Jul 2019 03:47:40: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:47:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:47:40: #1 tags after filtering in treatment: 10610930 INFO @ Sat, 06 Jul 2019 03:47:40: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:47:40: #1 finished! INFO @ Sat, 06 Jul 2019 03:47:40: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:47:40: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:47:40: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:47:40: #1 total tags in treatment: 16878602 INFO @ Sat, 06 Jul 2019 03:47:40: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:47:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:47:41: #1 tags after filtering in treatment: 10610930 INFO @ Sat, 06 Jul 2019 03:47:41: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:47:41: #1 finished! INFO @ Sat, 06 Jul 2019 03:47:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:47:41: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:47:41: 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 @ Sat, 06 Jul 2019 03:47:41: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:47:42: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:47:42: 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 @ Sat, 06 Jul 2019 03:47:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.05_model.r’pass1 - making usageList (0 chroms): No such file or directory: 4 millis rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.10_model.r’: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184)rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560560/SRX4560560.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling