Job ID = 1308454 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:45:54 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T13:45:54 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra76/SRR/008340/SRR8540847' 2019-06-03T13:45:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8540847' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:46:08 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T13:46:08 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra76/SRR/008340/SRR8540847' 2019-06-03T13:46:08 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR8540847' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:46:08 fasterq-dump.2.9.6 err: invalid accession 'SRR8540847' spots read : 38,894,571 reads read : 77,789,142 reads written : 38,894,571 reads 0-length : 38,894,571 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:22:35 38894571 reads; of these: 38894571 (100.00%) were unpaired; of these: 1328421 (3.42%) aligned 0 times 25408964 (65.33%) aligned exactly 1 time 12157186 (31.26%) aligned >1 times 96.58% overall alignment rate Time searching: 00:22:35 Overall time: 00:22:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5457856 / 37566150 = 0.1453 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 @ Mon, 03 Jun 2019 23:40:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 23:40:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:40:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:40:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 23:40:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:40:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:40:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 23:40:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:40:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:40:43: 1000000 INFO @ Mon, 03 Jun 2019 23:40:44: 1000000 INFO @ Mon, 03 Jun 2019 23:40:45: 1000000 INFO @ Mon, 03 Jun 2019 23:40:51: 2000000 INFO @ Mon, 03 Jun 2019 23:40:54: 2000000 INFO @ Mon, 03 Jun 2019 23:40:55: 2000000 INFO @ Mon, 03 Jun 2019 23:40:59: 3000000 INFO @ Mon, 03 Jun 2019 23:41:03: 3000000 INFO @ Mon, 03 Jun 2019 23:41:05: 3000000 INFO @ Mon, 03 Jun 2019 23:41:07: 4000000 INFO @ Mon, 03 Jun 2019 23:41:12: 4000000 INFO @ Mon, 03 Jun 2019 23:41:14: 5000000 INFO @ Mon, 03 Jun 2019 23:41:14: 4000000 INFO @ Mon, 03 Jun 2019 23:41:21: 5000000 INFO @ Mon, 03 Jun 2019 23:41:22: 6000000 INFO @ Mon, 03 Jun 2019 23:41:23: 5000000 INFO @ Mon, 03 Jun 2019 23:41:30: 7000000 INFO @ Mon, 03 Jun 2019 23:41:30: 6000000 INFO @ Mon, 03 Jun 2019 23:41:33: 6000000 INFO @ Mon, 03 Jun 2019 23:41:37: 8000000 INFO @ Mon, 03 Jun 2019 23:41:39: 7000000 INFO @ Mon, 03 Jun 2019 23:41:43: 7000000 INFO @ Mon, 03 Jun 2019 23:41:45: 9000000 INFO @ Mon, 03 Jun 2019 23:41:48: 8000000 INFO @ Mon, 03 Jun 2019 23:41:53: 10000000 INFO @ Mon, 03 Jun 2019 23:41:53: 8000000 INFO @ Mon, 03 Jun 2019 23:41:57: 9000000 INFO @ Mon, 03 Jun 2019 23:42:01: 11000000 INFO @ Mon, 03 Jun 2019 23:42:03: 9000000 INFO @ Mon, 03 Jun 2019 23:42:05: 10000000 INFO @ Mon, 03 Jun 2019 23:42:08: 12000000 INFO @ Mon, 03 Jun 2019 23:42:12: 10000000 INFO @ Mon, 03 Jun 2019 23:42:14: 11000000 INFO @ Mon, 03 Jun 2019 23:42:16: 13000000 INFO @ Mon, 03 Jun 2019 23:42:21: 11000000 INFO @ Mon, 03 Jun 2019 23:42:23: 12000000 INFO @ Mon, 03 Jun 2019 23:42:24: 14000000 INFO @ Mon, 03 Jun 2019 23:42:31: 12000000 INFO @ Mon, 03 Jun 2019 23:42:32: 15000000 INFO @ Mon, 03 Jun 2019 23:42:32: 13000000 INFO @ Mon, 03 Jun 2019 23:42:40: 16000000 INFO @ Mon, 03 Jun 2019 23:42:40: 13000000 INFO @ Mon, 03 Jun 2019 23:42:41: 14000000 INFO @ Mon, 03 Jun 2019 23:42:48: 17000000 INFO @ Mon, 03 Jun 2019 23:42:49: 14000000 INFO @ Mon, 03 Jun 2019 23:42:50: 15000000 INFO @ Mon, 03 Jun 2019 23:42:56: 18000000 INFO @ Mon, 03 Jun 2019 23:42:59: 15000000 INFO @ Mon, 03 Jun 2019 23:42:59: 16000000 INFO @ Mon, 03 Jun 2019 23:43:03: 19000000 INFO @ Mon, 03 Jun 2019 23:43:08: 17000000 INFO @ Mon, 03 Jun 2019 23:43:08: 16000000 INFO @ Mon, 03 Jun 2019 23:43:11: 20000000 INFO @ Mon, 03 Jun 2019 23:43:16: 18000000 INFO @ Mon, 03 Jun 2019 23:43:18: 17000000 INFO @ Mon, 03 Jun 2019 23:43:19: 21000000 INFO @ Mon, 03 Jun 2019 23:43:25: 19000000 INFO @ Mon, 03 Jun 2019 23:43:26: 22000000 INFO @ Mon, 03 Jun 2019 23:43:27: 18000000 INFO @ Mon, 03 Jun 2019 23:43:34: 20000000 INFO @ Mon, 03 Jun 2019 23:43:34: 23000000 INFO @ Mon, 03 Jun 2019 23:43:36: 19000000 INFO @ Mon, 03 Jun 2019 23:43:42: 24000000 INFO @ Mon, 03 Jun 2019 23:43:43: 21000000 INFO @ Mon, 03 Jun 2019 23:43:45: 20000000 INFO @ Mon, 03 Jun 2019 23:43:49: 25000000 INFO @ Mon, 03 Jun 2019 23:43:51: 22000000 INFO @ Mon, 03 Jun 2019 23:43:54: 21000000 INFO @ Mon, 03 Jun 2019 23:43:57: 26000000 INFO @ Mon, 03 Jun 2019 23:44:00: 23000000 INFO @ Mon, 03 Jun 2019 23:44:03: 22000000 INFO @ Mon, 03 Jun 2019 23:44:05: 27000000 INFO @ Mon, 03 Jun 2019 23:44:09: 24000000 INFO @ Mon, 03 Jun 2019 23:44:12: 23000000 INFO @ Mon, 03 Jun 2019 23:44:12: 28000000 INFO @ Mon, 03 Jun 2019 23:44:17: 25000000 INFO @ Mon, 03 Jun 2019 23:44:20: 29000000 INFO @ Mon, 03 Jun 2019 23:44:22: 24000000 INFO @ Mon, 03 Jun 2019 23:44:26: 26000000 INFO @ Mon, 03 Jun 2019 23:44:28: 30000000 INFO @ Mon, 03 Jun 2019 23:44:31: 25000000 INFO @ Mon, 03 Jun 2019 23:44:35: 27000000 INFO @ Mon, 03 Jun 2019 23:44:36: 31000000 INFO @ Mon, 03 Jun 2019 23:44:41: 26000000 INFO @ Mon, 03 Jun 2019 23:44:43: 32000000 INFO @ Mon, 03 Jun 2019 23:44:43: 28000000 INFO @ Mon, 03 Jun 2019 23:44:45: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:44:45: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:44:45: #1 total tags in treatment: 32108294 INFO @ Mon, 03 Jun 2019 23:44:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:44:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:44:45: #1 tags after filtering in treatment: 32108294 INFO @ Mon, 03 Jun 2019 23:44:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:44:45: #1 finished! INFO @ Mon, 03 Jun 2019 23:44:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:44:48: #2 number of paired peaks: 43 WARNING @ Mon, 03 Jun 2019 23:44:48: Too few paired peaks (43) 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 @ Mon, 03 Jun 2019 23:44:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.05_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/dm3/SRX5343147/SRX5343147.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:44:51: 27000000 INFO @ Mon, 03 Jun 2019 23:44:52: 29000000 INFO @ Mon, 03 Jun 2019 23:45:01: 28000000 INFO @ Mon, 03 Jun 2019 23:45:01: 30000000 INFO @ Mon, 03 Jun 2019 23:45:09: 31000000 INFO @ Mon, 03 Jun 2019 23:45:10: 29000000 INFO @ Mon, 03 Jun 2019 23:45:18: 32000000 INFO @ Mon, 03 Jun 2019 23:45:19: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:45:19: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:45:19: #1 total tags in treatment: 32108294 INFO @ Mon, 03 Jun 2019 23:45:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:45:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:45:20: 30000000 INFO @ Mon, 03 Jun 2019 23:45:20: #1 tags after filtering in treatment: 32108294 INFO @ Mon, 03 Jun 2019 23:45:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:45:20: #1 finished! INFO @ Mon, 03 Jun 2019 23:45:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:45:23: #2 number of paired peaks: 43 WARNING @ Mon, 03 Jun 2019 23:45:23: Too few paired peaks (43) 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 @ Mon, 03 Jun 2019 23:45:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.10_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/dm3/SRX5343147/SRX5343147.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:45:29: 31000000 INFO @ Mon, 03 Jun 2019 23:45:39: 32000000 INFO @ Mon, 03 Jun 2019 23:45:40: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:45:40: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:45:40: #1 total tags in treatment: 32108294 INFO @ Mon, 03 Jun 2019 23:45:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:45:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:45:41: #1 tags after filtering in treatment: 32108294 INFO @ Mon, 03 Jun 2019 23:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:45:41: #1 finished! INFO @ Mon, 03 Jun 2019 23:45:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:45:44: #2 number of paired peaks: 43 WARNING @ Mon, 03 Jun 2019 23:45:44: Too few paired peaks (43) 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 @ Mon, 03 Jun 2019 23:45:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.20_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/dm3/SRX5343147/SRX5343147.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5343147/SRX5343147.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。