Job ID = 1304987 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:00:43 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' 2019-06-03T12:00:43 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/sra36/SRR/001170/SRR1198765' 2019-06-03T12:00:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1198765' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T12:00:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T12:05:14 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 ) 2019-06-03T12:14:54 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 ) 2019-06-03T12:31:52 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 ) 2019-06-03T12:33:18 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 : 29,388,689 reads read : 29,388,689 reads written : 29,388,689 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: 00:08:03 29388689 reads; of these: 29388689 (100.00%) were unpaired; of these: 1823592 (6.21%) aligned 0 times 24381726 (82.96%) aligned exactly 1 time 3183371 (10.83%) aligned >1 times 93.79% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 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 12 files... [bam_rmdupse_core] 6081878 / 27565097 = 0.2206 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 21:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.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 21:53:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:53:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.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 21:53:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:53:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.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 21:53:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:53:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:53:11: 1000000 INFO @ Mon, 03 Jun 2019 21:53:12: 1000000 INFO @ Mon, 03 Jun 2019 21:53:12: 1000000 INFO @ Mon, 03 Jun 2019 21:53:18: 2000000 INFO @ Mon, 03 Jun 2019 21:53:21: 2000000 INFO @ Mon, 03 Jun 2019 21:53:22: 2000000 INFO @ Mon, 03 Jun 2019 21:53:26: 3000000 INFO @ Mon, 03 Jun 2019 21:53:29: 3000000 INFO @ Mon, 03 Jun 2019 21:53:32: 3000000 INFO @ Mon, 03 Jun 2019 21:53:34: 4000000 INFO @ Mon, 03 Jun 2019 21:53:38: 4000000 INFO @ Mon, 03 Jun 2019 21:53:41: 5000000 INFO @ Mon, 03 Jun 2019 21:53:41: 4000000 INFO @ Mon, 03 Jun 2019 21:53:46: 5000000 INFO @ Mon, 03 Jun 2019 21:53:48: 6000000 INFO @ Mon, 03 Jun 2019 21:53:51: 5000000 INFO @ Mon, 03 Jun 2019 21:53:55: 6000000 INFO @ Mon, 03 Jun 2019 21:53:57: 7000000 INFO @ Mon, 03 Jun 2019 21:54:01: 6000000 INFO @ Mon, 03 Jun 2019 21:54:04: 7000000 INFO @ Mon, 03 Jun 2019 21:54:06: 8000000 INFO @ Mon, 03 Jun 2019 21:54:11: 7000000 INFO @ Mon, 03 Jun 2019 21:54:13: 8000000 INFO @ Mon, 03 Jun 2019 21:54:14: 9000000 INFO @ Mon, 03 Jun 2019 21:54:21: 8000000 INFO @ Mon, 03 Jun 2019 21:54:22: 10000000 INFO @ Mon, 03 Jun 2019 21:54:22: 9000000 INFO @ Mon, 03 Jun 2019 21:54:29: 11000000 INFO @ Mon, 03 Jun 2019 21:54:31: 10000000 INFO @ Mon, 03 Jun 2019 21:54:31: 9000000 INFO @ Mon, 03 Jun 2019 21:54:37: 12000000 INFO @ Mon, 03 Jun 2019 21:54:39: 11000000 INFO @ Mon, 03 Jun 2019 21:54:40: 10000000 INFO @ Mon, 03 Jun 2019 21:54:45: 13000000 INFO @ Mon, 03 Jun 2019 21:54:48: 12000000 INFO @ Mon, 03 Jun 2019 21:54:50: 11000000 INFO @ Mon, 03 Jun 2019 21:54:52: 14000000 INFO @ Mon, 03 Jun 2019 21:54:57: 13000000 INFO @ Mon, 03 Jun 2019 21:54:59: 15000000 INFO @ Mon, 03 Jun 2019 21:55:00: 12000000 INFO @ Mon, 03 Jun 2019 21:55:05: 14000000 INFO @ Mon, 03 Jun 2019 21:55:07: 16000000 INFO @ Mon, 03 Jun 2019 21:55:09: 13000000 INFO @ Mon, 03 Jun 2019 21:55:14: 15000000 INFO @ Mon, 03 Jun 2019 21:55:16: 17000000 INFO @ Mon, 03 Jun 2019 21:55:19: 14000000 INFO @ Mon, 03 Jun 2019 21:55:23: 16000000 INFO @ Mon, 03 Jun 2019 21:55:24: 18000000 INFO @ Mon, 03 Jun 2019 21:55:29: 15000000 INFO @ Mon, 03 Jun 2019 21:55:32: 17000000 INFO @ Mon, 03 Jun 2019 21:55:32: 19000000 INFO @ Mon, 03 Jun 2019 21:55:38: 16000000 INFO @ Mon, 03 Jun 2019 21:55:39: 20000000 INFO @ Mon, 03 Jun 2019 21:55:40: 18000000 INFO @ Mon, 03 Jun 2019 21:55:46: 21000000 INFO @ Mon, 03 Jun 2019 21:55:48: 17000000 INFO @ Mon, 03 Jun 2019 21:55:49: 19000000 INFO @ Mon, 03 Jun 2019 21:55:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:55:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:55:50: #1 total tags in treatment: 21483219 INFO @ Mon, 03 Jun 2019 21:55:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:55:50: #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 21:55:50: #1 tags after filtering in treatment: 21483219 INFO @ Mon, 03 Jun 2019 21:55:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:55:50: #1 finished! INFO @ Mon, 03 Jun 2019 21:55:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:55:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:55:52: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 21:55:52: 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 @ Mon, 03 Jun 2019 21:55:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.20_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/dm3/SRX495260/SRX495260.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:55:57: 20000000 INFO @ Mon, 03 Jun 2019 21:55:57: 18000000 INFO @ Mon, 03 Jun 2019 21:56:06: 21000000 INFO @ Mon, 03 Jun 2019 21:56:07: 19000000 INFO @ Mon, 03 Jun 2019 21:56:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:56:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:56:10: #1 total tags in treatment: 21483219 INFO @ Mon, 03 Jun 2019 21:56:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:56:10: #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 21:56:10: #1 tags after filtering in treatment: 21483219 INFO @ Mon, 03 Jun 2019 21:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:56:10: #1 finished! INFO @ Mon, 03 Jun 2019 21:56:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:56:12: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 21:56:12: 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 @ Mon, 03 Jun 2019 21:56:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.10_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/SRX495260/SRX495260.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:56:16: 20000000 INFO @ Mon, 03 Jun 2019 21:56:25: 21000000 INFO @ Mon, 03 Jun 2019 21:56:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:56:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:56:30: #1 total tags in treatment: 21483219 INFO @ Mon, 03 Jun 2019 21:56:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:56:30: #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 21:56:30: #1 tags after filtering in treatment: 21483219 INFO @ Mon, 03 Jun 2019 21:56:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:56:30: #1 finished! INFO @ Mon, 03 Jun 2019 21:56:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:56:32: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 21:56:32: 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 @ Mon, 03 Jun 2019 21:56:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.05_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/SRX495260/SRX495260.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495260/SRX495260.05_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。