Job ID = 1295760 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T06:20:33 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' 2019-06-03T06:20:33 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/sra20/SRR/001118/SRR1145607' 2019-06-03T06:20:42 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR1145607', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T06:20:47 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' 2019-06-03T06:20:47 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/sra20/SRR/001118/SRR1145607' 2019-06-03T06:20:47 fasterq-dump.2.9.6 err: invalid accession 'SRR1145607' spots read : 25,547,860 reads read : 25,547,860 reads written : 25,547,860 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: 00:05:15 25547860 reads; of these: 25547860 (100.00%) were unpaired; of these: 5067822 (19.84%) aligned 0 times 18932210 (74.10%) aligned exactly 1 time 1547828 (6.06%) aligned >1 times 80.16% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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 8 files... [bam_rmdupse_core] 4236038 / 20480038 = 0.2068 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 15:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.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 15:40:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:40:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:40:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.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 15:40:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.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 15:40:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:40:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:40:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:40:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:40:49: 1000000 INFO @ Mon, 03 Jun 2019 15:40:50: 1000000 INFO @ Mon, 03 Jun 2019 15:40:50: 1000000 INFO @ Mon, 03 Jun 2019 15:40:56: 2000000 INFO @ Mon, 03 Jun 2019 15:40:57: 2000000 INFO @ Mon, 03 Jun 2019 15:40:57: 2000000 INFO @ Mon, 03 Jun 2019 15:41:02: 3000000 INFO @ Mon, 03 Jun 2019 15:41:04: 3000000 INFO @ Mon, 03 Jun 2019 15:41:04: 3000000 INFO @ Mon, 03 Jun 2019 15:41:09: 4000000 INFO @ Mon, 03 Jun 2019 15:41:10: 4000000 INFO @ Mon, 03 Jun 2019 15:41:10: 4000000 INFO @ Mon, 03 Jun 2019 15:41:15: 5000000 INFO @ Mon, 03 Jun 2019 15:41:17: 5000000 INFO @ Mon, 03 Jun 2019 15:41:17: 5000000 INFO @ Mon, 03 Jun 2019 15:41:22: 6000000 INFO @ Mon, 03 Jun 2019 15:41:24: 6000000 INFO @ Mon, 03 Jun 2019 15:41:24: 6000000 INFO @ Mon, 03 Jun 2019 15:41:28: 7000000 INFO @ Mon, 03 Jun 2019 15:41:31: 7000000 INFO @ Mon, 03 Jun 2019 15:41:31: 7000000 INFO @ Mon, 03 Jun 2019 15:41:34: 8000000 INFO @ Mon, 03 Jun 2019 15:41:37: 8000000 INFO @ Mon, 03 Jun 2019 15:41:37: 8000000 INFO @ Mon, 03 Jun 2019 15:41:41: 9000000 INFO @ Mon, 03 Jun 2019 15:41:44: 9000000 INFO @ Mon, 03 Jun 2019 15:41:44: 9000000 INFO @ Mon, 03 Jun 2019 15:41:47: 10000000 INFO @ Mon, 03 Jun 2019 15:41:50: 10000000 INFO @ Mon, 03 Jun 2019 15:41:50: 10000000 INFO @ Mon, 03 Jun 2019 15:41:53: 11000000 INFO @ Mon, 03 Jun 2019 15:41:56: 11000000 INFO @ Mon, 03 Jun 2019 15:41:57: 11000000 INFO @ Mon, 03 Jun 2019 15:42:00: 12000000 INFO @ Mon, 03 Jun 2019 15:42:03: 12000000 INFO @ Mon, 03 Jun 2019 15:42:03: 12000000 INFO @ Mon, 03 Jun 2019 15:42:06: 13000000 INFO @ Mon, 03 Jun 2019 15:42:09: 13000000 INFO @ Mon, 03 Jun 2019 15:42:09: 13000000 INFO @ Mon, 03 Jun 2019 15:42:13: 14000000 INFO @ Mon, 03 Jun 2019 15:42:15: 14000000 INFO @ Mon, 03 Jun 2019 15:42:16: 14000000 INFO @ Mon, 03 Jun 2019 15:42:19: 15000000 INFO @ Mon, 03 Jun 2019 15:42:22: 15000000 INFO @ Mon, 03 Jun 2019 15:42:23: 15000000 INFO @ Mon, 03 Jun 2019 15:42:25: 16000000 INFO @ Mon, 03 Jun 2019 15:42:27: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 15:42:27: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 15:42:27: #1 total tags in treatment: 16244000 INFO @ Mon, 03 Jun 2019 15:42:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:42:27: #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 15:42:27: #1 tags after filtering in treatment: 16244000 INFO @ Mon, 03 Jun 2019 15:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:42:27: #1 finished! INFO @ Mon, 03 Jun 2019 15:42:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:42:29: 16000000 INFO @ Mon, 03 Jun 2019 15:42:29: #2 number of paired peaks: 8 WARNING @ Mon, 03 Jun 2019 15:42:29: Too few paired peaks (8) 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 15:42:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.10_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/SRX450790/SRX450790.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:42:30: 16000000 INFO @ Mon, 03 Jun 2019 15:42:31: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 15:42:31: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 15:42:31: #1 total tags in treatment: 16244000 INFO @ Mon, 03 Jun 2019 15:42:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:42:31: #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 15:42:31: #1 tags after filtering in treatment: 16244000 INFO @ Mon, 03 Jun 2019 15:42:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:42:31: #1 finished! INFO @ Mon, 03 Jun 2019 15:42:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:42:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:42:31: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 15:42:31: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 15:42:31: #1 total tags in treatment: 16244000 INFO @ Mon, 03 Jun 2019 15:42:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:42:31: #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 15:42:32: #1 tags after filtering in treatment: 16244000 INFO @ Mon, 03 Jun 2019 15:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:42:32: #1 finished! INFO @ Mon, 03 Jun 2019 15:42:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:42:32: #2 number of paired peaks: 8 WARNING @ Mon, 03 Jun 2019 15:42:32: Too few paired peaks (8) 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 15:42:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.20_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/SRX450790/SRX450790.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:42:33: #2 number of paired peaks: 8 WARNING @ Mon, 03 Jun 2019 15:42:33: Too few paired peaks (8) 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 15:42:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.05_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/SRX450790/SRX450790.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX450790/SRX450790.05_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。