Job ID = 1292037 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T08:10:25 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' 2019-06-02T08:10:25 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/000913/SRR935757' 2019-06-02T08:10:35 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR935757', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T08:10:39 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' 2019-06-02T08:10:39 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/000913/SRR935757' 2019-06-02T08:10:39 fasterq-dump.2.9.6 err: invalid accession 'SRR935757' spots read : 13,687,820 reads read : 13,687,820 reads written : 13,687,820 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: 00:04:20 13687820 reads; of these: 13687820 (100.00%) were unpaired; of these: 1671977 (12.22%) aligned 0 times 10701388 (78.18%) aligned exactly 1 time 1314455 (9.60%) aligned >1 times 87.78% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3792162 / 12015843 = 0.3156 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 @ Sun, 02 Jun 2019 17:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 17:26:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:26:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 17:26:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:26:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 17:26:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:26:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:26:49: 1000000 INFO @ Sun, 02 Jun 2019 17:26:50: 1000000 INFO @ Sun, 02 Jun 2019 17:26:51: 1000000 INFO @ Sun, 02 Jun 2019 17:26:58: 2000000 INFO @ Sun, 02 Jun 2019 17:26:59: 2000000 INFO @ Sun, 02 Jun 2019 17:27:00: 2000000 INFO @ Sun, 02 Jun 2019 17:27:06: 3000000 INFO @ Sun, 02 Jun 2019 17:27:07: 3000000 INFO @ Sun, 02 Jun 2019 17:27:10: 3000000 INFO @ Sun, 02 Jun 2019 17:27:14: 4000000 INFO @ Sun, 02 Jun 2019 17:27:16: 4000000 INFO @ Sun, 02 Jun 2019 17:27:19: 4000000 INFO @ Sun, 02 Jun 2019 17:27:23: 5000000 INFO @ Sun, 02 Jun 2019 17:27:24: 5000000 INFO @ Sun, 02 Jun 2019 17:27:28: 5000000 INFO @ Sun, 02 Jun 2019 17:27:31: 6000000 INFO @ Sun, 02 Jun 2019 17:27:33: 6000000 INFO @ Sun, 02 Jun 2019 17:27:38: 6000000 INFO @ Sun, 02 Jun 2019 17:27:40: 7000000 INFO @ Sun, 02 Jun 2019 17:27:43: 7000000 INFO @ Sun, 02 Jun 2019 17:27:47: 7000000 INFO @ Sun, 02 Jun 2019 17:27:48: 8000000 INFO @ Sun, 02 Jun 2019 17:27:50: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:27:50: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:27:50: #1 total tags in treatment: 8223681 INFO @ Sun, 02 Jun 2019 17:27:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:27:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:27:50: #1 tags after filtering in treatment: 8223681 INFO @ Sun, 02 Jun 2019 17:27:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:27:50: #1 finished! INFO @ Sun, 02 Jun 2019 17:27:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:27:51: #2 number of paired peaks: 61 WARNING @ Sun, 02 Jun 2019 17:27:51: Too few paired peaks (61) 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 @ Sun, 02 Jun 2019 17:27:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.20_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/ce10/SRX323683/SRX323683.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:27:52: 8000000 INFO @ Sun, 02 Jun 2019 17:27:54: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:27:54: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:27:54: #1 total tags in treatment: 8223681 INFO @ Sun, 02 Jun 2019 17:27:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:27:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:27:54: #1 tags after filtering in treatment: 8223681 INFO @ Sun, 02 Jun 2019 17:27:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:27:54: #1 finished! INFO @ Sun, 02 Jun 2019 17:27:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:27:55: #2 number of paired peaks: 61 WARNING @ Sun, 02 Jun 2019 17:27:55: Too few paired peaks (61) 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 @ Sun, 02 Jun 2019 17:27:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.10_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/ce10/SRX323683/SRX323683.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:27:56: 8000000 INFO @ Sun, 02 Jun 2019 17:27:59: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:27:59: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:27:59: #1 total tags in treatment: 8223681 INFO @ Sun, 02 Jun 2019 17:27:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:27:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:27:59: #1 tags after filtering in treatment: 8223681 INFO @ Sun, 02 Jun 2019 17:27:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:27:59: #1 finished! INFO @ Sun, 02 Jun 2019 17:27:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:27:59: #2 number of paired peaks: 61 WARNING @ Sun, 02 Jun 2019 17:27:59: Too few paired peaks (61) 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 @ Sun, 02 Jun 2019 17:27:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.05_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/ce10/SRX323683/SRX323683.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX323683/SRX323683.05_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。