Job ID = 1292520 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T10:13:18 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' 2019-06-02T10:13:18 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/sos/sra-pub-run-1/SRR1163600/SRR1163600.1' 2019-06-02T10:13:29 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1163600' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T10:13:29 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 16,090,826 reads read : 16,090,826 reads written : 16,090,826 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: 00:03:31 16090826 reads; of these: 16090826 (100.00%) were unpaired; of these: 156674 (0.97%) aligned 0 times 13498502 (83.89%) aligned exactly 1 time 2435650 (15.14%) aligned >1 times 99.03% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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_rmdupse_core] 2343907 / 15934152 = 0.1471 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 19:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.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 19:24:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:24:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.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 19:24:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:24:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.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 19:24:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:24:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:24:21: 1000000 INFO @ Sun, 02 Jun 2019 19:24:22: 1000000 INFO @ Sun, 02 Jun 2019 19:24:22: 1000000 INFO @ Sun, 02 Jun 2019 19:24:28: 2000000 INFO @ Sun, 02 Jun 2019 19:24:30: 2000000 INFO @ Sun, 02 Jun 2019 19:24:30: 2000000 INFO @ Sun, 02 Jun 2019 19:24:35: 3000000 INFO @ Sun, 02 Jun 2019 19:24:38: 3000000 INFO @ Sun, 02 Jun 2019 19:24:38: 3000000 INFO @ Sun, 02 Jun 2019 19:24:43: 4000000 INFO @ Sun, 02 Jun 2019 19:24:46: 4000000 INFO @ Sun, 02 Jun 2019 19:24:47: 4000000 INFO @ Sun, 02 Jun 2019 19:24:50: 5000000 INFO @ Sun, 02 Jun 2019 19:24:55: 5000000 INFO @ Sun, 02 Jun 2019 19:24:55: 5000000 INFO @ Sun, 02 Jun 2019 19:24:58: 6000000 INFO @ Sun, 02 Jun 2019 19:25:03: 6000000 INFO @ Sun, 02 Jun 2019 19:25:03: 6000000 INFO @ Sun, 02 Jun 2019 19:25:06: 7000000 INFO @ Sun, 02 Jun 2019 19:25:11: 7000000 INFO @ Sun, 02 Jun 2019 19:25:11: 7000000 INFO @ Sun, 02 Jun 2019 19:25:13: 8000000 INFO @ Sun, 02 Jun 2019 19:25:19: 8000000 INFO @ Sun, 02 Jun 2019 19:25:19: 8000000 INFO @ Sun, 02 Jun 2019 19:25:20: 9000000 INFO @ Sun, 02 Jun 2019 19:25:27: 9000000 INFO @ Sun, 02 Jun 2019 19:25:27: 10000000 INFO @ Sun, 02 Jun 2019 19:25:27: 9000000 INFO @ Sun, 02 Jun 2019 19:25:35: 11000000 INFO @ Sun, 02 Jun 2019 19:25:35: 10000000 INFO @ Sun, 02 Jun 2019 19:25:36: 10000000 INFO @ Sun, 02 Jun 2019 19:25:42: 12000000 INFO @ Sun, 02 Jun 2019 19:25:43: 11000000 INFO @ Sun, 02 Jun 2019 19:25:46: 11000000 INFO @ Sun, 02 Jun 2019 19:25:49: 13000000 INFO @ Sun, 02 Jun 2019 19:25:51: 12000000 INFO @ Sun, 02 Jun 2019 19:25:54: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:25:54: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:25:54: #1 total tags in treatment: 13590245 INFO @ Sun, 02 Jun 2019 19:25:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:25:54: #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 19:25:54: #1 tags after filtering in treatment: 13590245 INFO @ Sun, 02 Jun 2019 19:25:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:25:54: #1 finished! INFO @ Sun, 02 Jun 2019 19:25:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:25:55: #2 number of paired peaks: 186 WARNING @ Sun, 02 Jun 2019 19:25:55: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 02 Jun 2019 19:25:55: start model_add_line... INFO @ Sun, 02 Jun 2019 19:25:55: start X-correlation... INFO @ Sun, 02 Jun 2019 19:25:55: end of X-cor INFO @ Sun, 02 Jun 2019 19:25:55: #2 finished! INFO @ Sun, 02 Jun 2019 19:25:55: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:25:55: #2 alternative fragment length(s) may be 2,39,554,580 bps INFO @ Sun, 02 Jun 2019 19:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.20_model.r WARNING @ Sun, 02 Jun 2019 19:25:55: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:25:55: #2 You may need to consider one of the other alternative d(s): 2,39,554,580 WARNING @ Sun, 02 Jun 2019 19:25:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:25:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:25:56: 12000000 INFO @ Sun, 02 Jun 2019 19:25:59: 13000000 INFO @ Sun, 02 Jun 2019 19:26:04: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:26:04: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:26:04: #1 total tags in treatment: 13590245 INFO @ Sun, 02 Jun 2019 19:26:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:26:04: #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 19:26:04: #1 tags after filtering in treatment: 13590245 INFO @ Sun, 02 Jun 2019 19:26:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:26:04: #1 finished! INFO @ Sun, 02 Jun 2019 19:26:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:26:05: 13000000 INFO @ Sun, 02 Jun 2019 19:26:05: #2 number of paired peaks: 186 WARNING @ Sun, 02 Jun 2019 19:26:05: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 02 Jun 2019 19:26:05: start model_add_line... INFO @ Sun, 02 Jun 2019 19:26:05: start X-correlation... INFO @ Sun, 02 Jun 2019 19:26:05: end of X-cor INFO @ Sun, 02 Jun 2019 19:26:05: #2 finished! INFO @ Sun, 02 Jun 2019 19:26:05: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:26:05: #2 alternative fragment length(s) may be 2,39,554,580 bps INFO @ Sun, 02 Jun 2019 19:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.10_model.r WARNING @ Sun, 02 Jun 2019 19:26:05: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:26:05: #2 You may need to consider one of the other alternative d(s): 2,39,554,580 WARNING @ Sun, 02 Jun 2019 19:26:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:26:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:26:11: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:26:11: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:26:11: #1 total tags in treatment: 13590245 INFO @ Sun, 02 Jun 2019 19:26:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:26:11: #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 19:26:11: #1 tags after filtering in treatment: 13590245 INFO @ Sun, 02 Jun 2019 19:26:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:26:11: #1 finished! INFO @ Sun, 02 Jun 2019 19:26:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:26:12: #2 number of paired peaks: 186 WARNING @ Sun, 02 Jun 2019 19:26:12: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 02 Jun 2019 19:26:12: start model_add_line... INFO @ Sun, 02 Jun 2019 19:26:12: start X-correlation... INFO @ Sun, 02 Jun 2019 19:26:12: end of X-cor INFO @ Sun, 02 Jun 2019 19:26:12: #2 finished! INFO @ Sun, 02 Jun 2019 19:26:12: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:26:12: #2 alternative fragment length(s) may be 2,39,554,580 bps INFO @ Sun, 02 Jun 2019 19:26:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.05_model.r WARNING @ Sun, 02 Jun 2019 19:26:12: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:26:12: #2 You may need to consider one of the other alternative d(s): 2,39,554,580 WARNING @ Sun, 02 Jun 2019 19:26:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:26:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:26:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:26:39: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:26:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:26:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:26:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.20_summits.bed INFO @ Sun, 02 Jun 2019 19:26:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:26:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:26:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.10_summits.bed INFO @ Sun, 02 Jun 2019 19:26:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466534/SRX466534.05_summits.bed INFO @ Sun, 02 Jun 2019 19:27:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (597 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。