Job ID = 1293079 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:40:44 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' 2019-06-02T12:40:44 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/SRR8201463/SRR8201463.1' 2019-06-02T12:40:55 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8201463' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T12:40:55 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 11,198,348 reads read : 11,198,348 reads written : 11,198,348 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: 00:02:55 11198348 reads; of these: 11198348 (100.00%) were unpaired; of these: 94210 (0.84%) aligned 0 times 9240651 (82.52%) aligned exactly 1 time 1863487 (16.64%) aligned >1 times 99.16% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 890761 / 11104138 = 0.0802 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 21:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.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 21:50:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:50:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.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 21:50:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:50:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.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 21:50:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:50:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:50:27: 1000000 INFO @ Sun, 02 Jun 2019 21:50:27: 1000000 INFO @ Sun, 02 Jun 2019 21:50:28: 1000000 INFO @ Sun, 02 Jun 2019 21:50:36: 2000000 INFO @ Sun, 02 Jun 2019 21:50:36: 2000000 INFO @ Sun, 02 Jun 2019 21:50:37: 2000000 INFO @ Sun, 02 Jun 2019 21:50:44: 3000000 INFO @ Sun, 02 Jun 2019 21:50:44: 3000000 INFO @ Sun, 02 Jun 2019 21:50:47: 3000000 INFO @ Sun, 02 Jun 2019 21:50:51: 4000000 INFO @ Sun, 02 Jun 2019 21:50:52: 4000000 INFO @ Sun, 02 Jun 2019 21:50:56: 4000000 INFO @ Sun, 02 Jun 2019 21:50:59: 5000000 INFO @ Sun, 02 Jun 2019 21:51:00: 5000000 INFO @ Sun, 02 Jun 2019 21:51:05: 5000000 INFO @ Sun, 02 Jun 2019 21:51:06: 6000000 INFO @ Sun, 02 Jun 2019 21:51:08: 6000000 INFO @ Sun, 02 Jun 2019 21:51:13: 7000000 INFO @ Sun, 02 Jun 2019 21:51:15: 6000000 INFO @ Sun, 02 Jun 2019 21:51:16: 7000000 INFO @ Sun, 02 Jun 2019 21:51:21: 8000000 INFO @ Sun, 02 Jun 2019 21:51:24: 7000000 INFO @ Sun, 02 Jun 2019 21:51:24: 8000000 INFO @ Sun, 02 Jun 2019 21:51:28: 9000000 INFO @ Sun, 02 Jun 2019 21:51:32: 9000000 INFO @ Sun, 02 Jun 2019 21:51:33: 8000000 INFO @ Sun, 02 Jun 2019 21:51:35: 10000000 INFO @ Sun, 02 Jun 2019 21:51:37: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:51:37: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:51:37: #1 total tags in treatment: 10213377 INFO @ Sun, 02 Jun 2019 21:51:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:51:37: #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 21:51:37: #1 tags after filtering in treatment: 10213377 INFO @ Sun, 02 Jun 2019 21:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:51:37: #1 finished! INFO @ Sun, 02 Jun 2019 21:51:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:51:38: #2 number of paired peaks: 330 WARNING @ Sun, 02 Jun 2019 21:51:38: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 02 Jun 2019 21:51:38: start model_add_line... INFO @ Sun, 02 Jun 2019 21:51:38: start X-correlation... INFO @ Sun, 02 Jun 2019 21:51:38: end of X-cor INFO @ Sun, 02 Jun 2019 21:51:38: #2 finished! INFO @ Sun, 02 Jun 2019 21:51:38: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 21:51:38: #2 alternative fragment length(s) may be 3,47,556 bps INFO @ Sun, 02 Jun 2019 21:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.20_model.r WARNING @ Sun, 02 Jun 2019 21:51:38: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:51:38: #2 You may need to consider one of the other alternative d(s): 3,47,556 WARNING @ Sun, 02 Jun 2019 21:51:38: #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 21:51:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:51:40: 10000000 INFO @ Sun, 02 Jun 2019 21:51:42: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:51:42: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:51:42: #1 total tags in treatment: 10213377 INFO @ Sun, 02 Jun 2019 21:51:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:51:42: #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 21:51:42: #1 tags after filtering in treatment: 10213377 INFO @ Sun, 02 Jun 2019 21:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:51:42: #1 finished! INFO @ Sun, 02 Jun 2019 21:51:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:51:42: 9000000 INFO @ Sun, 02 Jun 2019 21:51:43: #2 number of paired peaks: 330 WARNING @ Sun, 02 Jun 2019 21:51:43: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 02 Jun 2019 21:51:43: start model_add_line... INFO @ Sun, 02 Jun 2019 21:51:43: start X-correlation... INFO @ Sun, 02 Jun 2019 21:51:43: end of X-cor INFO @ Sun, 02 Jun 2019 21:51:43: #2 finished! INFO @ Sun, 02 Jun 2019 21:51:43: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 21:51:43: #2 alternative fragment length(s) may be 3,47,556 bps INFO @ Sun, 02 Jun 2019 21:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.05_model.r WARNING @ Sun, 02 Jun 2019 21:51:43: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:51:43: #2 You may need to consider one of the other alternative d(s): 3,47,556 WARNING @ Sun, 02 Jun 2019 21:51:43: #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 21:51:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:51:51: 10000000 INFO @ Sun, 02 Jun 2019 21:51:53: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:51:53: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:51:53: #1 total tags in treatment: 10213377 INFO @ Sun, 02 Jun 2019 21:51:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:51:53: #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 21:51:53: #1 tags after filtering in treatment: 10213377 INFO @ Sun, 02 Jun 2019 21:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:51:53: #1 finished! INFO @ Sun, 02 Jun 2019 21:51:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:51:54: #2 number of paired peaks: 330 WARNING @ Sun, 02 Jun 2019 21:51:54: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 02 Jun 2019 21:51:54: start model_add_line... INFO @ Sun, 02 Jun 2019 21:51:54: start X-correlation... INFO @ Sun, 02 Jun 2019 21:51:54: end of X-cor INFO @ Sun, 02 Jun 2019 21:51:54: #2 finished! INFO @ Sun, 02 Jun 2019 21:51:54: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 21:51:54: #2 alternative fragment length(s) may be 3,47,556 bps INFO @ Sun, 02 Jun 2019 21:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.10_model.r WARNING @ Sun, 02 Jun 2019 21:51:54: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:51:54: #2 You may need to consider one of the other alternative d(s): 3,47,556 WARNING @ Sun, 02 Jun 2019 21:51:54: #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 21:51:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:52:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:52:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.20_summits.bed INFO @ Sun, 02 Jun 2019 21:52:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:52:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:52:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:52:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.05_summits.bed INFO @ Sun, 02 Jun 2019 21:52:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (625 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020840/SRX5020840.10_summits.bed INFO @ Sun, 02 Jun 2019 21:52:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (416 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。