Job ID = 1292262 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T08:45:25 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' 2019-06-02T08:45:25 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/sos/sra-pub-run-1/SRR947529/SRR947529.2' 2019-06-02T08:45:36 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR947529' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T08:45:36 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 5,829,983 reads read : 5,829,983 reads written : 5,829,983 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: 00:00:43 5829983 reads; of these: 5829983 (100.00%) were unpaired; of these: 3144558 (53.94%) aligned 0 times 2202635 (37.78%) aligned exactly 1 time 482790 (8.28%) aligned >1 times 46.06% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 183419 / 2685425 = 0.0683 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 17:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.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 17:48:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:48:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.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 17:48:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:48:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.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 17:48:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:48:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:48:32: 1000000 INFO @ Sun, 02 Jun 2019 17:48:34: 1000000 INFO @ Sun, 02 Jun 2019 17:48:34: 1000000 INFO @ Sun, 02 Jun 2019 17:48:39: 2000000 INFO @ Sun, 02 Jun 2019 17:48:42: 2000000 INFO @ Sun, 02 Jun 2019 17:48:43: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:48:43: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:48:43: #1 total tags in treatment: 2502006 INFO @ Sun, 02 Jun 2019 17:48:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:48:43: #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 17:48:43: 2000000 INFO @ Sun, 02 Jun 2019 17:48:43: #1 tags after filtering in treatment: 2502006 INFO @ Sun, 02 Jun 2019 17:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:48:43: #1 finished! INFO @ Sun, 02 Jun 2019 17:48:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:48:43: #2 number of paired peaks: 495 WARNING @ Sun, 02 Jun 2019 17:48:43: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sun, 02 Jun 2019 17:48:43: start model_add_line... INFO @ Sun, 02 Jun 2019 17:48:43: start X-correlation... INFO @ Sun, 02 Jun 2019 17:48:43: end of X-cor INFO @ Sun, 02 Jun 2019 17:48:43: #2 finished! INFO @ Sun, 02 Jun 2019 17:48:43: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 17:48:43: #2 alternative fragment length(s) may be 41,535,574 bps INFO @ Sun, 02 Jun 2019 17:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.20_model.r WARNING @ Sun, 02 Jun 2019 17:48:43: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:48:43: #2 You may need to consider one of the other alternative d(s): 41,535,574 WARNING @ Sun, 02 Jun 2019 17:48:43: #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 17:48:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:48:46: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:48:46: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:48:46: #1 total tags in treatment: 2502006 INFO @ Sun, 02 Jun 2019 17:48:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:48:46: #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 17:48:46: #1 tags after filtering in treatment: 2502006 INFO @ Sun, 02 Jun 2019 17:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:48:46: #1 finished! INFO @ Sun, 02 Jun 2019 17:48:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:48:47: #2 number of paired peaks: 495 WARNING @ Sun, 02 Jun 2019 17:48:47: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sun, 02 Jun 2019 17:48:47: start model_add_line... INFO @ Sun, 02 Jun 2019 17:48:47: start X-correlation... INFO @ Sun, 02 Jun 2019 17:48:47: end of X-cor INFO @ Sun, 02 Jun 2019 17:48:47: #2 finished! INFO @ Sun, 02 Jun 2019 17:48:47: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 17:48:47: #2 alternative fragment length(s) may be 41,535,574 bps INFO @ Sun, 02 Jun 2019 17:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.05_model.r WARNING @ Sun, 02 Jun 2019 17:48:47: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:48:47: #2 You may need to consider one of the other alternative d(s): 41,535,574 WARNING @ Sun, 02 Jun 2019 17:48:47: #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 17:48:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:48:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:48:47: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:48:47: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:48:47: #1 total tags in treatment: 2502006 INFO @ Sun, 02 Jun 2019 17:48:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:48:47: #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 17:48:47: #1 tags after filtering in treatment: 2502006 INFO @ Sun, 02 Jun 2019 17:48:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:48:47: #1 finished! INFO @ Sun, 02 Jun 2019 17:48:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:48:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:48:47: #2 number of paired peaks: 495 WARNING @ Sun, 02 Jun 2019 17:48:47: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sun, 02 Jun 2019 17:48:47: start model_add_line... INFO @ Sun, 02 Jun 2019 17:48:47: start X-correlation... INFO @ Sun, 02 Jun 2019 17:48:47: end of X-cor INFO @ Sun, 02 Jun 2019 17:48:47: #2 finished! INFO @ Sun, 02 Jun 2019 17:48:47: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 17:48:47: #2 alternative fragment length(s) may be 41,535,574 bps INFO @ Sun, 02 Jun 2019 17:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.10_model.r WARNING @ Sun, 02 Jun 2019 17:48:47: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:48:47: #2 You may need to consider one of the other alternative d(s): 41,535,574 WARNING @ Sun, 02 Jun 2019 17:48:47: #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 17:48:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:48:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:48:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:48:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:48:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:48:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:48:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.20_summits.bed INFO @ Sun, 02 Jun 2019 17:48:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:48:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:48:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:48:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:48:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.05_summits.bed INFO @ Sun, 02 Jun 2019 17:48:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331292/SRX331292.10_summits.bed INFO @ Sun, 02 Jun 2019 17:48:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。