Job ID = 1293870 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:50:30 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' 2019-06-02T17:50:30 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-2/SRR447744/SRR447744.2' 2019-06-02T17:50:41 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR447744' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 44,491,533 reads read : 44,491,533 reads written : 44,491,533 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: 00:07:20 44491533 reads; of these: 44491533 (100.00%) were unpaired; of these: 37116660 (83.42%) aligned 0 times 5731644 (12.88%) aligned exactly 1 time 1643229 (3.69%) aligned >1 times 16.58% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 6710616 / 7374873 = 0.9099 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 03:03:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.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 03:03:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:03:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:03:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.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 03:03:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:03:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:03:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.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 03:03:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:03:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:03:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:03:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:03:35: #1 total tags in treatment: 664257 INFO @ Mon, 03 Jun 2019 03:03:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:03:35: #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 03:03:35: #1 tags after filtering in treatment: 664257 INFO @ Mon, 03 Jun 2019 03:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:03:35: #1 finished! INFO @ Mon, 03 Jun 2019 03:03:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:03:35: #2 number of paired peaks: 2906 INFO @ Mon, 03 Jun 2019 03:03:35: start model_add_line... INFO @ Mon, 03 Jun 2019 03:03:35: start X-correlation... INFO @ Mon, 03 Jun 2019 03:03:35: end of X-cor INFO @ Mon, 03 Jun 2019 03:03:35: #2 finished! INFO @ Mon, 03 Jun 2019 03:03:35: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 03:03:35: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 03 Jun 2019 03:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.05_model.r WARNING @ Mon, 03 Jun 2019 03:03:35: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:03:35: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 03 Jun 2019 03:03:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 03:03:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:03:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:03:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:03:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:03:36: #1 total tags in treatment: 664257 INFO @ Mon, 03 Jun 2019 03:03:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:03:36: #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 03:03:36: #1 tags after filtering in treatment: 664257 INFO @ Mon, 03 Jun 2019 03:03:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:03:36: #1 finished! INFO @ Mon, 03 Jun 2019 03:03:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:03:36: #2 number of paired peaks: 2906 INFO @ Mon, 03 Jun 2019 03:03:36: start model_add_line... INFO @ Mon, 03 Jun 2019 03:03:36: start X-correlation... INFO @ Mon, 03 Jun 2019 03:03:36: end of X-cor INFO @ Mon, 03 Jun 2019 03:03:36: #2 finished! INFO @ Mon, 03 Jun 2019 03:03:36: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 03:03:36: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 03 Jun 2019 03:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.10_model.r WARNING @ Mon, 03 Jun 2019 03:03:36: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:03:36: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 03 Jun 2019 03:03:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 03:03:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:03:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:03:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:03:37: #1 total tags in treatment: 664257 INFO @ Mon, 03 Jun 2019 03:03:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:03:37: #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 03:03:37: #1 tags after filtering in treatment: 664257 INFO @ Mon, 03 Jun 2019 03:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:03:37: #1 finished! INFO @ Mon, 03 Jun 2019 03:03:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:03:37: #2 number of paired peaks: 2906 INFO @ Mon, 03 Jun 2019 03:03:37: start model_add_line... INFO @ Mon, 03 Jun 2019 03:03:37: start X-correlation... INFO @ Mon, 03 Jun 2019 03:03:37: end of X-cor INFO @ Mon, 03 Jun 2019 03:03:37: #2 finished! INFO @ Mon, 03 Jun 2019 03:03:37: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 03:03:37: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 03 Jun 2019 03:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.20_model.r WARNING @ Mon, 03 Jun 2019 03:03:37: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:03:37: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 03 Jun 2019 03:03:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 03:03:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:03:37: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 03:03:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:03:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:03:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:03:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:03:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.05_summits.bed INFO @ Mon, 03 Jun 2019 03:03:39: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1589 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:03:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 03:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.10_summits.bed INFO @ Mon, 03 Jun 2019 03:03:40: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (977 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX131081/SRX131081.20_summits.bed INFO @ Mon, 03 Jun 2019 03:03:40: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (621 records, 4 fields): 3 millis CompletedMACS2peakCalling