Job ID = 1295045 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:20:36 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' 2019-06-03T02:20:36 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/sra52/SRR/005873/SRR6014244' 2019-06-03T02:20:46 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR6014244' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T02:20:46 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 11,548,577 reads read : 11,548,577 reads written : 11,548,577 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: 00:05:28 11548577 reads; of these: 11548577 (100.00%) were unpaired; of these: 1338579 (11.59%) aligned 0 times 6632711 (57.43%) aligned exactly 1 time 3577287 (30.98%) aligned >1 times 88.41% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6379200 / 10209998 = 0.6248 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 11:42:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.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 11:42:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:42:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:42:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.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 11:42:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:42:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:42:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.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 11:42:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:42:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:42:14: 1000000 INFO @ Mon, 03 Jun 2019 11:42:16: 1000000 INFO @ Mon, 03 Jun 2019 11:42:16: 1000000 INFO @ Mon, 03 Jun 2019 11:42:22: 2000000 INFO @ Mon, 03 Jun 2019 11:42:24: 2000000 INFO @ Mon, 03 Jun 2019 11:42:25: 2000000 INFO @ Mon, 03 Jun 2019 11:42:30: 3000000 INFO @ Mon, 03 Jun 2019 11:42:34: 3000000 INFO @ Mon, 03 Jun 2019 11:42:34: 3000000 INFO @ Mon, 03 Jun 2019 11:42:36: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:42:36: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:42:36: #1 total tags in treatment: 3830798 INFO @ Mon, 03 Jun 2019 11:42:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:42:36: #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 11:42:36: #1 tags after filtering in treatment: 3830798 INFO @ Mon, 03 Jun 2019 11:42:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:42:36: #1 finished! INFO @ Mon, 03 Jun 2019 11:42:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:42:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:42:37: #2 number of paired peaks: 1857 INFO @ Mon, 03 Jun 2019 11:42:37: start model_add_line... INFO @ Mon, 03 Jun 2019 11:42:37: start X-correlation... INFO @ Mon, 03 Jun 2019 11:42:37: end of X-cor INFO @ Mon, 03 Jun 2019 11:42:37: #2 finished! INFO @ Mon, 03 Jun 2019 11:42:37: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 11:42:37: #2 alternative fragment length(s) may be 58 bps INFO @ Mon, 03 Jun 2019 11:42:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.10_model.r WARNING @ Mon, 03 Jun 2019 11:42:37: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:42:37: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Mon, 03 Jun 2019 11:42:37: #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 11:42:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:42:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:42:41: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:42:41: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:42:41: #1 total tags in treatment: 3830798 INFO @ Mon, 03 Jun 2019 11:42:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:42:41: #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 11:42:41: #1 tags after filtering in treatment: 3830798 INFO @ Mon, 03 Jun 2019 11:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:42:41: #1 finished! INFO @ Mon, 03 Jun 2019 11:42:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:42:41: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:42:41: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:42:41: #1 total tags in treatment: 3830798 INFO @ Mon, 03 Jun 2019 11:42:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:42:41: #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 11:42:41: #1 tags after filtering in treatment: 3830798 INFO @ Mon, 03 Jun 2019 11:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:42:41: #1 finished! INFO @ Mon, 03 Jun 2019 11:42:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:42:42: #2 number of paired peaks: 1857 INFO @ Mon, 03 Jun 2019 11:42:42: start model_add_line... INFO @ Mon, 03 Jun 2019 11:42:42: start X-correlation... INFO @ Mon, 03 Jun 2019 11:42:42: end of X-cor INFO @ Mon, 03 Jun 2019 11:42:42: #2 finished! INFO @ Mon, 03 Jun 2019 11:42:42: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 11:42:42: #2 alternative fragment length(s) may be 58 bps INFO @ Mon, 03 Jun 2019 11:42:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.20_model.r WARNING @ Mon, 03 Jun 2019 11:42:42: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:42:42: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Mon, 03 Jun 2019 11:42:42: #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 11:42:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:42:42: #2 number of paired peaks: 1857 INFO @ Mon, 03 Jun 2019 11:42:42: start model_add_line... INFO @ Mon, 03 Jun 2019 11:42:42: start X-correlation... INFO @ Mon, 03 Jun 2019 11:42:42: end of X-cor INFO @ Mon, 03 Jun 2019 11:42:42: #2 finished! INFO @ Mon, 03 Jun 2019 11:42:42: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 11:42:42: #2 alternative fragment length(s) may be 58 bps INFO @ Mon, 03 Jun 2019 11:42:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.05_model.r WARNING @ Mon, 03 Jun 2019 11:42:42: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:42:42: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Mon, 03 Jun 2019 11:42:42: #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 11:42:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:42:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.10_summits.bed INFO @ Mon, 03 Jun 2019 11:42:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1255 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:42:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:42:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:42:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.20_summits.bed INFO @ Mon, 03 Jun 2019 11:42:59: Done! INFO @ Mon, 03 Jun 2019 11:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167241/SRX3167241.05_summits.bed pass1 - making usageList (12 chroms): 1 millis INFO @ Mon, 03 Jun 2019 11:43:00: Done! pass2 - checking and writing primary data (859 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2260 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。