Job ID = 1309213 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:06:53 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' 2019-06-03T14:06:53 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/sra24/SRR/001697/SRR1737835' 2019-06-03T14:07:03 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1737835' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T14:07:03 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 17,762,885 reads read : 17,762,885 reads written : 17,762,885 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: 00:03:44 17762885 reads; of these: 17762885 (100.00%) were unpaired; of these: 3565238 (20.07%) aligned 0 times 12718021 (71.60%) aligned exactly 1 time 1479626 (8.33%) aligned >1 times 79.93% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 4120579 / 14197647 = 0.2902 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 23:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.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 23:29:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.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 23:29:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.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 23:29:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:25: 1000000 INFO @ Mon, 03 Jun 2019 23:29:25: 1000000 INFO @ Mon, 03 Jun 2019 23:29:25: 1000000 INFO @ Mon, 03 Jun 2019 23:29:32: 2000000 INFO @ Mon, 03 Jun 2019 23:29:32: 2000000 INFO @ Mon, 03 Jun 2019 23:29:32: 2000000 INFO @ Mon, 03 Jun 2019 23:29:38: 3000000 INFO @ Mon, 03 Jun 2019 23:29:39: 3000000 INFO @ Mon, 03 Jun 2019 23:29:39: 3000000 INFO @ Mon, 03 Jun 2019 23:29:45: 4000000 INFO @ Mon, 03 Jun 2019 23:29:46: 4000000 INFO @ Mon, 03 Jun 2019 23:29:46: 4000000 INFO @ Mon, 03 Jun 2019 23:29:52: 5000000 INFO @ Mon, 03 Jun 2019 23:29:53: 5000000 INFO @ Mon, 03 Jun 2019 23:29:53: 5000000 INFO @ Mon, 03 Jun 2019 23:29:59: 6000000 INFO @ Mon, 03 Jun 2019 23:30:01: 6000000 INFO @ Mon, 03 Jun 2019 23:30:01: 6000000 INFO @ Mon, 03 Jun 2019 23:30:06: 7000000 INFO @ Mon, 03 Jun 2019 23:30:08: 7000000 INFO @ Mon, 03 Jun 2019 23:30:08: 7000000 INFO @ Mon, 03 Jun 2019 23:30:13: 8000000 INFO @ Mon, 03 Jun 2019 23:30:15: 8000000 INFO @ Mon, 03 Jun 2019 23:30:15: 8000000 INFO @ Mon, 03 Jun 2019 23:30:19: 9000000 INFO @ Mon, 03 Jun 2019 23:30:22: 9000000 INFO @ Mon, 03 Jun 2019 23:30:22: 9000000 INFO @ Mon, 03 Jun 2019 23:30:26: 10000000 INFO @ Mon, 03 Jun 2019 23:30:27: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:30:27: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:30:27: #1 total tags in treatment: 10077068 INFO @ Mon, 03 Jun 2019 23:30:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:30:27: #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 23:30:27: #1 tags after filtering in treatment: 10077068 INFO @ Mon, 03 Jun 2019 23:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:30:27: #1 finished! INFO @ Mon, 03 Jun 2019 23:30:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:30:28: #2 number of paired peaks: 1977 INFO @ Mon, 03 Jun 2019 23:30:28: start model_add_line... INFO @ Mon, 03 Jun 2019 23:30:28: start X-correlation... INFO @ Mon, 03 Jun 2019 23:30:28: end of X-cor INFO @ Mon, 03 Jun 2019 23:30:28: #2 finished! INFO @ Mon, 03 Jun 2019 23:30:28: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 23:30:28: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 03 Jun 2019 23:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.20_model.r INFO @ Mon, 03 Jun 2019 23:30:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:30:28: 10000000 INFO @ Mon, 03 Jun 2019 23:30:28: 10000000 INFO @ Mon, 03 Jun 2019 23:30:29: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:30:29: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:30:29: #1 total tags in treatment: 10077068 INFO @ Mon, 03 Jun 2019 23:30:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:30:29: #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 23:30:29: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:30:29: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:30:29: #1 total tags in treatment: 10077068 INFO @ Mon, 03 Jun 2019 23:30:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:30:29: #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 23:30:29: #1 tags after filtering in treatment: 10077068 INFO @ Mon, 03 Jun 2019 23:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:30:29: #1 finished! INFO @ Mon, 03 Jun 2019 23:30:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:30:29: #1 tags after filtering in treatment: 10077068 INFO @ Mon, 03 Jun 2019 23:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:30:29: #1 finished! INFO @ Mon, 03 Jun 2019 23:30:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:30:30: #2 number of paired peaks: 1977 INFO @ Mon, 03 Jun 2019 23:30:30: start model_add_line... INFO @ Mon, 03 Jun 2019 23:30:30: #2 number of paired peaks: 1977 INFO @ Mon, 03 Jun 2019 23:30:30: start model_add_line... INFO @ Mon, 03 Jun 2019 23:30:30: start X-correlation... INFO @ Mon, 03 Jun 2019 23:30:30: start X-correlation... INFO @ Mon, 03 Jun 2019 23:30:30: end of X-cor INFO @ Mon, 03 Jun 2019 23:30:30: #2 finished! INFO @ Mon, 03 Jun 2019 23:30:30: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 23:30:30: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 03 Jun 2019 23:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.05_model.r INFO @ Mon, 03 Jun 2019 23:30:30: end of X-cor INFO @ Mon, 03 Jun 2019 23:30:30: #2 finished! INFO @ Mon, 03 Jun 2019 23:30:30: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 23:30:30: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 03 Jun 2019 23:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.10_model.r INFO @ Mon, 03 Jun 2019 23:30:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:30:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:30:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:31:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:31:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.20_summits.bed INFO @ Mon, 03 Jun 2019 23:31:14: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4024 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.10_summits.bed INFO @ Mon, 03 Jun 2019 23:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:31:18: Done! INFO @ Mon, 03 Jun 2019 23:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX826335/SRX826335.05_summits.bed INFO @ Mon, 03 Jun 2019 23:31:19: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6256 records, 4 fields): 13 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8644 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。