Job ID = 1294001 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:51:39 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' 2019-06-02T18:51:39 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/sra5/SRR/000508/SRR520453' 2019-06-02T18:51:48 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR520453' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:51:48 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 27,820,142 reads read : 27,820,142 reads written : 27,820,142 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: 00:08:46 27820142 reads; of these: 27820142 (100.00%) were unpaired; of these: 1522101 (5.47%) aligned 0 times 19467403 (69.98%) aligned exactly 1 time 6830638 (24.55%) aligned >1 times 94.53% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 6610352 / 26298041 = 0.2514 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 04:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.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 04:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.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 04:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.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 04:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:23:56: 1000000 INFO @ Mon, 03 Jun 2019 04:23:56: 1000000 INFO @ Mon, 03 Jun 2019 04:23:56: 1000000 INFO @ Mon, 03 Jun 2019 04:24:02: 2000000 INFO @ Mon, 03 Jun 2019 04:24:03: 2000000 INFO @ Mon, 03 Jun 2019 04:24:04: 2000000 INFO @ Mon, 03 Jun 2019 04:24:09: 3000000 INFO @ Mon, 03 Jun 2019 04:24:10: 3000000 INFO @ Mon, 03 Jun 2019 04:24:11: 3000000 INFO @ Mon, 03 Jun 2019 04:24:16: 4000000 INFO @ Mon, 03 Jun 2019 04:24:17: 4000000 INFO @ Mon, 03 Jun 2019 04:24:19: 4000000 INFO @ Mon, 03 Jun 2019 04:24:23: 5000000 INFO @ Mon, 03 Jun 2019 04:24:23: 5000000 INFO @ Mon, 03 Jun 2019 04:24:26: 5000000 INFO @ Mon, 03 Jun 2019 04:24:29: 6000000 INFO @ Mon, 03 Jun 2019 04:24:31: 6000000 INFO @ Mon, 03 Jun 2019 04:24:35: 6000000 INFO @ Mon, 03 Jun 2019 04:24:36: 7000000 INFO @ Mon, 03 Jun 2019 04:24:38: 7000000 INFO @ Mon, 03 Jun 2019 04:24:42: 8000000 INFO @ Mon, 03 Jun 2019 04:24:43: 7000000 INFO @ Mon, 03 Jun 2019 04:24:44: 8000000 INFO @ Mon, 03 Jun 2019 04:24:49: 9000000 INFO @ Mon, 03 Jun 2019 04:24:51: 8000000 INFO @ Mon, 03 Jun 2019 04:24:51: 9000000 INFO @ Mon, 03 Jun 2019 04:24:58: 10000000 INFO @ Mon, 03 Jun 2019 04:24:59: 9000000 INFO @ Mon, 03 Jun 2019 04:24:59: 10000000 INFO @ Mon, 03 Jun 2019 04:25:05: 11000000 INFO @ Mon, 03 Jun 2019 04:25:06: 11000000 INFO @ Mon, 03 Jun 2019 04:25:06: 10000000 INFO @ Mon, 03 Jun 2019 04:25:12: 12000000 INFO @ Mon, 03 Jun 2019 04:25:12: 12000000 INFO @ Mon, 03 Jun 2019 04:25:13: 11000000 INFO @ Mon, 03 Jun 2019 04:25:19: 13000000 INFO @ Mon, 03 Jun 2019 04:25:19: 13000000 INFO @ Mon, 03 Jun 2019 04:25:21: 12000000 INFO @ Mon, 03 Jun 2019 04:25:25: 14000000 INFO @ Mon, 03 Jun 2019 04:25:26: 14000000 INFO @ Mon, 03 Jun 2019 04:25:29: 13000000 INFO @ Mon, 03 Jun 2019 04:25:32: 15000000 INFO @ Mon, 03 Jun 2019 04:25:33: 15000000 INFO @ Mon, 03 Jun 2019 04:25:36: 14000000 INFO @ Mon, 03 Jun 2019 04:25:39: 16000000 INFO @ Mon, 03 Jun 2019 04:25:40: 16000000 INFO @ Mon, 03 Jun 2019 04:25:44: 15000000 INFO @ Mon, 03 Jun 2019 04:25:46: 17000000 INFO @ Mon, 03 Jun 2019 04:25:46: 17000000 INFO @ Mon, 03 Jun 2019 04:25:51: 16000000 INFO @ Mon, 03 Jun 2019 04:25:53: 18000000 INFO @ Mon, 03 Jun 2019 04:25:53: 18000000 INFO @ Mon, 03 Jun 2019 04:25:59: 17000000 INFO @ Mon, 03 Jun 2019 04:25:59: 19000000 INFO @ Mon, 03 Jun 2019 04:26:00: 19000000 INFO @ Mon, 03 Jun 2019 04:26:04: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:26:04: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:26:04: #1 total tags in treatment: 19687689 INFO @ Mon, 03 Jun 2019 04:26:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:26:04: #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 04:26:05: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:26:05: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:26:05: #1 total tags in treatment: 19687689 INFO @ Mon, 03 Jun 2019 04:26:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:26:05: #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 04:26:05: #1 tags after filtering in treatment: 19687689 INFO @ Mon, 03 Jun 2019 04:26:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:26:05: #1 finished! INFO @ Mon, 03 Jun 2019 04:26:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:26:05: #1 tags after filtering in treatment: 19687689 INFO @ Mon, 03 Jun 2019 04:26:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:26:05: #1 finished! INFO @ Mon, 03 Jun 2019 04:26:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:26:06: 18000000 INFO @ Mon, 03 Jun 2019 04:26:07: #2 number of paired peaks: 1817 INFO @ Mon, 03 Jun 2019 04:26:07: start model_add_line... INFO @ Mon, 03 Jun 2019 04:26:07: start X-correlation... INFO @ Mon, 03 Jun 2019 04:26:07: end of X-cor INFO @ Mon, 03 Jun 2019 04:26:07: #2 finished! INFO @ Mon, 03 Jun 2019 04:26:07: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 04:26:07: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 04:26:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.05_model.r INFO @ Mon, 03 Jun 2019 04:26:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:26:07: #2 number of paired peaks: 1817 INFO @ Mon, 03 Jun 2019 04:26:07: start model_add_line... INFO @ Mon, 03 Jun 2019 04:26:07: start X-correlation... INFO @ Mon, 03 Jun 2019 04:26:07: end of X-cor INFO @ Mon, 03 Jun 2019 04:26:07: #2 finished! INFO @ Mon, 03 Jun 2019 04:26:07: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 04:26:07: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 04:26:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.20_model.r INFO @ Mon, 03 Jun 2019 04:26:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:26:13: 19000000 INFO @ Mon, 03 Jun 2019 04:26:18: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:26:18: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:26:18: #1 total tags in treatment: 19687689 INFO @ Mon, 03 Jun 2019 04:26:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:26:18: #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 04:26:19: #1 tags after filtering in treatment: 19687689 INFO @ Mon, 03 Jun 2019 04:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:26:19: #1 finished! INFO @ Mon, 03 Jun 2019 04:26:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:26:21: #2 number of paired peaks: 1817 INFO @ Mon, 03 Jun 2019 04:26:21: start model_add_line... INFO @ Mon, 03 Jun 2019 04:26:21: start X-correlation... INFO @ Mon, 03 Jun 2019 04:26:21: end of X-cor INFO @ Mon, 03 Jun 2019 04:26:21: #2 finished! INFO @ Mon, 03 Jun 2019 04:26:21: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 04:26:21: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 04:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.10_model.r INFO @ Mon, 03 Jun 2019 04:26:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:27:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:27:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:27:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.05_summits.bed INFO @ Mon, 03 Jun 2019 04:27:31: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (13461 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:27:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.20_summits.bed INFO @ Mon, 03 Jun 2019 04:27:31: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6668 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159172/SRX159172.10_summits.bed INFO @ Mon, 03 Jun 2019 04:27:46: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9880 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。