Job ID = 1294937 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:45:49 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' 2019-06-03T01:45:49 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/sra11/SRR/000849/SRR870191' 2019-06-03T01:45:58 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR870191' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T01:45:58 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 19,989,146 reads read : 19,989,146 reads written : 19,989,146 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: 00:05:22 19989146 reads; of these: 19989146 (100.00%) were unpaired; of these: 1510434 (7.56%) aligned 0 times 16979101 (84.94%) aligned exactly 1 time 1499611 (7.50%) aligned >1 times 92.44% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 2404615 / 18478712 = 0.1301 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 11:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.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 11:18:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:18:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.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 11:18:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:18:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.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 11:18:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:18:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:18:45: 1000000 INFO @ Mon, 03 Jun 2019 11:18:46: 1000000 INFO @ Mon, 03 Jun 2019 11:18:46: 1000000 INFO @ Mon, 03 Jun 2019 11:18:52: 2000000 INFO @ Mon, 03 Jun 2019 11:18:54: 2000000 INFO @ Mon, 03 Jun 2019 11:18:54: 2000000 INFO @ Mon, 03 Jun 2019 11:18:59: 3000000 INFO @ Mon, 03 Jun 2019 11:19:02: 3000000 INFO @ Mon, 03 Jun 2019 11:19:03: 3000000 INFO @ Mon, 03 Jun 2019 11:19:06: 4000000 INFO @ Mon, 03 Jun 2019 11:19:11: 4000000 INFO @ Mon, 03 Jun 2019 11:19:11: 4000000 INFO @ Mon, 03 Jun 2019 11:19:13: 5000000 INFO @ Mon, 03 Jun 2019 11:19:19: 5000000 INFO @ Mon, 03 Jun 2019 11:19:19: 5000000 INFO @ Mon, 03 Jun 2019 11:19:21: 6000000 INFO @ Mon, 03 Jun 2019 11:19:27: 6000000 INFO @ Mon, 03 Jun 2019 11:19:27: 6000000 INFO @ Mon, 03 Jun 2019 11:19:28: 7000000 INFO @ Mon, 03 Jun 2019 11:19:35: 8000000 INFO @ Mon, 03 Jun 2019 11:19:35: 7000000 INFO @ Mon, 03 Jun 2019 11:19:36: 7000000 INFO @ Mon, 03 Jun 2019 11:19:42: 9000000 INFO @ Mon, 03 Jun 2019 11:19:43: 8000000 INFO @ Mon, 03 Jun 2019 11:19:44: 8000000 INFO @ Mon, 03 Jun 2019 11:19:49: 10000000 INFO @ Mon, 03 Jun 2019 11:19:51: 9000000 INFO @ Mon, 03 Jun 2019 11:19:52: 9000000 INFO @ Mon, 03 Jun 2019 11:19:56: 11000000 INFO @ Mon, 03 Jun 2019 11:19:59: 10000000 INFO @ Mon, 03 Jun 2019 11:20:00: 10000000 INFO @ Mon, 03 Jun 2019 11:20:04: 12000000 INFO @ Mon, 03 Jun 2019 11:20:07: 11000000 INFO @ Mon, 03 Jun 2019 11:20:07: 11000000 INFO @ Mon, 03 Jun 2019 11:20:11: 13000000 INFO @ Mon, 03 Jun 2019 11:20:15: 12000000 INFO @ Mon, 03 Jun 2019 11:20:16: 12000000 INFO @ Mon, 03 Jun 2019 11:20:18: 14000000 INFO @ Mon, 03 Jun 2019 11:20:23: 13000000 INFO @ Mon, 03 Jun 2019 11:20:24: 13000000 INFO @ Mon, 03 Jun 2019 11:20:26: 15000000 INFO @ Mon, 03 Jun 2019 11:20:32: 14000000 INFO @ Mon, 03 Jun 2019 11:20:32: 14000000 INFO @ Mon, 03 Jun 2019 11:20:33: 16000000 INFO @ Mon, 03 Jun 2019 11:20:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:20:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:20:34: #1 total tags in treatment: 16074097 INFO @ Mon, 03 Jun 2019 11:20:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:20:34: #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 11:20:34: #1 tags after filtering in treatment: 16074097 INFO @ Mon, 03 Jun 2019 11:20:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:20:34: #1 finished! INFO @ Mon, 03 Jun 2019 11:20:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:20:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:20:36: #2 number of paired peaks: 4130 INFO @ Mon, 03 Jun 2019 11:20:36: start model_add_line... INFO @ Mon, 03 Jun 2019 11:20:36: start X-correlation... INFO @ Mon, 03 Jun 2019 11:20:36: end of X-cor INFO @ Mon, 03 Jun 2019 11:20:36: #2 finished! INFO @ Mon, 03 Jun 2019 11:20:36: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 11:20:36: #2 alternative fragment length(s) may be 4,206 bps INFO @ Mon, 03 Jun 2019 11:20:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.20_model.r INFO @ Mon, 03 Jun 2019 11:20:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:20:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:20:40: 15000000 INFO @ Mon, 03 Jun 2019 11:20:41: 15000000 INFO @ Mon, 03 Jun 2019 11:20:48: 16000000 INFO @ Mon, 03 Jun 2019 11:20:49: 16000000 INFO @ Mon, 03 Jun 2019 11:20:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:20:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:20:49: #1 total tags in treatment: 16074097 INFO @ Mon, 03 Jun 2019 11:20:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:20:49: #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 11:20:49: #1 tags after filtering in treatment: 16074097 INFO @ Mon, 03 Jun 2019 11:20:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:20:49: #1 finished! INFO @ Mon, 03 Jun 2019 11:20:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:20:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:20:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:20:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:20:49: #1 total tags in treatment: 16074097 INFO @ Mon, 03 Jun 2019 11:20:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:20:49: #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 11:20:50: #1 tags after filtering in treatment: 16074097 INFO @ Mon, 03 Jun 2019 11:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:20:50: #1 finished! INFO @ Mon, 03 Jun 2019 11:20:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:20:51: #2 number of paired peaks: 4130 INFO @ Mon, 03 Jun 2019 11:20:51: start model_add_line... INFO @ Mon, 03 Jun 2019 11:20:51: start X-correlation... INFO @ Mon, 03 Jun 2019 11:20:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:20:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:20:52: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 11:20:52: #2 alternative fragment length(s) may be 4,206 bps INFO @ Mon, 03 Jun 2019 11:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.05_model.r INFO @ Mon, 03 Jun 2019 11:20:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:20:52: #2 number of paired peaks: 4130 INFO @ Mon, 03 Jun 2019 11:20:52: start model_add_line... INFO @ Mon, 03 Jun 2019 11:20:52: start X-correlation... INFO @ Mon, 03 Jun 2019 11:20:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:20:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:20:52: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 11:20:52: #2 alternative fragment length(s) may be 4,206 bps INFO @ Mon, 03 Jun 2019 11:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.10_model.r INFO @ Mon, 03 Jun 2019 11:20:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:21:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:21:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:21:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:21:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:21:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:21:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.20_summits.bed INFO @ Mon, 03 Jun 2019 11:21:51: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (2399 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.05_summits.bed INFO @ Mon, 03 Jun 2019 11:22:06: Done! INFO @ Mon, 03 Jun 2019 11:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.10_peaks.xls pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7903 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288002/SRX288002.10_summits.bed INFO @ Mon, 03 Jun 2019 11:22:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4867 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。