Job ID = 1295442 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T04:45:50 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' 2019-06-03T04:45:50 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-1/SRR6292545/SRR6292545.1' 2019-06-03T04:45:50 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR6292545' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T04:45:50 fasterq-dump.2.9.6 err: invalid accession 'SRR6292545' spots read : 24,458,272 reads read : 48,916,544 reads written : 48,916,544 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: 00:57:28 24458272 reads; of these: 24458272 (100.00%) were paired; of these: 4574488 (18.70%) aligned concordantly 0 times 14632947 (59.83%) aligned concordantly exactly 1 time 5250837 (21.47%) aligned concordantly >1 times ---- 4574488 pairs aligned concordantly 0 times; of these: 118183 (2.58%) aligned discordantly 1 time ---- 4456305 pairs aligned 0 times concordantly or discordantly; of these: 8912610 mates make up the pairs; of these: 7381496 (82.82%) aligned 0 times 676482 (7.59%) aligned exactly 1 time 854632 (9.59%) aligned >1 times 84.91% overall alignment rate Time searching: 00:57:28 Overall time: 00:57:28 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1980791 / 19987803 = 0.0991 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 15:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.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 15:06:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:06:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.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 15:06:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:06:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:06:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.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 15:06:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:06:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:06:42: 1000000 INFO @ Mon, 03 Jun 2019 15:06:43: 1000000 INFO @ Mon, 03 Jun 2019 15:06:43: 1000000 INFO @ Mon, 03 Jun 2019 15:06:48: 2000000 INFO @ Mon, 03 Jun 2019 15:06:50: 2000000 INFO @ Mon, 03 Jun 2019 15:06:50: 2000000 INFO @ Mon, 03 Jun 2019 15:06:54: 3000000 INFO @ Mon, 03 Jun 2019 15:06:57: 3000000 INFO @ Mon, 03 Jun 2019 15:06:57: 3000000 INFO @ Mon, 03 Jun 2019 15:07:00: 4000000 INFO @ Mon, 03 Jun 2019 15:07:04: 4000000 INFO @ Mon, 03 Jun 2019 15:07:04: 4000000 INFO @ Mon, 03 Jun 2019 15:07:06: 5000000 INFO @ Mon, 03 Jun 2019 15:07:11: 5000000 INFO @ Mon, 03 Jun 2019 15:07:11: 5000000 INFO @ Mon, 03 Jun 2019 15:07:12: 6000000 INFO @ Mon, 03 Jun 2019 15:07:18: 7000000 INFO @ Mon, 03 Jun 2019 15:07:18: 6000000 INFO @ Mon, 03 Jun 2019 15:07:18: 6000000 INFO @ Mon, 03 Jun 2019 15:07:24: 8000000 INFO @ Mon, 03 Jun 2019 15:07:25: 7000000 INFO @ Mon, 03 Jun 2019 15:07:25: 7000000 INFO @ Mon, 03 Jun 2019 15:07:30: 9000000 INFO @ Mon, 03 Jun 2019 15:07:32: 8000000 INFO @ Mon, 03 Jun 2019 15:07:32: 8000000 INFO @ Mon, 03 Jun 2019 15:07:36: 10000000 INFO @ Mon, 03 Jun 2019 15:07:39: 9000000 INFO @ Mon, 03 Jun 2019 15:07:40: 9000000 INFO @ Mon, 03 Jun 2019 15:07:42: 11000000 INFO @ Mon, 03 Jun 2019 15:07:45: 10000000 INFO @ Mon, 03 Jun 2019 15:07:47: 10000000 INFO @ Mon, 03 Jun 2019 15:07:48: 12000000 INFO @ Mon, 03 Jun 2019 15:07:52: 11000000 INFO @ Mon, 03 Jun 2019 15:07:54: 11000000 INFO @ Mon, 03 Jun 2019 15:07:54: 13000000 INFO @ Mon, 03 Jun 2019 15:07:58: 12000000 INFO @ Mon, 03 Jun 2019 15:08:00: 14000000 INFO @ Mon, 03 Jun 2019 15:08:00: 12000000 INFO @ Mon, 03 Jun 2019 15:08:05: 13000000 INFO @ Mon, 03 Jun 2019 15:08:05: 15000000 INFO @ Mon, 03 Jun 2019 15:08:07: 13000000 INFO @ Mon, 03 Jun 2019 15:08:12: 16000000 INFO @ Mon, 03 Jun 2019 15:08:12: 14000000 INFO @ Mon, 03 Jun 2019 15:08:13: 14000000 INFO @ Mon, 03 Jun 2019 15:08:18: 17000000 INFO @ Mon, 03 Jun 2019 15:08:18: 15000000 INFO @ Mon, 03 Jun 2019 15:08:20: 15000000 INFO @ Mon, 03 Jun 2019 15:08:24: 18000000 INFO @ Mon, 03 Jun 2019 15:08:25: 16000000 INFO @ Mon, 03 Jun 2019 15:08:27: 16000000 INFO @ Mon, 03 Jun 2019 15:08:30: 19000000 INFO @ Mon, 03 Jun 2019 15:08:32: 17000000 INFO @ Mon, 03 Jun 2019 15:08:33: 17000000 INFO @ Mon, 03 Jun 2019 15:08:36: 20000000 INFO @ Mon, 03 Jun 2019 15:08:38: 18000000 INFO @ Mon, 03 Jun 2019 15:08:40: 18000000 INFO @ Mon, 03 Jun 2019 15:08:42: 21000000 INFO @ Mon, 03 Jun 2019 15:08:45: 19000000 INFO @ Mon, 03 Jun 2019 15:08:47: 19000000 INFO @ Mon, 03 Jun 2019 15:08:48: 22000000 INFO @ Mon, 03 Jun 2019 15:08:52: 20000000 INFO @ Mon, 03 Jun 2019 15:08:53: 20000000 INFO @ Mon, 03 Jun 2019 15:08:53: 23000000 INFO @ Mon, 03 Jun 2019 15:08:58: 21000000 INFO @ Mon, 03 Jun 2019 15:08:59: 24000000 INFO @ Mon, 03 Jun 2019 15:09:00: 21000000 INFO @ Mon, 03 Jun 2019 15:09:05: 22000000 INFO @ Mon, 03 Jun 2019 15:09:06: 25000000 INFO @ Mon, 03 Jun 2019 15:09:07: 22000000 INFO @ Mon, 03 Jun 2019 15:09:11: 26000000 INFO @ Mon, 03 Jun 2019 15:09:12: 23000000 INFO @ Mon, 03 Jun 2019 15:09:13: 23000000 INFO @ Mon, 03 Jun 2019 15:09:17: 27000000 INFO @ Mon, 03 Jun 2019 15:09:18: 24000000 INFO @ Mon, 03 Jun 2019 15:09:20: 24000000 INFO @ Mon, 03 Jun 2019 15:09:23: 28000000 INFO @ Mon, 03 Jun 2019 15:09:25: 25000000 INFO @ Mon, 03 Jun 2019 15:09:26: 25000000 INFO @ Mon, 03 Jun 2019 15:09:29: 29000000 INFO @ Mon, 03 Jun 2019 15:09:32: 26000000 INFO @ Mon, 03 Jun 2019 15:09:33: 26000000 INFO @ Mon, 03 Jun 2019 15:09:35: 30000000 INFO @ Mon, 03 Jun 2019 15:09:38: 27000000 INFO @ Mon, 03 Jun 2019 15:09:40: 27000000 INFO @ Mon, 03 Jun 2019 15:09:41: 31000000 INFO @ Mon, 03 Jun 2019 15:09:45: 28000000 INFO @ Mon, 03 Jun 2019 15:09:46: 28000000 INFO @ Mon, 03 Jun 2019 15:09:47: 32000000 INFO @ Mon, 03 Jun 2019 15:09:52: 29000000 INFO @ Mon, 03 Jun 2019 15:09:53: 33000000 INFO @ Mon, 03 Jun 2019 15:09:53: 29000000 INFO @ Mon, 03 Jun 2019 15:09:58: 30000000 INFO @ Mon, 03 Jun 2019 15:09:59: 34000000 INFO @ Mon, 03 Jun 2019 15:10:01: 30000000 INFO @ Mon, 03 Jun 2019 15:10:05: 31000000 INFO @ Mon, 03 Jun 2019 15:10:05: 35000000 INFO @ Mon, 03 Jun 2019 15:10:07: 31000000 INFO @ Mon, 03 Jun 2019 15:10:11: 36000000 INFO @ Mon, 03 Jun 2019 15:10:12: 32000000 INFO @ Mon, 03 Jun 2019 15:10:14: 32000000 INFO @ Mon, 03 Jun 2019 15:10:17: 37000000 INFO @ Mon, 03 Jun 2019 15:10:18: 33000000 INFO @ Mon, 03 Jun 2019 15:10:20: 33000000 INFO @ Mon, 03 Jun 2019 15:10:21: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:10:21: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:10:21: #1 total tags in treatment: 17906572 INFO @ Mon, 03 Jun 2019 15:10:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:10:21: #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 15:10:21: #1 tags after filtering in treatment: 9208356 INFO @ Mon, 03 Jun 2019 15:10:21: #1 Redundant rate of treatment: 0.49 INFO @ Mon, 03 Jun 2019 15:10:21: #1 finished! INFO @ Mon, 03 Jun 2019 15:10:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:10:23: #2 number of paired peaks: 10300 INFO @ Mon, 03 Jun 2019 15:10:23: start model_add_line... INFO @ Mon, 03 Jun 2019 15:10:23: start X-correlation... INFO @ Mon, 03 Jun 2019 15:10:23: end of X-cor INFO @ Mon, 03 Jun 2019 15:10:23: #2 finished! INFO @ Mon, 03 Jun 2019 15:10:23: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 15:10:23: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 15:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.05_model.r INFO @ Mon, 03 Jun 2019 15:10:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:10:25: 34000000 INFO @ Mon, 03 Jun 2019 15:10:27: 34000000 INFO @ Mon, 03 Jun 2019 15:10:31: 35000000 INFO @ Mon, 03 Jun 2019 15:10:34: 35000000 INFO @ Mon, 03 Jun 2019 15:10:38: 36000000 INFO @ Mon, 03 Jun 2019 15:10:40: 36000000 INFO @ Mon, 03 Jun 2019 15:10:44: 37000000 INFO @ Mon, 03 Jun 2019 15:10:47: 37000000 INFO @ Mon, 03 Jun 2019 15:10:48: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:10:48: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:10:48: #1 total tags in treatment: 17906572 INFO @ Mon, 03 Jun 2019 15:10:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:10:48: #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 15:10:49: #1 tags after filtering in treatment: 9208356 INFO @ Mon, 03 Jun 2019 15:10:49: #1 Redundant rate of treatment: 0.49 INFO @ Mon, 03 Jun 2019 15:10:49: #1 finished! INFO @ Mon, 03 Jun 2019 15:10:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:10:51: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:10:51: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:10:51: #1 total tags in treatment: 17906572 INFO @ Mon, 03 Jun 2019 15:10:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:10:51: #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 15:10:51: #2 number of paired peaks: 10300 INFO @ Mon, 03 Jun 2019 15:10:51: start model_add_line... INFO @ Mon, 03 Jun 2019 15:10:51: #1 tags after filtering in treatment: 9208356 INFO @ Mon, 03 Jun 2019 15:10:51: #1 Redundant rate of treatment: 0.49 INFO @ Mon, 03 Jun 2019 15:10:51: #1 finished! INFO @ Mon, 03 Jun 2019 15:10:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:10:51: start X-correlation... INFO @ Mon, 03 Jun 2019 15:10:51: end of X-cor INFO @ Mon, 03 Jun 2019 15:10:51: #2 finished! INFO @ Mon, 03 Jun 2019 15:10:51: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 15:10:51: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 15:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.10_model.r INFO @ Mon, 03 Jun 2019 15:10:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:10:53: #2 number of paired peaks: 10300 INFO @ Mon, 03 Jun 2019 15:10:53: start model_add_line... INFO @ Mon, 03 Jun 2019 15:10:53: start X-correlation... INFO @ Mon, 03 Jun 2019 15:10:53: end of X-cor INFO @ Mon, 03 Jun 2019 15:10:53: #2 finished! INFO @ Mon, 03 Jun 2019 15:10:53: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 15:10:53: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 15:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.20_model.r INFO @ Mon, 03 Jun 2019 15:10:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:10:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:11:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.05_summits.bed INFO @ Mon, 03 Jun 2019 15:11:14: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10535 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:11:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:11:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:11:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:11:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:11:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.10_summits.bed INFO @ Mon, 03 Jun 2019 15:11:42: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9488 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393656/SRX3393656.20_summits.bed INFO @ Mon, 03 Jun 2019 15:11:44: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8337 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。