Job ID = 1294050 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T19:21:11 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' 2019-06-02T19:21:11 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/sra36/SRR/003427/SRR3509712' 2019-06-02T19:21:11 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR3509712' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T19:21:11 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 8,176,519 reads read : 16,353,038 reads written : 16,353,038 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: 00:23:22 8176519 reads; of these: 8176519 (100.00%) were paired; of these: 1054669 (12.90%) aligned concordantly 0 times 5672683 (69.38%) aligned concordantly exactly 1 time 1449167 (17.72%) aligned concordantly >1 times ---- 1054669 pairs aligned concordantly 0 times; of these: 501641 (47.56%) aligned discordantly 1 time ---- 553028 pairs aligned 0 times concordantly or discordantly; of these: 1106056 mates make up the pairs; of these: 624741 (56.48%) aligned 0 times 224400 (20.29%) aligned exactly 1 time 256915 (23.23%) aligned >1 times 96.18% overall alignment rate Time searching: 00:23:22 Overall time: 00:23:22 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_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] 208391 / 7607319 = 0.0274 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 05:14:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.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 05:14:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:14:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:14:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.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 05:14:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:14:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:14:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.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 05:14:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:14:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:14:52: 1000000 INFO @ Mon, 03 Jun 2019 05:14:54: 1000000 INFO @ Mon, 03 Jun 2019 05:14:54: 1000000 INFO @ Mon, 03 Jun 2019 05:15:00: 2000000 INFO @ Mon, 03 Jun 2019 05:15:05: 2000000 INFO @ Mon, 03 Jun 2019 05:15:05: 2000000 INFO @ Mon, 03 Jun 2019 05:15:09: 3000000 INFO @ Mon, 03 Jun 2019 05:15:16: 3000000 INFO @ Mon, 03 Jun 2019 05:15:16: 3000000 INFO @ Mon, 03 Jun 2019 05:15:18: 4000000 INFO @ Mon, 03 Jun 2019 05:15:26: 5000000 INFO @ Mon, 03 Jun 2019 05:15:27: 4000000 INFO @ Mon, 03 Jun 2019 05:15:27: 4000000 INFO @ Mon, 03 Jun 2019 05:15:35: 6000000 INFO @ Mon, 03 Jun 2019 05:15:38: 5000000 INFO @ Mon, 03 Jun 2019 05:15:38: 5000000 INFO @ Mon, 03 Jun 2019 05:15:43: 7000000 INFO @ Mon, 03 Jun 2019 05:15:49: 6000000 INFO @ Mon, 03 Jun 2019 05:15:49: 6000000 INFO @ Mon, 03 Jun 2019 05:15:52: 8000000 INFO @ Mon, 03 Jun 2019 05:16:00: 7000000 INFO @ Mon, 03 Jun 2019 05:16:00: 7000000 INFO @ Mon, 03 Jun 2019 05:16:00: 9000000 INFO @ Mon, 03 Jun 2019 05:16:10: 10000000 INFO @ Mon, 03 Jun 2019 05:16:11: 8000000 INFO @ Mon, 03 Jun 2019 05:16:11: 8000000 INFO @ Mon, 03 Jun 2019 05:16:19: 11000000 INFO @ Mon, 03 Jun 2019 05:16:22: 9000000 INFO @ Mon, 03 Jun 2019 05:16:22: 9000000 INFO @ Mon, 03 Jun 2019 05:16:29: 12000000 INFO @ Mon, 03 Jun 2019 05:16:32: 10000000 INFO @ Mon, 03 Jun 2019 05:16:33: 10000000 INFO @ Mon, 03 Jun 2019 05:16:39: 13000000 INFO @ Mon, 03 Jun 2019 05:16:44: 11000000 INFO @ Mon, 03 Jun 2019 05:16:44: 11000000 INFO @ Mon, 03 Jun 2019 05:16:48: 14000000 INFO @ Mon, 03 Jun 2019 05:16:55: 12000000 INFO @ Mon, 03 Jun 2019 05:16:56: 12000000 INFO @ Mon, 03 Jun 2019 05:16:57: 15000000 INFO @ Mon, 03 Jun 2019 05:17:00: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 05:17:00: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 05:17:00: #1 total tags in treatment: 6921103 INFO @ Mon, 03 Jun 2019 05:17:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:17:00: #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 05:17:00: #1 tags after filtering in treatment: 6706697 INFO @ Mon, 03 Jun 2019 05:17:00: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:17:00: #1 finished! INFO @ Mon, 03 Jun 2019 05:17:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:17:01: #2 number of paired peaks: 860 WARNING @ Mon, 03 Jun 2019 05:17:01: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Mon, 03 Jun 2019 05:17:01: start model_add_line... INFO @ Mon, 03 Jun 2019 05:17:01: start X-correlation... INFO @ Mon, 03 Jun 2019 05:17:01: end of X-cor INFO @ Mon, 03 Jun 2019 05:17:01: #2 finished! INFO @ Mon, 03 Jun 2019 05:17:01: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 05:17:01: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 05:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.10_model.r INFO @ Mon, 03 Jun 2019 05:17:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:17:07: 13000000 INFO @ Mon, 03 Jun 2019 05:17:07: 13000000 INFO @ Mon, 03 Jun 2019 05:17:18: 14000000 INFO @ Mon, 03 Jun 2019 05:17:19: 14000000 INFO @ Mon, 03 Jun 2019 05:17:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:17:29: 15000000 INFO @ Mon, 03 Jun 2019 05:17:30: 15000000 INFO @ Mon, 03 Jun 2019 05:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.10_summits.bed INFO @ Mon, 03 Jun 2019 05:17:32: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2368 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:17:32: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 05:17:32: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 05:17:32: #1 total tags in treatment: 6921103 INFO @ Mon, 03 Jun 2019 05:17:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:17:32: #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 05:17:32: #1 tags after filtering in treatment: 6706697 INFO @ Mon, 03 Jun 2019 05:17:32: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:17:32: #1 finished! INFO @ Mon, 03 Jun 2019 05:17:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:17:33: #1 tag size is determined as 82 bps INFO @ Mon, 03 Jun 2019 05:17:33: #1 tag size = 82 INFO @ Mon, 03 Jun 2019 05:17:33: #1 total tags in treatment: 6921103 INFO @ Mon, 03 Jun 2019 05:17:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:17:33: #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 05:17:33: #1 tags after filtering in treatment: 6706697 INFO @ Mon, 03 Jun 2019 05:17:33: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 05:17:33: #1 finished! INFO @ Mon, 03 Jun 2019 05:17:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:17:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:17:33: #2 number of paired peaks: 860 WARNING @ Mon, 03 Jun 2019 05:17:33: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Mon, 03 Jun 2019 05:17:33: start model_add_line... INFO @ Mon, 03 Jun 2019 05:17:33: start X-correlation... INFO @ Mon, 03 Jun 2019 05:17:33: end of X-cor INFO @ Mon, 03 Jun 2019 05:17:33: #2 finished! INFO @ Mon, 03 Jun 2019 05:17:33: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 05:17:33: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 05:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.20_model.r INFO @ Mon, 03 Jun 2019 05:17:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:17:34: #2 number of paired peaks: 860 WARNING @ Mon, 03 Jun 2019 05:17:34: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Mon, 03 Jun 2019 05:17:34: start model_add_line... INFO @ Mon, 03 Jun 2019 05:17:34: start X-correlation... INFO @ Mon, 03 Jun 2019 05:17:34: end of X-cor INFO @ Mon, 03 Jun 2019 05:17:34: #2 finished! INFO @ Mon, 03 Jun 2019 05:17:34: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 05:17:34: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 05:17:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.05_model.r INFO @ Mon, 03 Jun 2019 05:17:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:17:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:17:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:17:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:18:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:18:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:18:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.20_summits.bed INFO @ Mon, 03 Jun 2019 05:18:04: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1159 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763413/SRX1763413.05_summits.bed INFO @ Mon, 03 Jun 2019 05:18:05: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3923 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。