Job ID = 1295195 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:26:11 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' 2019-06-03T03:26:11 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/sra13/SRR/000925/SRR947617' 2019-06-03T03:26:20 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR947617' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T03:26:20 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 12,734,840 reads read : 12,734,840 reads written : 12,734,840 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: 00:04:02 12734840 reads; of these: 12734840 (100.00%) were unpaired; of these: 906868 (7.12%) aligned 0 times 9906361 (77.79%) aligned exactly 1 time 1921611 (15.09%) aligned >1 times 92.88% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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] 1687479 / 11827972 = 0.1427 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 12:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.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 12:47:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:47:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.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 12:47:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:47:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.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 12:47:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:47:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:47:55: 1000000 INFO @ Mon, 03 Jun 2019 12:47:55: 1000000 INFO @ Mon, 03 Jun 2019 12:47:58: 1000000 INFO @ Mon, 03 Jun 2019 12:48:03: 2000000 INFO @ Mon, 03 Jun 2019 12:48:03: 2000000 INFO @ Mon, 03 Jun 2019 12:48:09: 2000000 INFO @ Mon, 03 Jun 2019 12:48:11: 3000000 INFO @ Mon, 03 Jun 2019 12:48:11: 3000000 INFO @ Mon, 03 Jun 2019 12:48:19: 4000000 INFO @ Mon, 03 Jun 2019 12:48:19: 4000000 INFO @ Mon, 03 Jun 2019 12:48:21: 3000000 INFO @ Mon, 03 Jun 2019 12:48:27: 5000000 INFO @ Mon, 03 Jun 2019 12:48:28: 5000000 INFO @ Mon, 03 Jun 2019 12:48:32: 4000000 INFO @ Mon, 03 Jun 2019 12:48:35: 6000000 INFO @ Mon, 03 Jun 2019 12:48:36: 6000000 INFO @ Mon, 03 Jun 2019 12:48:43: 7000000 INFO @ Mon, 03 Jun 2019 12:48:43: 5000000 INFO @ Mon, 03 Jun 2019 12:48:44: 7000000 INFO @ Mon, 03 Jun 2019 12:48:51: 8000000 INFO @ Mon, 03 Jun 2019 12:48:52: 8000000 INFO @ Mon, 03 Jun 2019 12:48:54: 6000000 INFO @ Mon, 03 Jun 2019 12:48:59: 9000000 INFO @ Mon, 03 Jun 2019 12:49:00: 9000000 INFO @ Mon, 03 Jun 2019 12:49:06: 7000000 INFO @ Mon, 03 Jun 2019 12:49:07: 10000000 INFO @ Mon, 03 Jun 2019 12:49:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:49:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:49:08: #1 total tags in treatment: 10140493 INFO @ Mon, 03 Jun 2019 12:49:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:08: #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 12:49:08: #1 tags after filtering in treatment: 10140493 INFO @ Mon, 03 Jun 2019 12:49:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:08: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:08: 10000000 INFO @ Mon, 03 Jun 2019 12:49:09: #2 number of paired peaks: 2852 INFO @ Mon, 03 Jun 2019 12:49:09: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:09: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:09: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:09: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:09: #2 predicted fragment length is 242 bps INFO @ Mon, 03 Jun 2019 12:49:09: #2 alternative fragment length(s) may be 4,242 bps INFO @ Mon, 03 Jun 2019 12:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.20_model.r INFO @ Mon, 03 Jun 2019 12:49:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:49:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:49:10: #1 total tags in treatment: 10140493 INFO @ Mon, 03 Jun 2019 12:49:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:10: #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 12:49:10: #1 tags after filtering in treatment: 10140493 INFO @ Mon, 03 Jun 2019 12:49:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:10: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:49:11: #2 number of paired peaks: 2852 INFO @ Mon, 03 Jun 2019 12:49:11: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:11: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:11: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:11: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:11: #2 predicted fragment length is 242 bps INFO @ Mon, 03 Jun 2019 12:49:11: #2 alternative fragment length(s) may be 4,242 bps INFO @ Mon, 03 Jun 2019 12:49:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.10_model.r INFO @ Mon, 03 Jun 2019 12:49:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:49:17: 8000000 INFO @ Mon, 03 Jun 2019 12:49:27: 9000000 INFO @ Mon, 03 Jun 2019 12:49:36: 10000000 INFO @ Mon, 03 Jun 2019 12:49:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:49:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:49:37: #1 total tags in treatment: 10140493 INFO @ Mon, 03 Jun 2019 12:49:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:37: #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 12:49:37: #1 tags after filtering in treatment: 10140493 INFO @ Mon, 03 Jun 2019 12:49:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:37: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:39: #2 number of paired peaks: 2852 INFO @ Mon, 03 Jun 2019 12:49:39: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:39: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:39: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:39: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:39: #2 predicted fragment length is 242 bps INFO @ Mon, 03 Jun 2019 12:49:39: #2 alternative fragment length(s) may be 4,242 bps INFO @ Mon, 03 Jun 2019 12:49:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.05_model.r INFO @ Mon, 03 Jun 2019 12:49:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:49:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:49:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:49:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:49:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:49:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.20_summits.bed INFO @ Mon, 03 Jun 2019 12:49:59: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.10_summits.bed INFO @ Mon, 03 Jun 2019 12:50:00: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (559 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:50:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331380/SRX331380.05_summits.bed INFO @ Mon, 03 Jun 2019 12:50:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1052 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。