Job ID = 1293286 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:40:24 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' 2019-06-02T13:40:24 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/era10/ERR/ERR031/ERR031143' 2019-06-02T13:40:24 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR031143' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T13:40:24 fasterq-dump.2.9.6 err: perform_fastq_split_3_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 37,544,693 reads read : 37,544,693 reads written : 37,544,693 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: 00:08:00 37544693 reads; of these: 37544693 (100.00%) were unpaired; of these: 4963145 (13.22%) aligned 0 times 26903320 (71.66%) aligned exactly 1 time 5678228 (15.12%) aligned >1 times 86.78% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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 12 files... [bam_rmdupse_core] 22193898 / 32581548 = 0.6812 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 @ Sun, 02 Jun 2019 23:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.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 @ Sun, 02 Jun 2019 23:14:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:14:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.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 @ Sun, 02 Jun 2019 23:14:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:14:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.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 @ Sun, 02 Jun 2019 23:14:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:14:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:14:56: 1000000 INFO @ Sun, 02 Jun 2019 23:14:56: 1000000 INFO @ Sun, 02 Jun 2019 23:14:57: 1000000 INFO @ Sun, 02 Jun 2019 23:15:04: 2000000 INFO @ Sun, 02 Jun 2019 23:15:05: 2000000 INFO @ Sun, 02 Jun 2019 23:15:07: 2000000 INFO @ Sun, 02 Jun 2019 23:15:12: 3000000 INFO @ Sun, 02 Jun 2019 23:15:14: 3000000 INFO @ Sun, 02 Jun 2019 23:15:16: 3000000 INFO @ Sun, 02 Jun 2019 23:15:20: 4000000 INFO @ Sun, 02 Jun 2019 23:15:22: 4000000 INFO @ Sun, 02 Jun 2019 23:15:26: 4000000 INFO @ Sun, 02 Jun 2019 23:15:28: 5000000 INFO @ Sun, 02 Jun 2019 23:15:31: 5000000 INFO @ Sun, 02 Jun 2019 23:15:35: 5000000 INFO @ Sun, 02 Jun 2019 23:15:36: 6000000 INFO @ Sun, 02 Jun 2019 23:15:39: 6000000 INFO @ Sun, 02 Jun 2019 23:15:44: 7000000 INFO @ Sun, 02 Jun 2019 23:15:44: 6000000 INFO @ Sun, 02 Jun 2019 23:15:48: 7000000 INFO @ Sun, 02 Jun 2019 23:15:52: 8000000 INFO @ Sun, 02 Jun 2019 23:15:54: 7000000 INFO @ Sun, 02 Jun 2019 23:15:56: 8000000 INFO @ Sun, 02 Jun 2019 23:16:00: 9000000 INFO @ Sun, 02 Jun 2019 23:16:03: 8000000 INFO @ Sun, 02 Jun 2019 23:16:05: 9000000 INFO @ Sun, 02 Jun 2019 23:16:08: 10000000 INFO @ Sun, 02 Jun 2019 23:16:11: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:16:11: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:16:11: #1 total tags in treatment: 10387650 INFO @ Sun, 02 Jun 2019 23:16:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:16:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:16:11: #1 tags after filtering in treatment: 10387650 INFO @ Sun, 02 Jun 2019 23:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:16:11: #1 finished! INFO @ Sun, 02 Jun 2019 23:16:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:16:12: #2 number of paired peaks: 1830 INFO @ Sun, 02 Jun 2019 23:16:12: start model_add_line... INFO @ Sun, 02 Jun 2019 23:16:12: start X-correlation... INFO @ Sun, 02 Jun 2019 23:16:12: end of X-cor INFO @ Sun, 02 Jun 2019 23:16:12: #2 finished! INFO @ Sun, 02 Jun 2019 23:16:12: #2 predicted fragment length is 82 bps INFO @ Sun, 02 Jun 2019 23:16:12: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 02 Jun 2019 23:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.20_model.r INFO @ Sun, 02 Jun 2019 23:16:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:16:12: 9000000 INFO @ Sun, 02 Jun 2019 23:16:13: 10000000 INFO @ Sun, 02 Jun 2019 23:16:16: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:16:16: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:16:16: #1 total tags in treatment: 10387650 INFO @ Sun, 02 Jun 2019 23:16:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:16:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:16:16: #1 tags after filtering in treatment: 10387650 INFO @ Sun, 02 Jun 2019 23:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:16:16: #1 finished! INFO @ Sun, 02 Jun 2019 23:16:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:16:17: #2 number of paired peaks: 1830 INFO @ Sun, 02 Jun 2019 23:16:17: start model_add_line... INFO @ Sun, 02 Jun 2019 23:16:17: start X-correlation... INFO @ Sun, 02 Jun 2019 23:16:17: end of X-cor INFO @ Sun, 02 Jun 2019 23:16:17: #2 finished! INFO @ Sun, 02 Jun 2019 23:16:17: #2 predicted fragment length is 82 bps INFO @ Sun, 02 Jun 2019 23:16:17: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 02 Jun 2019 23:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.10_model.r INFO @ Sun, 02 Jun 2019 23:16:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:16:21: 10000000 INFO @ Sun, 02 Jun 2019 23:16:24: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:16:24: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:16:24: #1 total tags in treatment: 10387650 INFO @ Sun, 02 Jun 2019 23:16:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:16:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:16:24: #1 tags after filtering in treatment: 10387650 INFO @ Sun, 02 Jun 2019 23:16:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:16:24: #1 finished! INFO @ Sun, 02 Jun 2019 23:16:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:16:25: #2 number of paired peaks: 1830 INFO @ Sun, 02 Jun 2019 23:16:25: start model_add_line... INFO @ Sun, 02 Jun 2019 23:16:25: start X-correlation... INFO @ Sun, 02 Jun 2019 23:16:26: end of X-cor INFO @ Sun, 02 Jun 2019 23:16:26: #2 finished! INFO @ Sun, 02 Jun 2019 23:16:26: #2 predicted fragment length is 82 bps INFO @ Sun, 02 Jun 2019 23:16:26: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 02 Jun 2019 23:16:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.05_model.r INFO @ Sun, 02 Jun 2019 23:16:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:16:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:16:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:16:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:16:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.20_summits.bed INFO @ Sun, 02 Jun 2019 23:16:59: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3253 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.10_summits.bed INFO @ Sun, 02 Jun 2019 23:17:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6237 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011422/ERX011422.05_summits.bed INFO @ Sun, 02 Jun 2019 23:17:11: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12210 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。