Job ID = 1294156 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:06:11 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' 2019-06-02T20:06:11 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/sos/sra-pub-run-1/SRR585065/SRR585065.1' 2019-06-02T20:06:22 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR585065' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T20:06:22 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 27,008,870 reads read : 27,008,870 reads written : 27,008,870 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: 00:07:24 27008870 reads; of these: 27008870 (100.00%) were unpaired; of these: 966064 (3.58%) aligned 0 times 21871460 (80.98%) aligned exactly 1 time 4171346 (15.44%) aligned >1 times 96.42% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 8325204 / 26042806 = 0.3197 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 05:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.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 05:25:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:25:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.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 05:25:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:25:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:25:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.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 05:25:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:25:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:25:58: 1000000 INFO @ Mon, 03 Jun 2019 05:25:59: 1000000 INFO @ Mon, 03 Jun 2019 05:25:59: 1000000 INFO @ Mon, 03 Jun 2019 05:26:06: 2000000 INFO @ Mon, 03 Jun 2019 05:26:06: 2000000 INFO @ Mon, 03 Jun 2019 05:26:07: 2000000 INFO @ Mon, 03 Jun 2019 05:26:14: 3000000 INFO @ Mon, 03 Jun 2019 05:26:14: 3000000 INFO @ Mon, 03 Jun 2019 05:26:16: 3000000 INFO @ Mon, 03 Jun 2019 05:26:21: 4000000 INFO @ Mon, 03 Jun 2019 05:26:21: 4000000 INFO @ Mon, 03 Jun 2019 05:26:24: 4000000 INFO @ Mon, 03 Jun 2019 05:26:29: 5000000 INFO @ Mon, 03 Jun 2019 05:26:29: 5000000 INFO @ Mon, 03 Jun 2019 05:26:32: 5000000 INFO @ Mon, 03 Jun 2019 05:26:37: 6000000 INFO @ Mon, 03 Jun 2019 05:26:37: 6000000 INFO @ Mon, 03 Jun 2019 05:26:41: 6000000 INFO @ Mon, 03 Jun 2019 05:26:45: 7000000 INFO @ Mon, 03 Jun 2019 05:26:46: 7000000 INFO @ Mon, 03 Jun 2019 05:26:49: 7000000 INFO @ Mon, 03 Jun 2019 05:26:53: 8000000 INFO @ Mon, 03 Jun 2019 05:26:54: 8000000 INFO @ Mon, 03 Jun 2019 05:26:57: 8000000 INFO @ Mon, 03 Jun 2019 05:27:00: 9000000 INFO @ Mon, 03 Jun 2019 05:27:03: 9000000 INFO @ Mon, 03 Jun 2019 05:27:05: 9000000 INFO @ Mon, 03 Jun 2019 05:27:08: 10000000 INFO @ Mon, 03 Jun 2019 05:27:13: 10000000 INFO @ Mon, 03 Jun 2019 05:27:14: 10000000 INFO @ Mon, 03 Jun 2019 05:27:15: 11000000 INFO @ Mon, 03 Jun 2019 05:27:22: 11000000 INFO @ Mon, 03 Jun 2019 05:27:23: 11000000 INFO @ Mon, 03 Jun 2019 05:27:23: 12000000 INFO @ Mon, 03 Jun 2019 05:27:30: 13000000 INFO @ Mon, 03 Jun 2019 05:27:30: 12000000 INFO @ Mon, 03 Jun 2019 05:27:33: 12000000 INFO @ Mon, 03 Jun 2019 05:27:38: 14000000 INFO @ Mon, 03 Jun 2019 05:27:39: 13000000 INFO @ Mon, 03 Jun 2019 05:27:43: 13000000 INFO @ Mon, 03 Jun 2019 05:27:46: 15000000 INFO @ Mon, 03 Jun 2019 05:27:47: 14000000 INFO @ Mon, 03 Jun 2019 05:27:53: 14000000 INFO @ Mon, 03 Jun 2019 05:27:53: 16000000 INFO @ Mon, 03 Jun 2019 05:27:55: 15000000 INFO @ Mon, 03 Jun 2019 05:28:01: 17000000 INFO @ Mon, 03 Jun 2019 05:28:03: 15000000 INFO @ Mon, 03 Jun 2019 05:28:04: 16000000 INFO @ Mon, 03 Jun 2019 05:28:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:28:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:28:06: #1 total tags in treatment: 17717602 INFO @ Mon, 03 Jun 2019 05:28:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:28:06: #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 05:28:07: #1 tags after filtering in treatment: 17717602 INFO @ Mon, 03 Jun 2019 05:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:28:07: #1 finished! INFO @ Mon, 03 Jun 2019 05:28:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:28:10: #2 number of paired peaks: 11271 INFO @ Mon, 03 Jun 2019 05:28:10: start model_add_line... INFO @ Mon, 03 Jun 2019 05:28:10: start X-correlation... INFO @ Mon, 03 Jun 2019 05:28:10: end of X-cor INFO @ Mon, 03 Jun 2019 05:28:10: #2 finished! INFO @ Mon, 03 Jun 2019 05:28:10: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 05:28:10: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 03 Jun 2019 05:28:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.20_model.r INFO @ Mon, 03 Jun 2019 05:28:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:28:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:28:12: 17000000 INFO @ Mon, 03 Jun 2019 05:28:12: 16000000 INFO @ Mon, 03 Jun 2019 05:28:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:28:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:28:18: #1 total tags in treatment: 17717602 INFO @ Mon, 03 Jun 2019 05:28:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:28:18: #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 05:28:18: #1 tags after filtering in treatment: 17717602 INFO @ Mon, 03 Jun 2019 05:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:28:18: #1 finished! INFO @ Mon, 03 Jun 2019 05:28:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:28:21: #2 number of paired peaks: 11271 INFO @ Mon, 03 Jun 2019 05:28:21: start model_add_line... INFO @ Mon, 03 Jun 2019 05:28:22: start X-correlation... INFO @ Mon, 03 Jun 2019 05:28:22: end of X-cor INFO @ Mon, 03 Jun 2019 05:28:22: #2 finished! INFO @ Mon, 03 Jun 2019 05:28:22: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 05:28:22: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 03 Jun 2019 05:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.05_model.r INFO @ Mon, 03 Jun 2019 05:28:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:28:22: 17000000 INFO @ Mon, 03 Jun 2019 05:28:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:28:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:28:30: #1 total tags in treatment: 17717602 INFO @ Mon, 03 Jun 2019 05:28:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:28:30: #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 05:28:30: #1 tags after filtering in treatment: 17717602 INFO @ Mon, 03 Jun 2019 05:28:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:28:30: #1 finished! INFO @ Mon, 03 Jun 2019 05:28:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:28:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:28:33: #2 number of paired peaks: 11271 INFO @ Mon, 03 Jun 2019 05:28:33: start model_add_line... INFO @ Mon, 03 Jun 2019 05:28:34: start X-correlation... INFO @ Mon, 03 Jun 2019 05:28:34: end of X-cor INFO @ Mon, 03 Jun 2019 05:28:34: #2 finished! INFO @ Mon, 03 Jun 2019 05:28:34: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 05:28:34: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 03 Jun 2019 05:28:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.10_model.r INFO @ Mon, 03 Jun 2019 05:28:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:28:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:29:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:29:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.20_summits.bed INFO @ Mon, 03 Jun 2019 05:29:31: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7428 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:29:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.05_summits.bed INFO @ Mon, 03 Jun 2019 05:29:43: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12970 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:29:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193332/SRX193332.10_summits.bed INFO @ Mon, 03 Jun 2019 05:29:55: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10609 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。