Job ID = 1295823 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T06:41:01 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' 2019-06-03T06:41:01 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/SRR1153273/SRR1153273.1' 2019-06-03T06:41:12 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1153273' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T06:41:12 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 39,320,649 reads read : 39,320,649 reads written : 39,320,649 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: 00:00:01 Multiseed full-index search: 00:13:13 39320649 reads; of these: 39320649 (100.00%) were unpaired; of these: 1948094 (4.95%) aligned 0 times 31562628 (80.27%) aligned exactly 1 time 5809927 (14.78%) aligned >1 times 95.05% overall alignment rate Time searching: 00:13:14 Overall time: 00:13:14 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_rmdupse_core] 19579877 / 37372555 = 0.5239 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 16:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.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 16:10:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:10:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.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 16:10:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:10:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.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 16:10:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:10:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:10:58: 1000000 INFO @ Mon, 03 Jun 2019 16:10:59: 1000000 INFO @ Mon, 03 Jun 2019 16:11:00: 1000000 INFO @ Mon, 03 Jun 2019 16:11:06: 2000000 INFO @ Mon, 03 Jun 2019 16:11:08: 2000000 INFO @ Mon, 03 Jun 2019 16:11:08: 2000000 INFO @ Mon, 03 Jun 2019 16:11:13: 3000000 INFO @ Mon, 03 Jun 2019 16:11:16: 3000000 INFO @ Mon, 03 Jun 2019 16:11:16: 3000000 INFO @ Mon, 03 Jun 2019 16:11:21: 4000000 INFO @ Mon, 03 Jun 2019 16:11:24: 4000000 INFO @ Mon, 03 Jun 2019 16:11:24: 4000000 INFO @ Mon, 03 Jun 2019 16:11:28: 5000000 INFO @ Mon, 03 Jun 2019 16:11:33: 5000000 INFO @ Mon, 03 Jun 2019 16:11:33: 5000000 INFO @ Mon, 03 Jun 2019 16:11:36: 6000000 INFO @ Mon, 03 Jun 2019 16:11:41: 6000000 INFO @ Mon, 03 Jun 2019 16:11:41: 6000000 INFO @ Mon, 03 Jun 2019 16:11:43: 7000000 INFO @ Mon, 03 Jun 2019 16:11:49: 7000000 INFO @ Mon, 03 Jun 2019 16:11:50: 7000000 INFO @ Mon, 03 Jun 2019 16:11:51: 8000000 INFO @ Mon, 03 Jun 2019 16:11:58: 8000000 INFO @ Mon, 03 Jun 2019 16:11:58: 8000000 INFO @ Mon, 03 Jun 2019 16:11:58: 9000000 INFO @ Mon, 03 Jun 2019 16:12:06: 9000000 INFO @ Mon, 03 Jun 2019 16:12:06: 10000000 INFO @ Mon, 03 Jun 2019 16:12:06: 9000000 INFO @ Mon, 03 Jun 2019 16:12:13: 11000000 INFO @ Mon, 03 Jun 2019 16:12:14: 10000000 INFO @ Mon, 03 Jun 2019 16:12:14: 10000000 INFO @ Mon, 03 Jun 2019 16:12:21: 12000000 INFO @ Mon, 03 Jun 2019 16:12:22: 11000000 INFO @ Mon, 03 Jun 2019 16:12:23: 11000000 INFO @ Mon, 03 Jun 2019 16:12:28: 13000000 INFO @ Mon, 03 Jun 2019 16:12:30: 12000000 INFO @ Mon, 03 Jun 2019 16:12:31: 12000000 INFO @ Mon, 03 Jun 2019 16:12:36: 14000000 INFO @ Mon, 03 Jun 2019 16:12:39: 13000000 INFO @ Mon, 03 Jun 2019 16:12:39: 13000000 INFO @ Mon, 03 Jun 2019 16:12:43: 15000000 INFO @ Mon, 03 Jun 2019 16:12:47: 14000000 INFO @ Mon, 03 Jun 2019 16:12:47: 14000000 INFO @ Mon, 03 Jun 2019 16:12:51: 16000000 INFO @ Mon, 03 Jun 2019 16:12:55: 15000000 INFO @ Mon, 03 Jun 2019 16:12:55: 15000000 INFO @ Mon, 03 Jun 2019 16:12:58: 17000000 INFO @ Mon, 03 Jun 2019 16:13:03: 16000000 INFO @ Mon, 03 Jun 2019 16:13:03: 16000000 INFO @ Mon, 03 Jun 2019 16:13:04: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:13:04: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:13:04: #1 total tags in treatment: 17792678 INFO @ Mon, 03 Jun 2019 16:13:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:04: #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 16:13:04: #1 tags after filtering in treatment: 17792678 INFO @ Mon, 03 Jun 2019 16:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:13:04: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:06: #2 number of paired peaks: 1897 INFO @ Mon, 03 Jun 2019 16:13:06: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:07: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:07: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:07: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:07: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 16:13:07: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 16:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.10_model.r INFO @ Mon, 03 Jun 2019 16:13:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:13:11: 17000000 INFO @ Mon, 03 Jun 2019 16:13:11: 17000000 INFO @ Mon, 03 Jun 2019 16:13:18: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:13:18: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:13:18: #1 total tags in treatment: 17792678 INFO @ Mon, 03 Jun 2019 16:13:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:18: #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 16:13:18: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:13:18: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:13:18: #1 total tags in treatment: 17792678 INFO @ Mon, 03 Jun 2019 16:13:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:18: #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 16:13:18: #1 tags after filtering in treatment: 17792678 INFO @ Mon, 03 Jun 2019 16:13:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:13:18: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:18: #1 tags after filtering in treatment: 17792678 INFO @ Mon, 03 Jun 2019 16:13:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:13:18: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:20: #2 number of paired peaks: 1897 INFO @ Mon, 03 Jun 2019 16:13:20: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:20: #2 number of paired peaks: 1897 INFO @ Mon, 03 Jun 2019 16:13:20: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:20: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:20: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:20: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:20: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 16:13:20: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 16:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.05_model.r INFO @ Mon, 03 Jun 2019 16:13:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:13:21: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:21: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:21: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:21: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 16:13:21: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 16:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.20_model.r INFO @ Mon, 03 Jun 2019 16:13:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:13:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:14:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:14:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:14:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:14:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.10_summits.bed INFO @ Mon, 03 Jun 2019 16:14:23: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12651 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:14:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:14:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:14:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.20_summits.bed INFO @ Mon, 03 Jun 2019 16:14:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9112 records, 4 fields): 13 millis INFO @ Mon, 03 Jun 2019 16:14:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.05_peaks.xls CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:14:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:14:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457597/SRX457597.05_summits.bed INFO @ Mon, 03 Jun 2019 16:14:36: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (15393 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。