Job ID = 1294063 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:26:24 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' 2019-06-02T19:26:24 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/sra4/SRR/000535/SRR548158' 2019-06-02T19:26:33 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR548158' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T19:26:33 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 22,846,201 reads read : 22,846,201 reads written : 22,846,201 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: 00:05:01 22846201 reads; of these: 22846201 (100.00%) were unpaired; of these: 2005026 (8.78%) aligned 0 times 18462474 (80.81%) aligned exactly 1 time 2378701 (10.41%) aligned >1 times 91.22% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 14898261 / 20841175 = 0.7148 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 04:49:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.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 04:49:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:49:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:49:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.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 04:49:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:49:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.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 04:49:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:49:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:49:31: 1000000 INFO @ Mon, 03 Jun 2019 04:49:32: 1000000 INFO @ Mon, 03 Jun 2019 04:49:32: 1000000 INFO @ Mon, 03 Jun 2019 04:49:38: 2000000 INFO @ Mon, 03 Jun 2019 04:49:39: 2000000 INFO @ Mon, 03 Jun 2019 04:49:39: 2000000 INFO @ Mon, 03 Jun 2019 04:49:44: 3000000 INFO @ Mon, 03 Jun 2019 04:49:45: 3000000 INFO @ Mon, 03 Jun 2019 04:49:45: 3000000 INFO @ Mon, 03 Jun 2019 04:49:50: 4000000 INFO @ Mon, 03 Jun 2019 04:49:52: 4000000 INFO @ Mon, 03 Jun 2019 04:49:52: 4000000 INFO @ Mon, 03 Jun 2019 04:49:56: 5000000 INFO @ Mon, 03 Jun 2019 04:49:58: 5000000 INFO @ Mon, 03 Jun 2019 04:49:58: 5000000 INFO @ Mon, 03 Jun 2019 04:50:02: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:50:02: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:50:02: #1 total tags in treatment: 5942914 INFO @ Mon, 03 Jun 2019 04:50:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:50:02: #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 04:50:02: #1 tags after filtering in treatment: 5942914 INFO @ Mon, 03 Jun 2019 04:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:50:02: #1 finished! INFO @ Mon, 03 Jun 2019 04:50:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:50:03: #2 number of paired peaks: 1097 INFO @ Mon, 03 Jun 2019 04:50:03: start model_add_line... INFO @ Mon, 03 Jun 2019 04:50:03: start X-correlation... INFO @ Mon, 03 Jun 2019 04:50:03: end of X-cor INFO @ Mon, 03 Jun 2019 04:50:03: #2 finished! INFO @ Mon, 03 Jun 2019 04:50:03: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 04:50:03: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 04:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.20_model.r INFO @ Mon, 03 Jun 2019 04:50:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:50:05: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:50:05: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:50:05: #1 total tags in treatment: 5942914 INFO @ Mon, 03 Jun 2019 04:50:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:50:05: #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 04:50:05: #1 tags after filtering in treatment: 5942914 INFO @ Mon, 03 Jun 2019 04:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:50:05: #1 finished! INFO @ Mon, 03 Jun 2019 04:50:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:50:05: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:50:05: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:50:05: #1 total tags in treatment: 5942914 INFO @ Mon, 03 Jun 2019 04:50:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:50:05: #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 04:50:05: #1 tags after filtering in treatment: 5942914 INFO @ Mon, 03 Jun 2019 04:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:50:05: #1 finished! INFO @ Mon, 03 Jun 2019 04:50:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:50:05: #2 number of paired peaks: 1097 INFO @ Mon, 03 Jun 2019 04:50:05: start model_add_line... INFO @ Mon, 03 Jun 2019 04:50:05: start X-correlation... INFO @ Mon, 03 Jun 2019 04:50:05: end of X-cor INFO @ Mon, 03 Jun 2019 04:50:05: #2 finished! INFO @ Mon, 03 Jun 2019 04:50:05: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 04:50:05: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 04:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.05_model.r INFO @ Mon, 03 Jun 2019 04:50:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:50:06: #2 number of paired peaks: 1097 INFO @ Mon, 03 Jun 2019 04:50:06: start model_add_line... INFO @ Mon, 03 Jun 2019 04:50:06: start X-correlation... INFO @ Mon, 03 Jun 2019 04:50:06: end of X-cor INFO @ Mon, 03 Jun 2019 04:50:06: #2 finished! INFO @ Mon, 03 Jun 2019 04:50:06: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 04:50:06: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 04:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.10_model.r INFO @ Mon, 03 Jun 2019 04:50:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:50:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.20_summits.bed INFO @ Mon, 03 Jun 2019 04:50:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.05_summits.bed INFO @ Mon, 03 Jun 2019 04:50:34: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4674 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181421/SRX181421.10_summits.bed INFO @ Mon, 03 Jun 2019 04:50:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2395 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。