Job ID = 1293975 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-06-02T18:45:47 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' 2019-06-02T18:45:47 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/sra37/SRR/003057/SRR3130853' 2019-06-02T18:45:56 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR3130853', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 3,831,296 reads read : 3,831,296 reads written : 3,831,296 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: 00:03:11 23831296 reads; of these: 23831296 (100.00%) were unpaired; of these: 21792949 (91.45%) aligned 0 times 1605187 (6.74%) aligned exactly 1 time 433160 (1.82%) aligned >1 times 8.55% overall alignment rate Time searching: 00:03:11 Overall time: 00:03:11 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_rmdupse_core] 566131 / 2038347 = 0.2777 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 03:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.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 03:52:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:52:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.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 03:52:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:52:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.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 03:52:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:52:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:52:54: 1000000 INFO @ Mon, 03 Jun 2019 03:52:57: 1000000 INFO @ Mon, 03 Jun 2019 03:52:57: 1000000 INFO @ Mon, 03 Jun 2019 03:52:58: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:52:58: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:52:58: #1 total tags in treatment: 1472216 INFO @ Mon, 03 Jun 2019 03:52:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:52:58: #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 03:52:58: #1 tags after filtering in treatment: 1472216 INFO @ Mon, 03 Jun 2019 03:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:52:58: #1 finished! INFO @ Mon, 03 Jun 2019 03:52:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:52:58: #2 number of paired peaks: 1914 INFO @ Mon, 03 Jun 2019 03:52:58: start model_add_line... INFO @ Mon, 03 Jun 2019 03:52:58: start X-correlation... INFO @ Mon, 03 Jun 2019 03:52:58: end of X-cor INFO @ Mon, 03 Jun 2019 03:52:58: #2 finished! INFO @ Mon, 03 Jun 2019 03:52:58: #2 predicted fragment length is 104 bps INFO @ Mon, 03 Jun 2019 03:52:58: #2 alternative fragment length(s) may be 104 bps INFO @ Mon, 03 Jun 2019 03:52:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.05_model.r INFO @ Mon, 03 Jun 2019 03:52:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:53:02: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:53:02: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:53:02: #1 total tags in treatment: 1472216 INFO @ Mon, 03 Jun 2019 03:53:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:53:02: #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 03:53:02: #1 tags after filtering in treatment: 1472216 INFO @ Mon, 03 Jun 2019 03:53:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:53:02: #1 finished! INFO @ Mon, 03 Jun 2019 03:53:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:53:02: #2 number of paired peaks: 1914 INFO @ Mon, 03 Jun 2019 03:53:02: start model_add_line... INFO @ Mon, 03 Jun 2019 03:53:02: start X-correlation... INFO @ Mon, 03 Jun 2019 03:53:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:53:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:53:02: #2 predicted fragment length is 104 bps INFO @ Mon, 03 Jun 2019 03:53:02: #2 alternative fragment length(s) may be 104 bps INFO @ Mon, 03 Jun 2019 03:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.20_model.r INFO @ Mon, 03 Jun 2019 03:53:02: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:53:02: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:53:02: #1 total tags in treatment: 1472216 INFO @ Mon, 03 Jun 2019 03:53:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:53:02: #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 03:53:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:53:03: #1 tags after filtering in treatment: 1472216 INFO @ Mon, 03 Jun 2019 03:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:53:03: #1 finished! INFO @ Mon, 03 Jun 2019 03:53:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:53:03: #2 number of paired peaks: 1914 INFO @ Mon, 03 Jun 2019 03:53:03: start model_add_line... INFO @ Mon, 03 Jun 2019 03:53:03: start X-correlation... INFO @ Mon, 03 Jun 2019 03:53:03: end of X-cor INFO @ Mon, 03 Jun 2019 03:53:03: #2 finished! INFO @ Mon, 03 Jun 2019 03:53:03: #2 predicted fragment length is 104 bps INFO @ Mon, 03 Jun 2019 03:53:03: #2 alternative fragment length(s) may be 104 bps INFO @ Mon, 03 Jun 2019 03:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.10_model.r INFO @ Mon, 03 Jun 2019 03:53:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:53:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:53:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.05_summits.bed INFO @ Mon, 03 Jun 2019 03:53:06: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2217 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:53:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:53:08: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 03:53:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.20_summits.bed INFO @ Mon, 03 Jun 2019 03:53:10: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (620 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:53:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550609/SRX1550609.10_summits.bed INFO @ Mon, 03 Jun 2019 03:53:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1246 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。