Job ID = 1294090 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:41:18 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' 2019-06-02T19:41:18 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/000554/SRR567536' 2019-06-02T19:41:18 fasterq-dump.2.9.6 err: invalid accession 'SRR567536' 2019-06-02T19:45:15 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 26,129,655 reads read : 26,129,655 reads written : 26,129,655 spots read : 21,770,338 reads read : 21,770,338 reads written : 21,770,338 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: 00:10:37 47899993 reads; of these: 47899993 (100.00%) were unpaired; of these: 31705233 (66.19%) aligned 0 times 10889731 (22.73%) aligned exactly 1 time 5305029 (11.08%) aligned >1 times 33.81% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 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] 10604119 / 16194760 = 0.6548 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 05:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.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 05:18:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:18:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.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 05:18:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:18:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.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 05:18:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:18:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:18:40: 1000000 INFO @ Mon, 03 Jun 2019 05:18:40: 1000000 INFO @ Mon, 03 Jun 2019 05:18:42: 1000000 INFO @ Mon, 03 Jun 2019 05:18:48: 2000000 INFO @ Mon, 03 Jun 2019 05:18:48: 2000000 INFO @ Mon, 03 Jun 2019 05:18:54: 2000000 INFO @ Mon, 03 Jun 2019 05:18:56: 3000000 INFO @ Mon, 03 Jun 2019 05:18:56: 3000000 INFO @ Mon, 03 Jun 2019 05:19:05: 4000000 INFO @ Mon, 03 Jun 2019 05:19:05: 3000000 INFO @ Mon, 03 Jun 2019 05:19:05: 4000000 INFO @ Mon, 03 Jun 2019 05:19:13: 5000000 INFO @ Mon, 03 Jun 2019 05:19:13: 5000000 INFO @ Mon, 03 Jun 2019 05:19:16: 4000000 INFO @ Mon, 03 Jun 2019 05:19:17: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 05:19:17: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 05:19:17: #1 total tags in treatment: 5590641 INFO @ Mon, 03 Jun 2019 05:19:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:19:17: #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 05:19:17: #1 tags after filtering in treatment: 5590641 INFO @ Mon, 03 Jun 2019 05:19:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:19:17: #1 finished! INFO @ Mon, 03 Jun 2019 05:19:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:19:18: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 05:19:18: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 05:19:18: #1 total tags in treatment: 5590641 INFO @ Mon, 03 Jun 2019 05:19:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:19:18: #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 05:19:18: #1 tags after filtering in treatment: 5590641 INFO @ Mon, 03 Jun 2019 05:19:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:19:18: #1 finished! INFO @ Mon, 03 Jun 2019 05:19:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:19:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:19:18: #2 number of paired peaks: 5688 INFO @ Mon, 03 Jun 2019 05:19:18: start model_add_line... INFO @ Mon, 03 Jun 2019 05:19:18: start X-correlation... INFO @ Mon, 03 Jun 2019 05:19:18: end of X-cor INFO @ Mon, 03 Jun 2019 05:19:18: #2 finished! INFO @ Mon, 03 Jun 2019 05:19:18: #2 predicted fragment length is 152 bps INFO @ Mon, 03 Jun 2019 05:19:18: #2 alternative fragment length(s) may be 152 bps INFO @ Mon, 03 Jun 2019 05:19:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.20_model.r INFO @ Mon, 03 Jun 2019 05:19:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:19:19: #2 number of paired peaks: 5688 INFO @ Mon, 03 Jun 2019 05:19:19: start model_add_line... INFO @ Mon, 03 Jun 2019 05:19:19: start X-correlation... INFO @ Mon, 03 Jun 2019 05:19:19: end of X-cor INFO @ Mon, 03 Jun 2019 05:19:19: #2 finished! INFO @ Mon, 03 Jun 2019 05:19:19: #2 predicted fragment length is 152 bps INFO @ Mon, 03 Jun 2019 05:19:19: #2 alternative fragment length(s) may be 152 bps INFO @ Mon, 03 Jun 2019 05:19:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.05_model.r INFO @ Mon, 03 Jun 2019 05:19:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:19:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:19:26: 5000000 INFO @ Mon, 03 Jun 2019 05:19:32: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 05:19:32: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 05:19:32: #1 total tags in treatment: 5590641 INFO @ Mon, 03 Jun 2019 05:19:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:19:32: #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 05:19:32: #1 tags after filtering in treatment: 5590641 INFO @ Mon, 03 Jun 2019 05:19:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:19:32: #1 finished! INFO @ Mon, 03 Jun 2019 05:19:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:19:33: #2 number of paired peaks: 5688 INFO @ Mon, 03 Jun 2019 05:19:33: start model_add_line... INFO @ Mon, 03 Jun 2019 05:19:33: start X-correlation... INFO @ Mon, 03 Jun 2019 05:19:33: end of X-cor INFO @ Mon, 03 Jun 2019 05:19:33: #2 finished! INFO @ Mon, 03 Jun 2019 05:19:33: #2 predicted fragment length is 152 bps INFO @ Mon, 03 Jun 2019 05:19:33: #2 alternative fragment length(s) may be 152 bps INFO @ Mon, 03 Jun 2019 05:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.10_model.r INFO @ Mon, 03 Jun 2019 05:19:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:19:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:19:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:19:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.05_summits.bed INFO @ Mon, 03 Jun 2019 05:19:48: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (7455 records, 4 fields): 14 millis INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.20_peaks.xls CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.20_summits.bed INFO @ Mon, 03 Jun 2019 05:19:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4642 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:19:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183520/SRX183520.10_summits.bed INFO @ Mon, 03 Jun 2019 05:20:04: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5848 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。