Job ID = 1294427 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:42:40 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 ) 2019-06-02T22:43:54 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 : 14,182,606 reads read : 14,182,606 reads written : 14,182,606 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: 00:04:50 14182606 reads; of these: 14182606 (100.00%) were unpaired; of these: 591270 (4.17%) aligned 0 times 11505544 (81.12%) aligned exactly 1 time 2085792 (14.71%) aligned >1 times 95.83% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 5124296 / 13591336 = 0.3770 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 07:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.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 07:57:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.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 07:57:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.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 07:57:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:56: 1000000 INFO @ Mon, 03 Jun 2019 07:57:56: 1000000 INFO @ Mon, 03 Jun 2019 07:57:58: 1000000 INFO @ Mon, 03 Jun 2019 07:58:03: 2000000 INFO @ Mon, 03 Jun 2019 07:58:03: 2000000 INFO @ Mon, 03 Jun 2019 07:58:08: 2000000 INFO @ Mon, 03 Jun 2019 07:58:11: 3000000 INFO @ Mon, 03 Jun 2019 07:58:11: 3000000 INFO @ Mon, 03 Jun 2019 07:58:17: 3000000 INFO @ Mon, 03 Jun 2019 07:58:19: 4000000 INFO @ Mon, 03 Jun 2019 07:58:19: 4000000 INFO @ Mon, 03 Jun 2019 07:58:26: 5000000 INFO @ Mon, 03 Jun 2019 07:58:26: 5000000 INFO @ Mon, 03 Jun 2019 07:58:27: 4000000 INFO @ Mon, 03 Jun 2019 07:58:34: 6000000 INFO @ Mon, 03 Jun 2019 07:58:34: 6000000 INFO @ Mon, 03 Jun 2019 07:58:37: 5000000 INFO @ Mon, 03 Jun 2019 07:58:41: 7000000 INFO @ Mon, 03 Jun 2019 07:58:42: 7000000 INFO @ Mon, 03 Jun 2019 07:58:47: 6000000 INFO @ Mon, 03 Jun 2019 07:58:49: 8000000 INFO @ Mon, 03 Jun 2019 07:58:49: 8000000 INFO @ Mon, 03 Jun 2019 07:58:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:58:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:58:52: #1 total tags in treatment: 8467040 INFO @ Mon, 03 Jun 2019 07:58:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:58:52: #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 07:58:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:58:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:58:53: #1 total tags in treatment: 8467040 INFO @ Mon, 03 Jun 2019 07:58:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:58:53: #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 07:58:53: #1 tags after filtering in treatment: 8467040 INFO @ Mon, 03 Jun 2019 07:58:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:58:53: #1 finished! INFO @ Mon, 03 Jun 2019 07:58:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:58:53: #1 tags after filtering in treatment: 8467040 INFO @ Mon, 03 Jun 2019 07:58:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:58:53: #1 finished! INFO @ Mon, 03 Jun 2019 07:58:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:58:54: #2 number of paired peaks: 6419 INFO @ Mon, 03 Jun 2019 07:58:54: start model_add_line... INFO @ Mon, 03 Jun 2019 07:58:54: #2 number of paired peaks: 6419 INFO @ Mon, 03 Jun 2019 07:58:54: start model_add_line... INFO @ Mon, 03 Jun 2019 07:58:54: start X-correlation... INFO @ Mon, 03 Jun 2019 07:58:54: end of X-cor INFO @ Mon, 03 Jun 2019 07:58:54: #2 finished! INFO @ Mon, 03 Jun 2019 07:58:54: #2 predicted fragment length is 197 bps INFO @ Mon, 03 Jun 2019 07:58:54: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 03 Jun 2019 07:58:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.20_model.r INFO @ Mon, 03 Jun 2019 07:58:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:58:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:58:54: start X-correlation... INFO @ Mon, 03 Jun 2019 07:58:54: end of X-cor INFO @ Mon, 03 Jun 2019 07:58:54: #2 finished! INFO @ Mon, 03 Jun 2019 07:58:54: #2 predicted fragment length is 197 bps INFO @ Mon, 03 Jun 2019 07:58:54: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 03 Jun 2019 07:58:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.05_model.r INFO @ Mon, 03 Jun 2019 07:58:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:58:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:58:56: 7000000 INFO @ Mon, 03 Jun 2019 07:59:05: 8000000 INFO @ Mon, 03 Jun 2019 07:59:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:59:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:59:10: #1 total tags in treatment: 8467040 INFO @ Mon, 03 Jun 2019 07:59:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:59:10: #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 07:59:10: #1 tags after filtering in treatment: 8467040 INFO @ Mon, 03 Jun 2019 07:59:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:59:10: #1 finished! INFO @ Mon, 03 Jun 2019 07:59:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:59:11: #2 number of paired peaks: 6419 INFO @ Mon, 03 Jun 2019 07:59:11: start model_add_line... INFO @ Mon, 03 Jun 2019 07:59:11: start X-correlation... INFO @ Mon, 03 Jun 2019 07:59:11: end of X-cor INFO @ Mon, 03 Jun 2019 07:59:11: #2 finished! INFO @ Mon, 03 Jun 2019 07:59:11: #2 predicted fragment length is 197 bps INFO @ Mon, 03 Jun 2019 07:59:11: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 03 Jun 2019 07:59:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.10_model.r INFO @ Mon, 03 Jun 2019 07:59:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:59:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:59:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:59:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.20_summits.bed INFO @ Mon, 03 Jun 2019 07:59:38: Done! INFO @ Mon, 03 Jun 2019 07:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.05_peaks.xls pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6728 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.05_summits.bed INFO @ Mon, 03 Jun 2019 07:59:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10396 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:59:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:59:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:59:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:59:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287597/SRX287597.10_summits.bed INFO @ Mon, 03 Jun 2019 07:59:56: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8556 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。