Job ID = 1294274 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:06:53 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 : 21,817,500 reads read : 21,817,500 reads written : 21,817,500 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: 00:04:31 21817500 reads; of these: 21817500 (100.00%) were unpaired; of these: 1703238 (7.81%) aligned 0 times 18054527 (82.75%) aligned exactly 1 time 2059735 (9.44%) aligned >1 times 92.19% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 7898191 / 20114262 = 0.3927 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 06:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.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 06:22:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:22:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.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 06:22:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:22:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.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 06:22:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:22:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:22:35: 1000000 INFO @ Mon, 03 Jun 2019 06:22:35: 1000000 INFO @ Mon, 03 Jun 2019 06:22:35: 1000000 INFO @ Mon, 03 Jun 2019 06:22:42: 2000000 INFO @ Mon, 03 Jun 2019 06:22:42: 2000000 INFO @ Mon, 03 Jun 2019 06:22:43: 2000000 INFO @ Mon, 03 Jun 2019 06:22:49: 3000000 INFO @ Mon, 03 Jun 2019 06:22:49: 3000000 INFO @ Mon, 03 Jun 2019 06:22:50: 3000000 INFO @ Mon, 03 Jun 2019 06:22:56: 4000000 INFO @ Mon, 03 Jun 2019 06:22:56: 4000000 INFO @ Mon, 03 Jun 2019 06:22:58: 4000000 INFO @ Mon, 03 Jun 2019 06:23:03: 5000000 INFO @ Mon, 03 Jun 2019 06:23:03: 5000000 INFO @ Mon, 03 Jun 2019 06:23:05: 5000000 INFO @ Mon, 03 Jun 2019 06:23:09: 6000000 INFO @ Mon, 03 Jun 2019 06:23:10: 6000000 INFO @ Mon, 03 Jun 2019 06:23:12: 6000000 INFO @ Mon, 03 Jun 2019 06:23:16: 7000000 INFO @ Mon, 03 Jun 2019 06:23:16: 7000000 INFO @ Mon, 03 Jun 2019 06:23:19: 7000000 INFO @ Mon, 03 Jun 2019 06:23:23: 8000000 INFO @ Mon, 03 Jun 2019 06:23:23: 8000000 INFO @ Mon, 03 Jun 2019 06:23:26: 8000000 INFO @ Mon, 03 Jun 2019 06:23:30: 9000000 INFO @ Mon, 03 Jun 2019 06:23:30: 9000000 INFO @ Mon, 03 Jun 2019 06:23:33: 9000000 INFO @ Mon, 03 Jun 2019 06:23:36: 10000000 INFO @ Mon, 03 Jun 2019 06:23:36: 10000000 INFO @ Mon, 03 Jun 2019 06:23:40: 10000000 INFO @ Mon, 03 Jun 2019 06:23:43: 11000000 INFO @ Mon, 03 Jun 2019 06:23:43: 11000000 INFO @ Mon, 03 Jun 2019 06:23:47: 11000000 INFO @ Mon, 03 Jun 2019 06:23:49: 12000000 INFO @ Mon, 03 Jun 2019 06:23:49: 12000000 INFO @ Mon, 03 Jun 2019 06:23:51: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:23:51: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:23:51: #1 total tags in treatment: 12216071 INFO @ Mon, 03 Jun 2019 06:23:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:23:51: #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 06:23:51: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:23:51: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:23:51: #1 total tags in treatment: 12216071 INFO @ Mon, 03 Jun 2019 06:23:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:23:51: #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 06:23:51: #1 tags after filtering in treatment: 12216071 INFO @ Mon, 03 Jun 2019 06:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:23:51: #1 finished! INFO @ Mon, 03 Jun 2019 06:23:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:23:51: #1 tags after filtering in treatment: 12216071 INFO @ Mon, 03 Jun 2019 06:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:23:51: #1 finished! INFO @ Mon, 03 Jun 2019 06:23:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:23:53: #2 number of paired peaks: 5676 INFO @ Mon, 03 Jun 2019 06:23:53: start model_add_line... INFO @ Mon, 03 Jun 2019 06:23:53: #2 number of paired peaks: 5676 INFO @ Mon, 03 Jun 2019 06:23:53: start model_add_line... INFO @ Mon, 03 Jun 2019 06:23:53: start X-correlation... INFO @ Mon, 03 Jun 2019 06:23:53: end of X-cor INFO @ Mon, 03 Jun 2019 06:23:53: #2 finished! INFO @ Mon, 03 Jun 2019 06:23:53: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 06:23:53: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 06:23:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.10_model.r INFO @ Mon, 03 Jun 2019 06:23:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:23:53: start X-correlation... INFO @ Mon, 03 Jun 2019 06:23:53: end of X-cor INFO @ Mon, 03 Jun 2019 06:23:53: #2 finished! INFO @ Mon, 03 Jun 2019 06:23:53: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 06:23:53: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 06:23:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.20_model.r INFO @ Mon, 03 Jun 2019 06:23:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:23:55: 12000000 INFO @ Mon, 03 Jun 2019 06:23:56: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:23:56: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:23:56: #1 total tags in treatment: 12216071 INFO @ Mon, 03 Jun 2019 06:23:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:23:56: #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 06:23:56: #1 tags after filtering in treatment: 12216071 INFO @ Mon, 03 Jun 2019 06:23:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:23:56: #1 finished! INFO @ Mon, 03 Jun 2019 06:23:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:23:58: #2 number of paired peaks: 5676 INFO @ Mon, 03 Jun 2019 06:23:58: start model_add_line... INFO @ Mon, 03 Jun 2019 06:23:58: start X-correlation... INFO @ Mon, 03 Jun 2019 06:23:58: end of X-cor INFO @ Mon, 03 Jun 2019 06:23:58: #2 finished! INFO @ Mon, 03 Jun 2019 06:23:58: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 06:23:58: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 06:23:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.05_model.r INFO @ Mon, 03 Jun 2019 06:23:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:23:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:24:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:24:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:24:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.20_summits.bed INFO @ Mon, 03 Jun 2019 06:24:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4174 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.10_summits.bed INFO @ Mon, 03 Jun 2019 06:24:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6270 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220300/SRX220300.05_summits.bed INFO @ Mon, 03 Jun 2019 06:24:56: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9059 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。