Job ID = 1307702 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:27:31 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 : 24,653,565 reads read : 49,307,130 reads written : 24,653,565 reads 0-length : 24,653,565 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: 00:08:41 24653565 reads; of these: 24653565 (100.00%) were unpaired; of these: 5673645 (23.01%) aligned 0 times 15919945 (64.57%) aligned exactly 1 time 3059975 (12.41%) aligned >1 times 76.99% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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] 10460204 / 18979920 = 0.5511 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 22:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.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 22:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.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 22:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.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 22:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:50:21: 1000000 INFO @ Mon, 03 Jun 2019 22:50:21: 1000000 INFO @ Mon, 03 Jun 2019 22:50:23: 1000000 INFO @ Mon, 03 Jun 2019 22:50:31: 2000000 INFO @ Mon, 03 Jun 2019 22:50:31: 2000000 INFO @ Mon, 03 Jun 2019 22:50:35: 2000000 INFO @ Mon, 03 Jun 2019 22:50:41: 3000000 INFO @ Mon, 03 Jun 2019 22:50:42: 3000000 INFO @ Mon, 03 Jun 2019 22:50:47: 3000000 INFO @ Mon, 03 Jun 2019 22:50:52: 4000000 INFO @ Mon, 03 Jun 2019 22:50:52: 4000000 INFO @ Mon, 03 Jun 2019 22:51:00: 4000000 INFO @ Mon, 03 Jun 2019 22:51:01: 5000000 INFO @ Mon, 03 Jun 2019 22:51:01: 5000000 INFO @ Mon, 03 Jun 2019 22:51:11: 6000000 INFO @ Mon, 03 Jun 2019 22:51:11: 5000000 INFO @ Mon, 03 Jun 2019 22:51:11: 6000000 INFO @ Mon, 03 Jun 2019 22:51:21: 7000000 INFO @ Mon, 03 Jun 2019 22:51:21: 7000000 INFO @ Mon, 03 Jun 2019 22:51:22: 6000000 INFO @ Mon, 03 Jun 2019 22:51:31: 8000000 INFO @ Mon, 03 Jun 2019 22:51:31: 8000000 INFO @ Mon, 03 Jun 2019 22:51:34: 7000000 INFO @ Mon, 03 Jun 2019 22:51:36: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:51:36: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:51:36: #1 total tags in treatment: 8519716 INFO @ Mon, 03 Jun 2019 22:51:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:51:36: #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 22:51:36: #1 tags after filtering in treatment: 8519716 INFO @ Mon, 03 Jun 2019 22:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:51:36: #1 finished! INFO @ Mon, 03 Jun 2019 22:51:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:51:37: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:51:37: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:51:37: #1 total tags in treatment: 8519716 INFO @ Mon, 03 Jun 2019 22:51:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:51:37: #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 22:51:37: #1 tags after filtering in treatment: 8519716 INFO @ Mon, 03 Jun 2019 22:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:51:37: #1 finished! INFO @ Mon, 03 Jun 2019 22:51:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:51:38: #2 number of paired peaks: 7118 INFO @ Mon, 03 Jun 2019 22:51:38: start model_add_line... INFO @ Mon, 03 Jun 2019 22:51:38: start X-correlation... INFO @ Mon, 03 Jun 2019 22:51:38: end of X-cor INFO @ Mon, 03 Jun 2019 22:51:38: #2 finished! INFO @ Mon, 03 Jun 2019 22:51:38: #2 predicted fragment length is 172 bps INFO @ Mon, 03 Jun 2019 22:51:38: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 03 Jun 2019 22:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.05_model.r INFO @ Mon, 03 Jun 2019 22:51:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:51:38: #2 number of paired peaks: 7118 INFO @ Mon, 03 Jun 2019 22:51:38: start model_add_line... INFO @ Mon, 03 Jun 2019 22:51:38: start X-correlation... INFO @ Mon, 03 Jun 2019 22:51:38: end of X-cor INFO @ Mon, 03 Jun 2019 22:51:38: #2 finished! INFO @ Mon, 03 Jun 2019 22:51:38: #2 predicted fragment length is 172 bps INFO @ Mon, 03 Jun 2019 22:51:38: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 03 Jun 2019 22:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.10_model.r INFO @ Mon, 03 Jun 2019 22:51:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:51:46: 8000000 INFO @ Mon, 03 Jun 2019 22:51:52: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:51:52: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:51:52: #1 total tags in treatment: 8519716 INFO @ Mon, 03 Jun 2019 22:51:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:51:52: #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 22:51:52: #1 tags after filtering in treatment: 8519716 INFO @ Mon, 03 Jun 2019 22:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:51:52: #1 finished! INFO @ Mon, 03 Jun 2019 22:51:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:51:54: #2 number of paired peaks: 7118 INFO @ Mon, 03 Jun 2019 22:51:54: start model_add_line... INFO @ Mon, 03 Jun 2019 22:51:54: start X-correlation... INFO @ Mon, 03 Jun 2019 22:51:54: end of X-cor INFO @ Mon, 03 Jun 2019 22:51:54: #2 finished! INFO @ Mon, 03 Jun 2019 22:51:54: #2 predicted fragment length is 172 bps INFO @ Mon, 03 Jun 2019 22:51:54: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 03 Jun 2019 22:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.20_model.r INFO @ Mon, 03 Jun 2019 22:51:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:52:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:52:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:52:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:52:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.05_summits.bed INFO @ Mon, 03 Jun 2019 22:52:18: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8238 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.10_summits.bed INFO @ Mon, 03 Jun 2019 22:52:20: Done! INFO @ Mon, 03 Jun 2019 22:52:20: #3 Call peaks for each chromosome... pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7355 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343114/SRX5343114.20_summits.bed INFO @ Mon, 03 Jun 2019 22:52:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5877 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。