Job ID = 1294576 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:00:54 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 ) 2019-06-03T00:00:54 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 ) 2019-06-03T00:06:21 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 : 22,422,337 reads read : 22,422,337 reads written : 22,422,337 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: 00:09:39 22422337 reads; of these: 22422337 (100.00%) were unpaired; of these: 1018988 (4.54%) aligned 0 times 15498432 (69.12%) aligned exactly 1 time 5904917 (26.33%) aligned >1 times 95.46% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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 12 files... [bam_rmdupse_core] 2777310 / 21403349 = 0.1298 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 09:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.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 09:28:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:28:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.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 09:28:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:28:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.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 09:28:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:28:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:29:02: 1000000 INFO @ Mon, 03 Jun 2019 09:29:03: 1000000 INFO @ Mon, 03 Jun 2019 09:29:03: 1000000 INFO @ Mon, 03 Jun 2019 09:29:10: 2000000 INFO @ Mon, 03 Jun 2019 09:29:11: 2000000 INFO @ Mon, 03 Jun 2019 09:29:11: 2000000 INFO @ Mon, 03 Jun 2019 09:29:17: 3000000 INFO @ Mon, 03 Jun 2019 09:29:19: 3000000 INFO @ Mon, 03 Jun 2019 09:29:19: 3000000 INFO @ Mon, 03 Jun 2019 09:29:24: 4000000 INFO @ Mon, 03 Jun 2019 09:29:26: 4000000 INFO @ Mon, 03 Jun 2019 09:29:27: 4000000 INFO @ Mon, 03 Jun 2019 09:29:32: 5000000 INFO @ Mon, 03 Jun 2019 09:29:34: 5000000 INFO @ Mon, 03 Jun 2019 09:29:35: 5000000 INFO @ Mon, 03 Jun 2019 09:29:39: 6000000 INFO @ Mon, 03 Jun 2019 09:29:42: 6000000 INFO @ Mon, 03 Jun 2019 09:29:43: 6000000 INFO @ Mon, 03 Jun 2019 09:29:47: 7000000 INFO @ Mon, 03 Jun 2019 09:29:51: 7000000 INFO @ Mon, 03 Jun 2019 09:29:51: 7000000 INFO @ Mon, 03 Jun 2019 09:29:55: 8000000 INFO @ Mon, 03 Jun 2019 09:29:59: 8000000 INFO @ Mon, 03 Jun 2019 09:29:59: 8000000 INFO @ Mon, 03 Jun 2019 09:30:03: 9000000 INFO @ Mon, 03 Jun 2019 09:30:07: 9000000 INFO @ Mon, 03 Jun 2019 09:30:07: 9000000 INFO @ Mon, 03 Jun 2019 09:30:10: 10000000 INFO @ Mon, 03 Jun 2019 09:30:14: 10000000 INFO @ Mon, 03 Jun 2019 09:30:14: 10000000 INFO @ Mon, 03 Jun 2019 09:30:17: 11000000 INFO @ Mon, 03 Jun 2019 09:30:22: 11000000 INFO @ Mon, 03 Jun 2019 09:30:22: 11000000 INFO @ Mon, 03 Jun 2019 09:30:24: 12000000 INFO @ Mon, 03 Jun 2019 09:30:30: 12000000 INFO @ Mon, 03 Jun 2019 09:30:30: 12000000 INFO @ Mon, 03 Jun 2019 09:30:32: 13000000 INFO @ Mon, 03 Jun 2019 09:30:37: 13000000 INFO @ Mon, 03 Jun 2019 09:30:38: 13000000 INFO @ Mon, 03 Jun 2019 09:30:39: 14000000 INFO @ Mon, 03 Jun 2019 09:30:45: 14000000 INFO @ Mon, 03 Jun 2019 09:30:46: 14000000 INFO @ Mon, 03 Jun 2019 09:30:46: 15000000 INFO @ Mon, 03 Jun 2019 09:30:53: 15000000 INFO @ Mon, 03 Jun 2019 09:30:54: 15000000 INFO @ Mon, 03 Jun 2019 09:30:54: 16000000 INFO @ Mon, 03 Jun 2019 09:31:01: 17000000 INFO @ Mon, 03 Jun 2019 09:31:01: 16000000 INFO @ Mon, 03 Jun 2019 09:31:01: 16000000 INFO @ Mon, 03 Jun 2019 09:31:08: 18000000 INFO @ Mon, 03 Jun 2019 09:31:09: 17000000 INFO @ Mon, 03 Jun 2019 09:31:09: 17000000 INFO @ Mon, 03 Jun 2019 09:31:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:31:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:31:13: #1 total tags in treatment: 18626039 INFO @ Mon, 03 Jun 2019 09:31:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:31:13: #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 09:31:13: #1 tags after filtering in treatment: 18626039 INFO @ Mon, 03 Jun 2019 09:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:31:13: #1 finished! INFO @ Mon, 03 Jun 2019 09:31:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:31:15: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 09:31:15: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 09:31:15: start model_add_line... INFO @ Mon, 03 Jun 2019 09:31:15: start X-correlation... INFO @ Mon, 03 Jun 2019 09:31:15: end of X-cor INFO @ Mon, 03 Jun 2019 09:31:15: #2 finished! INFO @ Mon, 03 Jun 2019 09:31:15: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 09:31:15: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 09:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.20_model.r INFO @ Mon, 03 Jun 2019 09:31:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:31:17: 18000000 INFO @ Mon, 03 Jun 2019 09:31:17: 18000000 INFO @ Mon, 03 Jun 2019 09:31:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:31:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:31:21: #1 total tags in treatment: 18626039 INFO @ Mon, 03 Jun 2019 09:31:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:31:21: #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 09:31:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:31:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:31:22: #1 total tags in treatment: 18626039 INFO @ Mon, 03 Jun 2019 09:31:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:31:22: #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 09:31:22: #1 tags after filtering in treatment: 18626039 INFO @ Mon, 03 Jun 2019 09:31:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:31:22: #1 finished! INFO @ Mon, 03 Jun 2019 09:31:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:31:22: #1 tags after filtering in treatment: 18626039 INFO @ Mon, 03 Jun 2019 09:31:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:31:22: #1 finished! INFO @ Mon, 03 Jun 2019 09:31:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:31:23: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 09:31:23: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 09:31:23: start model_add_line... INFO @ Mon, 03 Jun 2019 09:31:24: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 09:31:24: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 09:31:24: start model_add_line... INFO @ Mon, 03 Jun 2019 09:31:24: start X-correlation... INFO @ Mon, 03 Jun 2019 09:31:24: end of X-cor INFO @ Mon, 03 Jun 2019 09:31:24: #2 finished! INFO @ Mon, 03 Jun 2019 09:31:24: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 09:31:24: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 09:31:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.10_model.r INFO @ Mon, 03 Jun 2019 09:31:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:31:24: start X-correlation... INFO @ Mon, 03 Jun 2019 09:31:24: end of X-cor INFO @ Mon, 03 Jun 2019 09:31:24: #2 finished! INFO @ Mon, 03 Jun 2019 09:31:24: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 09:31:24: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 09:31:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.05_model.r INFO @ Mon, 03 Jun 2019 09:31:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:32:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:32:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:32:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:32:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:32:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.20_summits.bed INFO @ Mon, 03 Jun 2019 09:32:28: Done! pass1 - making usageList (13 chroms): 7 millis pass2 - checking and writing primary data (1544 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.10_summits.bed INFO @ Mon, 03 Jun 2019 09:32:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2268 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:32:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:32:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:32:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287751/SRX287751.05_summits.bed INFO @ Mon, 03 Jun 2019 09:32:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3209 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。