Job ID = 4288908 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:35:20 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 ) 2019-12-10T03:36:12 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 ) 2019-12-10T03:36:12 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 ) 2019-12-10T03:36:12 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 ) 2019-12-10T03:36:31 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 ) 2019-12-10T03:36:31 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 : 21,825,591 reads read : 43,651,182 reads written : 21,825,591 reads 0-length : 21,825,591 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:42 21825591 reads; of these: 21825591 (100.00%) were unpaired; of these: 1418232 (6.50%) aligned 0 times 17776922 (81.45%) aligned exactly 1 time 2630437 (12.05%) aligned >1 times 93.50% overall alignment rate Time searching: 00:23:43 Overall time: 00:23:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2552499 / 20407359 = 0.1251 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Tue, 10 Dec 2019 13:19:52: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:19:52: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:20:00: 1000000 INFO @ Tue, 10 Dec 2019 13:20:08: 2000000 INFO @ Tue, 10 Dec 2019 13:20:17: 3000000 INFO @ Tue, 10 Dec 2019 13:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Tue, 10 Dec 2019 13:20:22: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:20:22: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:20:25: 4000000 INFO @ Tue, 10 Dec 2019 13:20:32: 1000000 INFO @ Tue, 10 Dec 2019 13:20:33: 5000000 INFO @ Tue, 10 Dec 2019 13:20:41: 6000000 INFO @ Tue, 10 Dec 2019 13:20:42: 2000000 INFO @ Tue, 10 Dec 2019 13:20:49: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Tue, 10 Dec 2019 13:20:52: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:20:52: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:20:52: 3000000 INFO @ Tue, 10 Dec 2019 13:20:58: 8000000 INFO @ Tue, 10 Dec 2019 13:21:00: 1000000 INFO @ Tue, 10 Dec 2019 13:21:03: 4000000 INFO @ Tue, 10 Dec 2019 13:21:06: 9000000 INFO @ Tue, 10 Dec 2019 13:21:09: 2000000 INFO @ Tue, 10 Dec 2019 13:21:12: 5000000 INFO @ Tue, 10 Dec 2019 13:21:14: 10000000 INFO @ Tue, 10 Dec 2019 13:21:17: 3000000 INFO @ Tue, 10 Dec 2019 13:21:22: 6000000 INFO @ Tue, 10 Dec 2019 13:21:22: 11000000 INFO @ Tue, 10 Dec 2019 13:21:26: 4000000 INFO @ Tue, 10 Dec 2019 13:21:30: 12000000 INFO @ Tue, 10 Dec 2019 13:21:31: 7000000 INFO @ Tue, 10 Dec 2019 13:21:34: 5000000 INFO @ Tue, 10 Dec 2019 13:21:38: 13000000 INFO @ Tue, 10 Dec 2019 13:21:41: 8000000 INFO @ Tue, 10 Dec 2019 13:21:42: 6000000 INFO @ Tue, 10 Dec 2019 13:21:46: 14000000 INFO @ Tue, 10 Dec 2019 13:21:50: 7000000 INFO @ Tue, 10 Dec 2019 13:21:51: 9000000 INFO @ Tue, 10 Dec 2019 13:21:55: 15000000 INFO @ Tue, 10 Dec 2019 13:21:58: 8000000 INFO @ Tue, 10 Dec 2019 13:22:01: 10000000 INFO @ Tue, 10 Dec 2019 13:22:03: 16000000 INFO @ Tue, 10 Dec 2019 13:22:06: 9000000 INFO @ Tue, 10 Dec 2019 13:22:10: 11000000 INFO @ Tue, 10 Dec 2019 13:22:11: 17000000 INFO @ Tue, 10 Dec 2019 13:22:14: 10000000 INFO @ Tue, 10 Dec 2019 13:22:18: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:22:18: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:22:18: #1 total tags in treatment: 17854860 INFO @ Tue, 10 Dec 2019 13:22:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:22:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:22:19: #1 tags after filtering in treatment: 17854663 INFO @ Tue, 10 Dec 2019 13:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:22:19: #1 finished! INFO @ Tue, 10 Dec 2019 13:22:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:22:20: 12000000 INFO @ Tue, 10 Dec 2019 13:22:22: 11000000 INFO @ Tue, 10 Dec 2019 13:22:24: #2 number of paired peaks: 100549 INFO @ Tue, 10 Dec 2019 13:22:24: start model_add_line... INFO @ Tue, 10 Dec 2019 13:22:25: start X-correlation... INFO @ Tue, 10 Dec 2019 13:22:25: end of X-cor INFO @ Tue, 10 Dec 2019 13:22:25: #2 finished! INFO @ Tue, 10 Dec 2019 13:22:25: #2 predicted fragment length is 184 bps INFO @ Tue, 10 Dec 2019 13:22:25: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 10 Dec 2019 13:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.05_model.r INFO @ Tue, 10 Dec 2019 13:22:25: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:22:29: 13000000 INFO @ Tue, 10 Dec 2019 13:22:31: 12000000 INFO @ Tue, 10 Dec 2019 13:22:38: 13000000 INFO @ Tue, 10 Dec 2019 13:22:39: 14000000 INFO @ Tue, 10 Dec 2019 13:22:46: 14000000 INFO @ Tue, 10 Dec 2019 13:22:48: 15000000 INFO @ Tue, 10 Dec 2019 13:22:54: 15000000 INFO @ Tue, 10 Dec 2019 13:22:57: 16000000 INFO @ Tue, 10 Dec 2019 13:23:02: 16000000 INFO @ Tue, 10 Dec 2019 13:23:07: 17000000 INFO @ Tue, 10 Dec 2019 13:23:10: 17000000 INFO @ Tue, 10 Dec 2019 13:23:16: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:23:16: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:23:16: #1 total tags in treatment: 17854860 INFO @ Tue, 10 Dec 2019 13:23:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:23:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:23:16: #1 tags after filtering in treatment: 17854663 INFO @ Tue, 10 Dec 2019 13:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:23:16: #1 finished! INFO @ Tue, 10 Dec 2019 13:23:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:23:17: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:23:17: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:23:17: #1 total tags in treatment: 17854860 INFO @ Tue, 10 Dec 2019 13:23:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:23:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:23:18: #1 tags after filtering in treatment: 17854663 INFO @ Tue, 10 Dec 2019 13:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:23:18: #1 finished! INFO @ Tue, 10 Dec 2019 13:23:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:23:22: #2 number of paired peaks: 100549 INFO @ Tue, 10 Dec 2019 13:23:22: start model_add_line... INFO @ Tue, 10 Dec 2019 13:23:22: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:23:22: start X-correlation... INFO @ Tue, 10 Dec 2019 13:23:22: end of X-cor INFO @ Tue, 10 Dec 2019 13:23:22: #2 finished! INFO @ Tue, 10 Dec 2019 13:23:22: #2 predicted fragment length is 184 bps INFO @ Tue, 10 Dec 2019 13:23:22: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 10 Dec 2019 13:23:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.10_model.r INFO @ Tue, 10 Dec 2019 13:23:22: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:23:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:23:23: #2 number of paired peaks: 100549 INFO @ Tue, 10 Dec 2019 13:23:23: start model_add_line... INFO @ Tue, 10 Dec 2019 13:23:23: start X-correlation... INFO @ Tue, 10 Dec 2019 13:23:23: end of X-cor INFO @ Tue, 10 Dec 2019 13:23:23: #2 finished! INFO @ Tue, 10 Dec 2019 13:23:23: #2 predicted fragment length is 184 bps INFO @ Tue, 10 Dec 2019 13:23:23: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 10 Dec 2019 13:23:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.20_model.r INFO @ Tue, 10 Dec 2019 13:23:23: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:23:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:23:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.05_summits.bed INFO @ Tue, 10 Dec 2019 13:23:55: Done! pass1 - making usageList (141 chroms): 22 millis pass2 - checking and writing primary data (81498 records, 4 fields): 102 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:24:20: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:24:20: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.20_summits.bed INFO @ Tue, 10 Dec 2019 13:24:51: Done! pass1 - making usageList (57 chroms): 5 millis INFO @ Tue, 10 Dec 2019 13:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.10_peaks.xls pass2 - checking and writing primary data (19679 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460561/SRX5460561.10_summits.bed INFO @ Tue, 10 Dec 2019 13:24:52: Done! pass1 - making usageList (88 chroms): 14 millis pass2 - checking and writing primary data (45388 records, 4 fields): 58 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。