Job ID = 2640490 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:17:33 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 : 11,069,978 reads read : 22,139,956 reads written : 11,069,978 reads 0-length : 11,069,978 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:38 11069978 reads; of these: 11069978 (100.00%) were unpaired; of these: 687919 (6.21%) aligned 0 times 7917660 (71.52%) aligned exactly 1 time 2464399 (22.26%) aligned >1 times 93.79% 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: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1176287 / 10382059 = 0.1133 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.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 @ Sat, 24 Aug 2019 17:34:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:34:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:35:05: 1000000 INFO @ Sat, 24 Aug 2019 17:35:11: 2000000 INFO @ Sat, 24 Aug 2019 17:35:18: 3000000 INFO @ Sat, 24 Aug 2019 17:35:24: 4000000 INFO @ Sat, 24 Aug 2019 17:35:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.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 @ Sat, 24 Aug 2019 17:35:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:35:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:35:31: 5000000 INFO @ Sat, 24 Aug 2019 17:35:35: 1000000 INFO @ Sat, 24 Aug 2019 17:35:38: 6000000 INFO @ Sat, 24 Aug 2019 17:35:42: 2000000 INFO @ Sat, 24 Aug 2019 17:35:44: 7000000 INFO @ Sat, 24 Aug 2019 17:35:49: 3000000 INFO @ Sat, 24 Aug 2019 17:35:51: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:35:56: 4000000 INFO @ Sat, 24 Aug 2019 17:35:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.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 @ Sat, 24 Aug 2019 17:35:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:35:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:35:59: 9000000 INFO @ Sat, 24 Aug 2019 17:36:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:36:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:36:00: #1 total tags in treatment: 9205772 INFO @ Sat, 24 Aug 2019 17:36:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:36:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:36:01: #1 tags after filtering in treatment: 9205524 INFO @ Sat, 24 Aug 2019 17:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:36:01: #1 finished! INFO @ Sat, 24 Aug 2019 17:36:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:36:03: #2 number of paired peaks: 38182 INFO @ Sat, 24 Aug 2019 17:36:03: start model_add_line... INFO @ Sat, 24 Aug 2019 17:36:03: 5000000 INFO @ Sat, 24 Aug 2019 17:36:03: start X-correlation... INFO @ Sat, 24 Aug 2019 17:36:03: end of X-cor INFO @ Sat, 24 Aug 2019 17:36:03: #2 finished! INFO @ Sat, 24 Aug 2019 17:36:03: #2 predicted fragment length is 136 bps INFO @ Sat, 24 Aug 2019 17:36:03: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 24 Aug 2019 17:36:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.05_model.r INFO @ Sat, 24 Aug 2019 17:36:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:36:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:36:05: 1000000 INFO @ Sat, 24 Aug 2019 17:36:09: 6000000 INFO @ Sat, 24 Aug 2019 17:36:12: 2000000 INFO @ Sat, 24 Aug 2019 17:36:16: 7000000 INFO @ Sat, 24 Aug 2019 17:36:19: 3000000 INFO @ Sat, 24 Aug 2019 17:36:22: 8000000 INFO @ Sat, 24 Aug 2019 17:36:26: 4000000 INFO @ Sat, 24 Aug 2019 17:36:29: 9000000 INFO @ Sat, 24 Aug 2019 17:36:31: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:36:31: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:36:31: #1 total tags in treatment: 9205772 INFO @ Sat, 24 Aug 2019 17:36:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:36:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:36:31: #1 tags after filtering in treatment: 9205524 INFO @ Sat, 24 Aug 2019 17:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:36:31: #1 finished! INFO @ Sat, 24 Aug 2019 17:36:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:36:33: 5000000 INFO @ Sat, 24 Aug 2019 17:36:33: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:36:33: #2 number of paired peaks: 38182 INFO @ Sat, 24 Aug 2019 17:36:33: start model_add_line... INFO @ Sat, 24 Aug 2019 17:36:34: start X-correlation... INFO @ Sat, 24 Aug 2019 17:36:34: end of X-cor INFO @ Sat, 24 Aug 2019 17:36:34: #2 finished! INFO @ Sat, 24 Aug 2019 17:36:34: #2 predicted fragment length is 136 bps INFO @ Sat, 24 Aug 2019 17:36:34: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 24 Aug 2019 17:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.10_model.r INFO @ Sat, 24 Aug 2019 17:36:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:36:40: 6000000 INFO @ Sat, 24 Aug 2019 17:36:47: 7000000 INFO @ Sat, 24 Aug 2019 17:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.05_summits.bed INFO @ Sat, 24 Aug 2019 17:36:48: Done! pass1 - making usageList (83 chroms): 5 millis pass2 - checking and writing primary data (12584 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:36:53: 8000000 INFO @ Sat, 24 Aug 2019 17:37:00: 9000000 INFO @ Sat, 24 Aug 2019 17:37:02: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:37:02: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:37:02: #1 total tags in treatment: 9205772 INFO @ Sat, 24 Aug 2019 17:37:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:37:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:37:02: #1 tags after filtering in treatment: 9205524 INFO @ Sat, 24 Aug 2019 17:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:37:02: #1 finished! INFO @ Sat, 24 Aug 2019 17:37:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:37:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:37:05: #2 number of paired peaks: 38182 INFO @ Sat, 24 Aug 2019 17:37:05: start model_add_line... INFO @ Sat, 24 Aug 2019 17:37:05: start X-correlation... INFO @ Sat, 24 Aug 2019 17:37:05: end of X-cor INFO @ Sat, 24 Aug 2019 17:37:05: #2 finished! INFO @ Sat, 24 Aug 2019 17:37:05: #2 predicted fragment length is 136 bps INFO @ Sat, 24 Aug 2019 17:37:05: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 24 Aug 2019 17:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.20_model.r INFO @ Sat, 24 Aug 2019 17:37:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.10_summits.bed INFO @ Sat, 24 Aug 2019 17:37:18: Done! pass1 - making usageList (51 chroms): 4 millis pass2 - checking and writing primary data (5591 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:37:34: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374997/SRX5374997.20_summits.bed INFO @ Sat, 24 Aug 2019 17:37:48: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1868 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。