Job ID = 2640561 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:40:00 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 ) 2019-08-24T08:40:00 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 ) 2019-08-24T08:40:15 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 ) 2019-08-24T08:40:58 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 ) 2019-08-24T08:41:46 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 ) 2019-08-24T08:41:46 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 : 24,536,264 reads read : 49,072,528 reads written : 24,536,264 reads 0-length : 24,536,264 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: 00:00:01 Multiseed full-index search: 00:17:41 24536264 reads; of these: 24536264 (100.00%) were unpaired; of these: 599830 (2.44%) aligned 0 times 18515366 (75.46%) aligned exactly 1 time 5421068 (22.09%) aligned >1 times 97.56% overall alignment rate Time searching: 00:17:43 Overall time: 00:17:43 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] 4491109 / 23936434 = 0.1876 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:17:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.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 18:17:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:17:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:17:22: 1000000 INFO @ Sat, 24 Aug 2019 18:17:29: 2000000 INFO @ Sat, 24 Aug 2019 18:17:36: 3000000 INFO @ Sat, 24 Aug 2019 18:17:43: 4000000 INFO @ Sat, 24 Aug 2019 18:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.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 18:17:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:17:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:17:49: 5000000 INFO @ Sat, 24 Aug 2019 18:17:52: 1000000 INFO @ Sat, 24 Aug 2019 18:17:56: 6000000 INFO @ Sat, 24 Aug 2019 18:18:00: 2000000 INFO @ Sat, 24 Aug 2019 18:18:03: 7000000 INFO @ Sat, 24 Aug 2019 18:18:07: 3000000 INFO @ Sat, 24 Aug 2019 18:18:10: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.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 18:18:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:18:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:18:15: 4000000 INFO @ Sat, 24 Aug 2019 18:18:17: 9000000 INFO @ Sat, 24 Aug 2019 18:18:21: 1000000 INFO @ Sat, 24 Aug 2019 18:18:23: 5000000 INFO @ Sat, 24 Aug 2019 18:18:25: 10000000 INFO @ Sat, 24 Aug 2019 18:18:28: 2000000 INFO @ Sat, 24 Aug 2019 18:18:30: 6000000 INFO @ Sat, 24 Aug 2019 18:18:32: 11000000 INFO @ Sat, 24 Aug 2019 18:18:35: 3000000 INFO @ Sat, 24 Aug 2019 18:18:38: 7000000 INFO @ Sat, 24 Aug 2019 18:18:39: 12000000 INFO @ Sat, 24 Aug 2019 18:18:42: 4000000 INFO @ Sat, 24 Aug 2019 18:18:46: 13000000 INFO @ Sat, 24 Aug 2019 18:18:46: 8000000 INFO @ Sat, 24 Aug 2019 18:18:49: 5000000 INFO @ Sat, 24 Aug 2019 18:18:53: 14000000 INFO @ Sat, 24 Aug 2019 18:18:54: 9000000 INFO @ Sat, 24 Aug 2019 18:18:56: 6000000 INFO @ Sat, 24 Aug 2019 18:19:00: 15000000 INFO @ Sat, 24 Aug 2019 18:19:02: 10000000 INFO @ Sat, 24 Aug 2019 18:19:03: 7000000 INFO @ Sat, 24 Aug 2019 18:19:07: 16000000 INFO @ Sat, 24 Aug 2019 18:19:10: 11000000 INFO @ Sat, 24 Aug 2019 18:19:10: 8000000 INFO @ Sat, 24 Aug 2019 18:19:14: 17000000 INFO @ Sat, 24 Aug 2019 18:19:17: 9000000 INFO @ Sat, 24 Aug 2019 18:19:18: 12000000 INFO @ Sat, 24 Aug 2019 18:19:21: 18000000 INFO @ Sat, 24 Aug 2019 18:19:24: 10000000 INFO @ Sat, 24 Aug 2019 18:19:25: 13000000 INFO @ Sat, 24 Aug 2019 18:19:28: 19000000 INFO @ Sat, 24 Aug 2019 18:19:31: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:19:31: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:19:31: #1 total tags in treatment: 19445325 INFO @ Sat, 24 Aug 2019 18:19:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:19:31: #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 18:19:32: 11000000 INFO @ Sat, 24 Aug 2019 18:19:32: #1 tags after filtering in treatment: 19445154 INFO @ Sat, 24 Aug 2019 18:19:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:19:32: #1 finished! INFO @ Sat, 24 Aug 2019 18:19:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:19:33: 14000000 INFO @ Sat, 24 Aug 2019 18:19:35: #2 number of paired peaks: 34531 INFO @ Sat, 24 Aug 2019 18:19:35: start model_add_line... INFO @ Sat, 24 Aug 2019 18:19:36: start X-correlation... INFO @ Sat, 24 Aug 2019 18:19:36: end of X-cor INFO @ Sat, 24 Aug 2019 18:19:36: #2 finished! INFO @ Sat, 24 Aug 2019 18:19:36: #2 predicted fragment length is 166 bps INFO @ Sat, 24 Aug 2019 18:19:36: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 24 Aug 2019 18:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.05_model.r INFO @ Sat, 24 Aug 2019 18:19:36: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:19:38: 12000000 INFO @ Sat, 24 Aug 2019 18:19:41: 15000000 INFO @ Sat, 24 Aug 2019 18:19:45: 13000000 INFO @ Sat, 24 Aug 2019 18:19:48: 16000000 INFO @ Sat, 24 Aug 2019 18:19:52: 14000000 INFO @ Sat, 24 Aug 2019 18:19:56: 17000000 INFO @ Sat, 24 Aug 2019 18:19:59: 15000000 INFO @ Sat, 24 Aug 2019 18:20:04: 18000000 INFO @ Sat, 24 Aug 2019 18:20:06: 16000000 INFO @ Sat, 24 Aug 2019 18:20:11: 19000000 INFO @ Sat, 24 Aug 2019 18:20:13: 17000000 INFO @ Sat, 24 Aug 2019 18:20:15: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:20:15: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:20:15: #1 total tags in treatment: 19445325 INFO @ Sat, 24 Aug 2019 18:20:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:20:15: #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 18:20:15: #1 tags after filtering in treatment: 19445154 INFO @ Sat, 24 Aug 2019 18:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:20:15: #1 finished! INFO @ Sat, 24 Aug 2019 18:20:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:20:19: #2 number of paired peaks: 34531 INFO @ Sat, 24 Aug 2019 18:20:19: start model_add_line... INFO @ Sat, 24 Aug 2019 18:20:19: start X-correlation... INFO @ Sat, 24 Aug 2019 18:20:19: end of X-cor INFO @ Sat, 24 Aug 2019 18:20:19: #2 finished! INFO @ Sat, 24 Aug 2019 18:20:19: #2 predicted fragment length is 166 bps INFO @ Sat, 24 Aug 2019 18:20:19: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 24 Aug 2019 18:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.10_model.r INFO @ Sat, 24 Aug 2019 18:20:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:20:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:20:20: 18000000 INFO @ Sat, 24 Aug 2019 18:20:27: 19000000 INFO @ Sat, 24 Aug 2019 18:20:31: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:20:31: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:20:31: #1 total tags in treatment: 19445325 INFO @ Sat, 24 Aug 2019 18:20:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:20:31: #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 18:20:31: #1 tags after filtering in treatment: 19445154 INFO @ Sat, 24 Aug 2019 18:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:20:31: #1 finished! INFO @ Sat, 24 Aug 2019 18:20:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:20:34: #2 number of paired peaks: 34531 INFO @ Sat, 24 Aug 2019 18:20:34: start model_add_line... INFO @ Sat, 24 Aug 2019 18:20:35: start X-correlation... INFO @ Sat, 24 Aug 2019 18:20:35: end of X-cor INFO @ Sat, 24 Aug 2019 18:20:35: #2 finished! INFO @ Sat, 24 Aug 2019 18:20:35: #2 predicted fragment length is 166 bps INFO @ Sat, 24 Aug 2019 18:20:35: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 24 Aug 2019 18:20:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.20_model.r INFO @ Sat, 24 Aug 2019 18:20:35: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:20:37: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.05_summits.bed INFO @ Sat, 24 Aug 2019 18:21:09: Done! pass1 - making usageList (94 chroms): 7 millis pass2 - checking and writing primary data (17302 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:21:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:21:36: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.10_summits.bed INFO @ Sat, 24 Aug 2019 18:21:55: Done! pass1 - making usageList (76 chroms): 6 millis pass2 - checking and writing primary data (12170 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:22:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:22:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:22:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375012/SRX5375012.20_summits.bed INFO @ Sat, 24 Aug 2019 18:22:08: Done! pass1 - making usageList (51 chroms): 3 millis pass2 - checking and writing primary data (6931 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。