Job ID = 2640478 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:10:36 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-08-24T08:10:36 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.51' 2019-08-24T08:10:36 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.24) from '172.19.7.51' 2019-08-24T08:10:36 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/008373/SRR8574046' 2019-08-24T08:10:36 fasterq-dump.2.9.6 err: invalid accession 'SRR8574046' spots read : 13,122,570 reads read : 26,245,140 reads written : 13,122,570 reads 0-length : 13,122,570 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: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:11:00 13122570 reads; of these: 13122570 (100.00%) were unpaired; of these: 302561 (2.31%) aligned 0 times 10903507 (83.09%) aligned exactly 1 time 1916502 (14.60%) aligned >1 times 97.69% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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] 4385275 / 12820009 = 0.3421 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.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 17:30:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:30:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:30:18: 1000000 INFO @ Sat, 24 Aug 2019 17:30:25: 2000000 INFO @ Sat, 24 Aug 2019 17:30:32: 3000000 INFO @ Sat, 24 Aug 2019 17:30:38: 4000000 INFO @ Sat, 24 Aug 2019 17:30:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.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 17:30:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:30:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:30:45: 5000000 INFO @ Sat, 24 Aug 2019 17:30:50: 1000000 INFO @ Sat, 24 Aug 2019 17:30:52: 6000000 INFO @ Sat, 24 Aug 2019 17:30:59: 2000000 INFO @ Sat, 24 Aug 2019 17:30:59: 7000000 INFO @ Sat, 24 Aug 2019 17:31:06: 8000000 INFO @ Sat, 24 Aug 2019 17:31:08: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:31:09: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:31:09: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:31:09: #1 total tags in treatment: 8434734 INFO @ Sat, 24 Aug 2019 17:31:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:31:09: #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 17:31:09: #1 tags after filtering in treatment: 8434469 INFO @ Sat, 24 Aug 2019 17:31:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:31:09: #1 finished! INFO @ Sat, 24 Aug 2019 17:31:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:31:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.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 17:31:10: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:31:10: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:31:13: #2 number of paired peaks: 97030 INFO @ Sat, 24 Aug 2019 17:31:13: start model_add_line... INFO @ Sat, 24 Aug 2019 17:31:14: start X-correlation... INFO @ Sat, 24 Aug 2019 17:31:14: end of X-cor INFO @ Sat, 24 Aug 2019 17:31:14: #2 finished! INFO @ Sat, 24 Aug 2019 17:31:14: #2 predicted fragment length is 168 bps INFO @ Sat, 24 Aug 2019 17:31:14: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 24 Aug 2019 17:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.05_model.r INFO @ Sat, 24 Aug 2019 17:31:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:31:17: 4000000 INFO @ Sat, 24 Aug 2019 17:31:18: 1000000 INFO @ Sat, 24 Aug 2019 17:31:26: 2000000 INFO @ Sat, 24 Aug 2019 17:31:26: 5000000 INFO @ Sat, 24 Aug 2019 17:31:34: 3000000 INFO @ Sat, 24 Aug 2019 17:31:35: 6000000 INFO @ Sat, 24 Aug 2019 17:31:41: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:31:41: 4000000 INFO @ Sat, 24 Aug 2019 17:31:44: 7000000 INFO @ Sat, 24 Aug 2019 17:31:49: 5000000 INFO @ Sat, 24 Aug 2019 17:31:53: 8000000 INFO @ Sat, 24 Aug 2019 17:31:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:31:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:31:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.05_summits.bed INFO @ Sat, 24 Aug 2019 17:31:55: Done! pass1 - making usageList (90 chroms): 10 millis pass2 - checking and writing primary data (23147 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:31:57: 6000000 INFO @ Sat, 24 Aug 2019 17:31:57: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:31:57: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:31:57: #1 total tags in treatment: 8434734 INFO @ Sat, 24 Aug 2019 17:31:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:31:57: #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 17:31:57: #1 tags after filtering in treatment: 8434469 INFO @ Sat, 24 Aug 2019 17:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:31:57: #1 finished! INFO @ Sat, 24 Aug 2019 17:31:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:32:01: #2 number of paired peaks: 97030 INFO @ Sat, 24 Aug 2019 17:32:01: start model_add_line... INFO @ Sat, 24 Aug 2019 17:32:02: start X-correlation... INFO @ Sat, 24 Aug 2019 17:32:02: end of X-cor INFO @ Sat, 24 Aug 2019 17:32:02: #2 finished! INFO @ Sat, 24 Aug 2019 17:32:02: #2 predicted fragment length is 168 bps INFO @ Sat, 24 Aug 2019 17:32:02: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 24 Aug 2019 17:32:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.10_model.r INFO @ Sat, 24 Aug 2019 17:32:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:32:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:32:04: 7000000 INFO @ Sat, 24 Aug 2019 17:32:12: 8000000 INFO @ Sat, 24 Aug 2019 17:32:15: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:32:15: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:32:15: #1 total tags in treatment: 8434734 INFO @ Sat, 24 Aug 2019 17:32:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:32:15: #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 17:32:15: #1 tags after filtering in treatment: 8434469 INFO @ Sat, 24 Aug 2019 17:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:32:15: #1 finished! INFO @ Sat, 24 Aug 2019 17:32:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:32:19: #2 number of paired peaks: 97030 INFO @ Sat, 24 Aug 2019 17:32:19: start model_add_line... INFO @ Sat, 24 Aug 2019 17:32:19: start X-correlation... INFO @ Sat, 24 Aug 2019 17:32:19: end of X-cor INFO @ Sat, 24 Aug 2019 17:32:19: #2 finished! INFO @ Sat, 24 Aug 2019 17:32:19: #2 predicted fragment length is 168 bps INFO @ Sat, 24 Aug 2019 17:32:19: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 24 Aug 2019 17:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.20_model.r INFO @ Sat, 24 Aug 2019 17:32:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:32:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:32:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:32:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:32:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.10_summits.bed INFO @ Sat, 24 Aug 2019 17:32:42: Done! pass1 - making usageList (60 chroms): 5 millis pass2 - checking and writing primary data (9165 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:32:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374991/SRX5374991.20_summits.bed INFO @ Sat, 24 Aug 2019 17:32:59: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (1318 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。