Job ID = 1301470 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:45:29 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T10:45:29 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra17/SRR/001160/SRR1187974' 2019-06-03T10:45:29 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_table_names( 'SRR1187974' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T10:45:34 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T10:45:34 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra17/SRR/001160/SRR1187974' 2019-06-03T10:45:34 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR1187974' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T10:56:44 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 ) 2019-06-03T10:56:44 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 : 22,256,853 reads read : 22,256,853 reads written : 22,256,853 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: 00:09:30 22256853 reads; of these: 22256853 (100.00%) were unpaired; of these: 1062320 (4.77%) aligned 0 times 12607335 (56.64%) aligned exactly 1 time 8587198 (38.58%) aligned >1 times 95.23% overall alignment rate Time searching: 00:09:30 Overall time: 00:09:30 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] 5981659 / 21194533 = 0.2822 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 20:13:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.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 20:13:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:13:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:13:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.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 20:13:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:13:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:13:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.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 20:13:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:13:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:13:36: 1000000 INFO @ Mon, 03 Jun 2019 20:13:36: 1000000 INFO @ Mon, 03 Jun 2019 20:13:36: 1000000 INFO @ Mon, 03 Jun 2019 20:13:44: 2000000 INFO @ Mon, 03 Jun 2019 20:13:44: 2000000 INFO @ Mon, 03 Jun 2019 20:13:45: 2000000 INFO @ Mon, 03 Jun 2019 20:13:52: 3000000 INFO @ Mon, 03 Jun 2019 20:13:52: 3000000 INFO @ Mon, 03 Jun 2019 20:13:54: 3000000 INFO @ Mon, 03 Jun 2019 20:13:59: 4000000 INFO @ Mon, 03 Jun 2019 20:13:59: 4000000 INFO @ Mon, 03 Jun 2019 20:14:02: 4000000 INFO @ Mon, 03 Jun 2019 20:14:06: 5000000 INFO @ Mon, 03 Jun 2019 20:14:07: 5000000 INFO @ Mon, 03 Jun 2019 20:14:10: 5000000 INFO @ Mon, 03 Jun 2019 20:14:13: 6000000 INFO @ Mon, 03 Jun 2019 20:14:14: 6000000 INFO @ Mon, 03 Jun 2019 20:14:18: 6000000 INFO @ Mon, 03 Jun 2019 20:14:20: 7000000 INFO @ Mon, 03 Jun 2019 20:14:21: 7000000 INFO @ Mon, 03 Jun 2019 20:14:27: 7000000 INFO @ Mon, 03 Jun 2019 20:14:27: 8000000 INFO @ Mon, 03 Jun 2019 20:14:29: 8000000 INFO @ Mon, 03 Jun 2019 20:14:34: 9000000 INFO @ Mon, 03 Jun 2019 20:14:35: 8000000 INFO @ Mon, 03 Jun 2019 20:14:37: 9000000 INFO @ Mon, 03 Jun 2019 20:14:41: 10000000 INFO @ Mon, 03 Jun 2019 20:14:43: 9000000 INFO @ Mon, 03 Jun 2019 20:14:45: 10000000 INFO @ Mon, 03 Jun 2019 20:14:48: 11000000 INFO @ Mon, 03 Jun 2019 20:14:52: 10000000 INFO @ Mon, 03 Jun 2019 20:14:52: 11000000 INFO @ Mon, 03 Jun 2019 20:14:56: 12000000 INFO @ Mon, 03 Jun 2019 20:15:00: 12000000 INFO @ Mon, 03 Jun 2019 20:15:00: 11000000 INFO @ Mon, 03 Jun 2019 20:15:03: 13000000 INFO @ Mon, 03 Jun 2019 20:15:07: 13000000 INFO @ Mon, 03 Jun 2019 20:15:08: 12000000 INFO @ Mon, 03 Jun 2019 20:15:10: 14000000 INFO @ Mon, 03 Jun 2019 20:15:14: 14000000 INFO @ Mon, 03 Jun 2019 20:15:16: 13000000 INFO @ Mon, 03 Jun 2019 20:15:17: 15000000 INFO @ Mon, 03 Jun 2019 20:15:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:15:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:15:18: #1 total tags in treatment: 15212874 INFO @ Mon, 03 Jun 2019 20:15:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:15:18: #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 20:15:19: #1 tags after filtering in treatment: 15212874 INFO @ Mon, 03 Jun 2019 20:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:15:19: #1 finished! INFO @ Mon, 03 Jun 2019 20:15:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:15:20: #2 number of paired peaks: 1333 INFO @ Mon, 03 Jun 2019 20:15:20: start model_add_line... INFO @ Mon, 03 Jun 2019 20:15:20: start X-correlation... INFO @ Mon, 03 Jun 2019 20:15:20: end of X-cor INFO @ Mon, 03 Jun 2019 20:15:20: #2 finished! INFO @ Mon, 03 Jun 2019 20:15:20: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 20:15:20: #2 alternative fragment length(s) may be 179 bps INFO @ Mon, 03 Jun 2019 20:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.20_model.r INFO @ Mon, 03 Jun 2019 20:15:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:15:21: 15000000 INFO @ Mon, 03 Jun 2019 20:15:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:15:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:15:23: #1 total tags in treatment: 15212874 INFO @ Mon, 03 Jun 2019 20:15:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:15:23: #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 20:15:23: #1 tags after filtering in treatment: 15212874 INFO @ Mon, 03 Jun 2019 20:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:15:23: #1 finished! INFO @ Mon, 03 Jun 2019 20:15:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:15:24: 14000000 INFO @ Mon, 03 Jun 2019 20:15:24: #2 number of paired peaks: 1333 INFO @ Mon, 03 Jun 2019 20:15:24: start model_add_line... INFO @ Mon, 03 Jun 2019 20:15:25: start X-correlation... INFO @ Mon, 03 Jun 2019 20:15:25: end of X-cor INFO @ Mon, 03 Jun 2019 20:15:25: #2 finished! INFO @ Mon, 03 Jun 2019 20:15:25: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 20:15:25: #2 alternative fragment length(s) may be 179 bps INFO @ Mon, 03 Jun 2019 20:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.10_model.r INFO @ Mon, 03 Jun 2019 20:15:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:15:32: 15000000 INFO @ Mon, 03 Jun 2019 20:15:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:15:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:15:34: #1 total tags in treatment: 15212874 INFO @ Mon, 03 Jun 2019 20:15:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:15:34: #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 20:15:34: #1 tags after filtering in treatment: 15212874 INFO @ Mon, 03 Jun 2019 20:15:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:15:34: #1 finished! INFO @ Mon, 03 Jun 2019 20:15:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:15:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:15:36: #2 number of paired peaks: 1333 INFO @ Mon, 03 Jun 2019 20:15:36: start model_add_line... INFO @ Mon, 03 Jun 2019 20:15:36: start X-correlation... INFO @ Mon, 03 Jun 2019 20:15:36: end of X-cor INFO @ Mon, 03 Jun 2019 20:15:36: #2 finished! INFO @ Mon, 03 Jun 2019 20:15:36: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 20:15:36: #2 alternative fragment length(s) may be 179 bps INFO @ Mon, 03 Jun 2019 20:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.05_model.r INFO @ Mon, 03 Jun 2019 20:15:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:16:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:16:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:16:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:16:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:16:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:16:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.20_summits.bed INFO @ Mon, 03 Jun 2019 20:16:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3568 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.10_summits.bed INFO @ Mon, 03 Jun 2019 20:16:33: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7859 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:16:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485216/SRX485216.05_summits.bed INFO @ Mon, 03 Jun 2019 20:16:45: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (13644 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。