Job ID = 2001134 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:18:16 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-04T18:18:16 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR022309/ERR022309.1' 2019-07-04T18:18:16 fasterq-dump.2.9.6 err: invalid accession 'ERR022309' 2019-07-04T18:18:31 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-04T18:18:31 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR022309/ERR022309.1' 2019-07-04T18:18:31 fasterq-dump.2.9.6 err: invalid accession 'ERR022309' spots read : 30,917,716 reads read : 30,917,716 reads written : 30,917,716 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR022309.sra.cache’: 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:14 30917716 reads; of these: 30917716 (100.00%) were unpaired; of these: 1288948 (4.17%) aligned 0 times 21397024 (69.21%) aligned exactly 1 time 8231744 (26.62%) aligned >1 times 95.83% overall alignment rate Time searching: 00:12:18 Overall time: 00:12:18 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] 3027005 / 29628768 = 0.1022 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 @ Fri, 05 Jul 2019 03:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.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 @ Fri, 05 Jul 2019 03:42:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:42:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.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 @ Fri, 05 Jul 2019 03:42:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:42:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:42:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.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 @ Fri, 05 Jul 2019 03:42:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:42:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:42:46: 1000000 INFO @ Fri, 05 Jul 2019 03:42:47: 1000000 INFO @ Fri, 05 Jul 2019 03:42:48: 1000000 INFO @ Fri, 05 Jul 2019 03:42:53: 2000000 INFO @ Fri, 05 Jul 2019 03:42:54: 2000000 INFO @ Fri, 05 Jul 2019 03:42:55: 2000000 INFO @ Fri, 05 Jul 2019 03:43:01: 3000000 INFO @ Fri, 05 Jul 2019 03:43:02: 3000000 INFO @ Fri, 05 Jul 2019 03:43:02: 3000000 INFO @ Fri, 05 Jul 2019 03:43:08: 4000000 INFO @ Fri, 05 Jul 2019 03:43:08: 4000000 INFO @ Fri, 05 Jul 2019 03:43:09: 4000000 INFO @ Fri, 05 Jul 2019 03:43:15: 5000000 INFO @ Fri, 05 Jul 2019 03:43:15: 5000000 INFO @ Fri, 05 Jul 2019 03:43:17: 5000000 INFO @ Fri, 05 Jul 2019 03:43:22: 6000000 INFO @ Fri, 05 Jul 2019 03:43:23: 6000000 INFO @ Fri, 05 Jul 2019 03:43:24: 6000000 INFO @ Fri, 05 Jul 2019 03:43:29: 7000000 INFO @ Fri, 05 Jul 2019 03:43:31: 7000000 INFO @ Fri, 05 Jul 2019 03:43:32: 7000000 INFO @ Fri, 05 Jul 2019 03:43:36: 8000000 INFO @ Fri, 05 Jul 2019 03:43:39: 8000000 INFO @ Fri, 05 Jul 2019 03:43:40: 8000000 INFO @ Fri, 05 Jul 2019 03:43:42: 9000000 INFO @ Fri, 05 Jul 2019 03:43:47: 9000000 INFO @ Fri, 05 Jul 2019 03:43:48: 9000000 INFO @ Fri, 05 Jul 2019 03:43:49: 10000000 INFO @ Fri, 05 Jul 2019 03:43:55: 10000000 INFO @ Fri, 05 Jul 2019 03:43:56: 11000000 INFO @ Fri, 05 Jul 2019 03:43:56: 10000000 INFO @ Fri, 05 Jul 2019 03:44:02: 12000000 INFO @ Fri, 05 Jul 2019 03:44:03: 11000000 INFO @ Fri, 05 Jul 2019 03:44:04: 11000000 INFO @ Fri, 05 Jul 2019 03:44:09: 13000000 INFO @ Fri, 05 Jul 2019 03:44:11: 12000000 INFO @ Fri, 05 Jul 2019 03:44:12: 12000000 INFO @ Fri, 05 Jul 2019 03:44:16: 14000000 INFO @ Fri, 05 Jul 2019 03:44:19: 13000000 INFO @ Fri, 05 Jul 2019 03:44:20: 13000000 INFO @ Fri, 05 Jul 2019 03:44:23: 15000000 INFO @ Fri, 05 Jul 2019 03:44:27: 14000000 INFO @ Fri, 05 Jul 2019 03:44:28: 14000000 INFO @ Fri, 05 Jul 2019 03:44:30: 16000000 INFO @ Fri, 05 Jul 2019 03:44:35: 15000000 INFO @ Fri, 05 Jul 2019 03:44:36: 15000000 INFO @ Fri, 05 Jul 2019 03:44:37: 17000000 INFO @ Fri, 05 Jul 2019 03:44:43: 16000000 INFO @ Fri, 05 Jul 2019 03:44:44: 18000000 INFO @ Fri, 05 Jul 2019 03:44:44: 16000000 INFO @ Fri, 05 Jul 2019 03:44:52: 19000000 INFO @ Fri, 05 Jul 2019 03:44:52: 17000000 INFO @ Fri, 05 Jul 2019 03:44:53: 17000000 INFO @ Fri, 05 Jul 2019 03:44:59: 20000000 INFO @ Fri, 05 Jul 2019 03:45:00: 18000000 INFO @ Fri, 05 Jul 2019 03:45:01: 18000000 INFO @ Fri, 05 Jul 2019 03:45:07: 21000000 INFO @ Fri, 05 Jul 2019 03:45:08: 19000000 INFO @ Fri, 05 Jul 2019 03:45:09: 19000000 INFO @ Fri, 05 Jul 2019 03:45:14: 22000000 INFO @ Fri, 05 Jul 2019 03:45:17: 20000000 INFO @ Fri, 05 Jul 2019 03:45:18: 20000000 INFO @ Fri, 05 Jul 2019 03:45:21: 23000000 INFO @ Fri, 05 Jul 2019 03:45:25: 21000000 INFO @ Fri, 05 Jul 2019 03:45:26: 21000000 INFO @ Fri, 05 Jul 2019 03:45:29: 24000000 INFO @ Fri, 05 Jul 2019 03:45:33: 22000000 INFO @ Fri, 05 Jul 2019 03:45:34: 22000000 INFO @ Fri, 05 Jul 2019 03:45:36: 25000000 INFO @ Fri, 05 Jul 2019 03:45:41: 23000000 INFO @ Fri, 05 Jul 2019 03:45:42: 23000000 INFO @ Fri, 05 Jul 2019 03:45:44: 26000000 INFO @ Fri, 05 Jul 2019 03:45:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:49: #1 total tags in treatment: 26601763 INFO @ Fri, 05 Jul 2019 03:45:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 03:45:49: 24000000 INFO @ Fri, 05 Jul 2019 03:45:50: #1 tags after filtering in treatment: 26601641 INFO @ Fri, 05 Jul 2019 03:45:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:50: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:51: 24000000 INFO @ Fri, 05 Jul 2019 03:45:54: #2 number of paired peaks: 37367 INFO @ Fri, 05 Jul 2019 03:45:54: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:55: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:55: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:55: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:55: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 03:45:55: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 05 Jul 2019 03:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.20_model.r INFO @ Fri, 05 Jul 2019 03:45:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:57: 25000000 INFO @ Fri, 05 Jul 2019 03:45:58: 25000000 INFO @ Fri, 05 Jul 2019 03:46:04: 26000000 INFO @ Fri, 05 Jul 2019 03:46:05: 26000000 INFO @ Fri, 05 Jul 2019 03:46:08: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:46:08: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:46:08: #1 total tags in treatment: 26601763 INFO @ Fri, 05 Jul 2019 03:46:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:46:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 03:46:09: #1 tags after filtering in treatment: 26601641 INFO @ Fri, 05 Jul 2019 03:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:46:09: #1 finished! INFO @ Fri, 05 Jul 2019 03:46:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:46:10: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:46:10: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:46:10: #1 total tags in treatment: 26601763 INFO @ Fri, 05 Jul 2019 03:46:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:46:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 03:46:10: #1 tags after filtering in treatment: 26601641 INFO @ Fri, 05 Jul 2019 03:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:46:10: #1 finished! INFO @ Fri, 05 Jul 2019 03:46:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:46:14: #2 number of paired peaks: 37367 INFO @ Fri, 05 Jul 2019 03:46:14: start model_add_line... INFO @ Fri, 05 Jul 2019 03:46:14: start X-correlation... INFO @ Fri, 05 Jul 2019 03:46:14: end of X-cor INFO @ Fri, 05 Jul 2019 03:46:14: #2 finished! INFO @ Fri, 05 Jul 2019 03:46:14: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 03:46:14: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 05 Jul 2019 03:46:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.05_model.r INFO @ Fri, 05 Jul 2019 03:46:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:46:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:46:15: #2 number of paired peaks: 37367 INFO @ Fri, 05 Jul 2019 03:46:15: start model_add_line... INFO @ Fri, 05 Jul 2019 03:46:15: start X-correlation... INFO @ Fri, 05 Jul 2019 03:46:15: end of X-cor INFO @ Fri, 05 Jul 2019 03:46:15: #2 finished! INFO @ Fri, 05 Jul 2019 03:46:15: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 03:46:15: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 05 Jul 2019 03:46:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.10_model.r INFO @ Fri, 05 Jul 2019 03:46:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:47:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:48:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.20_peaks.xls INFO @ Fri, 05 Jul 2019 03:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.20_summits.bed INFO @ Fri, 05 Jul 2019 03:48:08: Done! pass1 - making usageList (104 chroms): 6 millis pass2 - checking and writing primary data (24940 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:48:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.10_peaks.xls INFO @ Fri, 05 Jul 2019 03:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.10_summits.bed INFO @ Fri, 05 Jul 2019 03:48:32: Done! pass1 - making usageList (132 chroms): 12 millis pass2 - checking and writing primary data (32383 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.05_peaks.xls INFO @ Fri, 05 Jul 2019 03:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:48:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008724/ERX008724.05_summits.bed INFO @ Fri, 05 Jul 2019 03:48:35: Done! pass1 - making usageList (166 chroms): 8 millis pass2 - checking and writing primary data (40241 records, 4 fields): 57 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。