Job ID = 2001136 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-1/ERR022308/ERR022308.1' 2019-07-04T18:18:16 fasterq-dump.2.9.6 err: invalid accession 'ERR022308' 2019-07-04T18:18:32 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' 2019-07-04T18:18:32 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-1/ERR022308/ERR022308.1' 2019-07-04T18:18:32 fasterq-dump.2.9.6 err: invalid accession 'ERR022308' spots read : 31,589,944 reads read : 31,589,944 reads written : 31,589,944 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR022308.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:02 31589944 reads; of these: 31589944 (100.00%) were unpaired; of these: 1266633 (4.01%) aligned 0 times 22150261 (70.12%) aligned exactly 1 time 8173050 (25.87%) aligned >1 times 95.99% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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] 3751197 / 30323311 = 0.1237 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 03:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.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 03:41:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.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 03:41:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.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 03:41:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:55: 1000000 INFO @ Fri, 05 Jul 2019 03:41:55: 1000000 INFO @ Fri, 05 Jul 2019 03:41:56: 1000000 INFO @ Fri, 05 Jul 2019 03:42:02: 2000000 INFO @ Fri, 05 Jul 2019 03:42:02: 2000000 INFO @ Fri, 05 Jul 2019 03:42:04: 2000000 INFO @ Fri, 05 Jul 2019 03:42:09: 3000000 INFO @ Fri, 05 Jul 2019 03:42:09: 3000000 INFO @ Fri, 05 Jul 2019 03:42:11: 3000000 INFO @ Fri, 05 Jul 2019 03:42:16: 4000000 INFO @ Fri, 05 Jul 2019 03:42:16: 4000000 INFO @ Fri, 05 Jul 2019 03:42:19: 4000000 INFO @ Fri, 05 Jul 2019 03:42:24: 5000000 INFO @ Fri, 05 Jul 2019 03:42:24: 5000000 INFO @ Fri, 05 Jul 2019 03:42:27: 5000000 INFO @ Fri, 05 Jul 2019 03:42:31: 6000000 INFO @ Fri, 05 Jul 2019 03:42:31: 6000000 INFO @ Fri, 05 Jul 2019 03:42:35: 6000000 INFO @ Fri, 05 Jul 2019 03:42:38: 7000000 INFO @ Fri, 05 Jul 2019 03:42:38: 7000000 INFO @ Fri, 05 Jul 2019 03:42:43: 7000000 INFO @ Fri, 05 Jul 2019 03:42:46: 8000000 INFO @ Fri, 05 Jul 2019 03:42:46: 8000000 INFO @ Fri, 05 Jul 2019 03:42:50: 8000000 INFO @ Fri, 05 Jul 2019 03:42:53: 9000000 INFO @ Fri, 05 Jul 2019 03:42:53: 9000000 INFO @ Fri, 05 Jul 2019 03:42:58: 9000000 INFO @ Fri, 05 Jul 2019 03:43:00: 10000000 INFO @ Fri, 05 Jul 2019 03:43:00: 10000000 INFO @ Fri, 05 Jul 2019 03:43:06: 10000000 INFO @ Fri, 05 Jul 2019 03:43:07: 11000000 INFO @ Fri, 05 Jul 2019 03:43:07: 11000000 INFO @ Fri, 05 Jul 2019 03:43:14: 12000000 INFO @ Fri, 05 Jul 2019 03:43:14: 12000000 INFO @ Fri, 05 Jul 2019 03:43:14: 11000000 INFO @ Fri, 05 Jul 2019 03:43:21: 13000000 INFO @ Fri, 05 Jul 2019 03:43:21: 13000000 INFO @ Fri, 05 Jul 2019 03:43:22: 12000000 INFO @ Fri, 05 Jul 2019 03:43:28: 14000000 INFO @ Fri, 05 Jul 2019 03:43:28: 14000000 INFO @ Fri, 05 Jul 2019 03:43:30: 13000000 INFO @ Fri, 05 Jul 2019 03:43:35: 15000000 INFO @ Fri, 05 Jul 2019 03:43:35: 15000000 INFO @ Fri, 05 Jul 2019 03:43:38: 14000000 INFO @ Fri, 05 Jul 2019 03:43:42: 16000000 INFO @ Fri, 05 Jul 2019 03:43:43: 16000000 INFO @ Fri, 05 Jul 2019 03:43:46: 15000000 INFO @ Fri, 05 Jul 2019 03:43:50: 17000000 INFO @ Fri, 05 Jul 2019 03:43:50: 17000000 INFO @ Fri, 05 Jul 2019 03:43:54: 16000000 INFO @ Fri, 05 Jul 2019 03:43:57: 18000000 INFO @ Fri, 05 Jul 2019 03:43:57: 18000000 INFO @ Fri, 05 Jul 2019 03:44:02: 17000000 INFO @ Fri, 05 Jul 2019 03:44:04: 19000000 INFO @ Fri, 05 Jul 2019 03:44:04: 19000000 INFO @ Fri, 05 Jul 2019 03:44:09: 18000000 INFO @ Fri, 05 Jul 2019 03:44:11: 20000000 INFO @ Fri, 05 Jul 2019 03:44:11: 20000000 INFO @ Fri, 05 Jul 2019 03:44:17: 19000000 INFO @ Fri, 05 Jul 2019 03:44:18: 21000000 INFO @ Fri, 05 Jul 2019 03:44:19: 21000000 INFO @ Fri, 05 Jul 2019 03:44:25: 22000000 INFO @ Fri, 05 Jul 2019 03:44:25: 20000000 INFO @ Fri, 05 Jul 2019 03:44:26: 22000000 INFO @ Fri, 05 Jul 2019 03:44:32: 23000000 INFO @ Fri, 05 Jul 2019 03:44:33: 21000000 INFO @ Fri, 05 Jul 2019 03:44:33: 23000000 INFO @ Fri, 05 Jul 2019 03:44:39: 24000000 INFO @ Fri, 05 Jul 2019 03:44:40: 24000000 INFO @ Fri, 05 Jul 2019 03:44:41: 22000000 INFO @ Fri, 05 Jul 2019 03:44:46: 25000000 INFO @ Fri, 05 Jul 2019 03:44:48: 25000000 INFO @ Fri, 05 Jul 2019 03:44:49: 23000000 INFO @ Fri, 05 Jul 2019 03:44:53: 26000000 INFO @ Fri, 05 Jul 2019 03:44:55: 26000000 INFO @ Fri, 05 Jul 2019 03:44:57: 24000000 INFO @ Fri, 05 Jul 2019 03:44:58: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:44:58: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:44:58: #1 total tags in treatment: 26572114 INFO @ Fri, 05 Jul 2019 03:44:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:44:58: #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 03:44:58: #1 tags after filtering in treatment: 26572021 INFO @ Fri, 05 Jul 2019 03:44:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:44:58: #1 finished! INFO @ Fri, 05 Jul 2019 03:44:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:00: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:00: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:00: #1 total tags in treatment: 26572114 INFO @ Fri, 05 Jul 2019 03:45:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:00: #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 03:45:00: #1 tags after filtering in treatment: 26572021 INFO @ Fri, 05 Jul 2019 03:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:00: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:03: #2 number of paired peaks: 41321 INFO @ Fri, 05 Jul 2019 03:45:03: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:03: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:03: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:03: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:03: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 03:45:03: #2 alternative fragment length(s) may be 106 bps INFO @ Fri, 05 Jul 2019 03:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.20_model.r INFO @ Fri, 05 Jul 2019 03:45:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:04: 25000000 INFO @ Fri, 05 Jul 2019 03:45:05: #2 number of paired peaks: 41321 INFO @ Fri, 05 Jul 2019 03:45:05: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:05: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:05: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:05: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:05: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 03:45:05: #2 alternative fragment length(s) may be 106 bps INFO @ Fri, 05 Jul 2019 03:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.10_model.r INFO @ Fri, 05 Jul 2019 03:45:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:12: 26000000 INFO @ Fri, 05 Jul 2019 03:45:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:17: #1 total tags in treatment: 26572114 INFO @ Fri, 05 Jul 2019 03:45:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:17: #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 03:45:18: #1 tags after filtering in treatment: 26572021 INFO @ Fri, 05 Jul 2019 03:45:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:18: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:22: #2 number of paired peaks: 41321 INFO @ Fri, 05 Jul 2019 03:45:22: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:23: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:23: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:23: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:23: #2 predicted fragment length is 106 bps INFO @ Fri, 05 Jul 2019 03:45:23: #2 alternative fragment length(s) may be 106 bps INFO @ Fri, 05 Jul 2019 03:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.05_model.r INFO @ Fri, 05 Jul 2019 03:45:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:46:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:46:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:46:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.20_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.20_summits.bed INFO @ Fri, 05 Jul 2019 03:47:09: Done! pass1 - making usageList (116 chroms): 11 millis pass2 - checking and writing primary data (28242 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:47:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.10_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.10_summits.bed INFO @ Fri, 05 Jul 2019 03:47:11: Done! pass1 - making usageList (154 chroms): 8 millis pass2 - checking and writing primary data (35967 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.05_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008733/ERX008733.05_summits.bed INFO @ Fri, 05 Jul 2019 03:47:29: Done! pass1 - making usageList (187 chroms): 9 millis pass2 - checking and writing primary data (44427 records, 4 fields): 63 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。