Job ID = 2001137 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:18:31 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/ERR022311/ERR022311.1' 2019-07-04T18:18:31 fasterq-dump.2.9.6 err: invalid accession 'ERR022311' spots read : 28,444,779 reads read : 28,444,779 reads written : 28,444,779 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR022311.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: 00:11:08 28444779 reads; of these: 28444779 (100.00%) were unpaired; of these: 4610892 (16.21%) aligned 0 times 16692788 (58.68%) aligned exactly 1 time 7141099 (25.11%) aligned >1 times 83.79% overall alignment rate Time searching: 00:11:12 Overall time: 00:11:13 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] 409645 / 23833887 = 0.0172 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 03:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.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 03:41:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.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 03:41:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.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 03:41:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:37: 1000000 INFO @ Fri, 05 Jul 2019 03:41:38: 1000000 INFO @ Fri, 05 Jul 2019 03:41:39: 1000000 INFO @ Fri, 05 Jul 2019 03:41:47: 2000000 INFO @ Fri, 05 Jul 2019 03:41:50: 2000000 INFO @ Fri, 05 Jul 2019 03:41:50: 2000000 INFO @ Fri, 05 Jul 2019 03:41:56: 3000000 INFO @ Fri, 05 Jul 2019 03:41:59: 3000000 INFO @ Fri, 05 Jul 2019 03:42:02: 3000000 INFO @ Fri, 05 Jul 2019 03:42:06: 4000000 INFO @ Fri, 05 Jul 2019 03:42:09: 4000000 INFO @ Fri, 05 Jul 2019 03:42:13: 4000000 INFO @ Fri, 05 Jul 2019 03:42:16: 5000000 INFO @ Fri, 05 Jul 2019 03:42:19: 5000000 INFO @ Fri, 05 Jul 2019 03:42:25: 5000000 INFO @ Fri, 05 Jul 2019 03:42:25: 6000000 INFO @ Fri, 05 Jul 2019 03:42:28: 6000000 INFO @ Fri, 05 Jul 2019 03:42:35: 7000000 INFO @ Fri, 05 Jul 2019 03:42:37: 6000000 INFO @ Fri, 05 Jul 2019 03:42:38: 7000000 INFO @ Fri, 05 Jul 2019 03:42:44: 8000000 INFO @ Fri, 05 Jul 2019 03:42:48: 8000000 INFO @ Fri, 05 Jul 2019 03:42:48: 7000000 INFO @ Fri, 05 Jul 2019 03:42:54: 9000000 INFO @ Fri, 05 Jul 2019 03:42:57: 9000000 INFO @ Fri, 05 Jul 2019 03:42:59: 8000000 INFO @ Fri, 05 Jul 2019 03:43:04: 10000000 INFO @ Fri, 05 Jul 2019 03:43:07: 10000000 INFO @ Fri, 05 Jul 2019 03:43:10: 9000000 INFO @ Fri, 05 Jul 2019 03:43:13: 11000000 INFO @ Fri, 05 Jul 2019 03:43:17: 11000000 INFO @ Fri, 05 Jul 2019 03:43:21: 10000000 INFO @ Fri, 05 Jul 2019 03:43:23: 12000000 INFO @ Fri, 05 Jul 2019 03:43:26: 12000000 INFO @ Fri, 05 Jul 2019 03:43:32: 11000000 INFO @ Fri, 05 Jul 2019 03:43:33: 13000000 INFO @ Fri, 05 Jul 2019 03:43:36: 13000000 INFO @ Fri, 05 Jul 2019 03:43:42: 14000000 INFO @ Fri, 05 Jul 2019 03:43:43: 12000000 INFO @ Fri, 05 Jul 2019 03:43:45: 14000000 INFO @ Fri, 05 Jul 2019 03:43:52: 15000000 INFO @ Fri, 05 Jul 2019 03:43:54: 15000000 INFO @ Fri, 05 Jul 2019 03:43:55: 13000000 INFO @ Fri, 05 Jul 2019 03:44:01: 16000000 INFO @ Fri, 05 Jul 2019 03:44:04: 16000000 INFO @ Fri, 05 Jul 2019 03:44:06: 14000000 INFO @ Fri, 05 Jul 2019 03:44:11: 17000000 INFO @ Fri, 05 Jul 2019 03:44:14: 17000000 INFO @ Fri, 05 Jul 2019 03:44:16: 15000000 INFO @ Fri, 05 Jul 2019 03:44:21: 18000000 INFO @ Fri, 05 Jul 2019 03:44:24: 18000000 INFO @ Fri, 05 Jul 2019 03:44:27: 16000000 INFO @ Fri, 05 Jul 2019 03:44:32: 19000000 INFO @ Fri, 05 Jul 2019 03:44:35: 19000000 INFO @ Fri, 05 Jul 2019 03:44:39: 17000000 INFO @ Fri, 05 Jul 2019 03:44:42: 20000000 INFO @ Fri, 05 Jul 2019 03:44:45: 20000000 INFO @ Fri, 05 Jul 2019 03:44:50: 18000000 INFO @ Fri, 05 Jul 2019 03:44:53: 21000000 INFO @ Fri, 05 Jul 2019 03:44:56: 21000000 INFO @ Fri, 05 Jul 2019 03:45:02: 19000000 INFO @ Fri, 05 Jul 2019 03:45:03: 22000000 INFO @ Fri, 05 Jul 2019 03:45:06: 22000000 INFO @ Fri, 05 Jul 2019 03:45:12: 20000000 INFO @ Fri, 05 Jul 2019 03:45:13: 23000000 INFO @ Fri, 05 Jul 2019 03:45:17: 23000000 INFO @ Fri, 05 Jul 2019 03:45:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:18: #1 total tags in treatment: 23424242 INFO @ Fri, 05 Jul 2019 03:45:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:18: #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 03:45:19: #1 tags after filtering in treatment: 23424126 INFO @ Fri, 05 Jul 2019 03:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:19: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:21: #1 total tags in treatment: 23424242 INFO @ Fri, 05 Jul 2019 03:45:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:21: #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 03:45:22: #1 tags after filtering in treatment: 23424126 INFO @ Fri, 05 Jul 2019 03:45:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:22: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:22: #2 number of paired peaks: 5919 INFO @ Fri, 05 Jul 2019 03:45:22: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:22: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:22: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:22: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:22: #2 predicted fragment length is 37 bps INFO @ Fri, 05 Jul 2019 03:45:22: #2 alternative fragment length(s) may be 37,516 bps INFO @ Fri, 05 Jul 2019 03:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.10_model.r WARNING @ Fri, 05 Jul 2019 03:45:22: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:45:22: #2 You may need to consider one of the other alternative d(s): 37,516 WARNING @ Fri, 05 Jul 2019 03:45:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 03:45:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:24: 21000000 INFO @ Fri, 05 Jul 2019 03:45:25: #2 number of paired peaks: 5919 INFO @ Fri, 05 Jul 2019 03:45:25: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:25: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:26: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:26: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:26: #2 predicted fragment length is 37 bps INFO @ Fri, 05 Jul 2019 03:45:26: #2 alternative fragment length(s) may be 37,516 bps INFO @ Fri, 05 Jul 2019 03:45:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.20_model.r WARNING @ Fri, 05 Jul 2019 03:45:26: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:45:26: #2 You may need to consider one of the other alternative d(s): 37,516 WARNING @ Fri, 05 Jul 2019 03:45:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 03:45:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:35: 22000000 INFO @ Fri, 05 Jul 2019 03:45:46: 23000000 INFO @ Fri, 05 Jul 2019 03:45:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:51: #1 total tags in treatment: 23424242 INFO @ Fri, 05 Jul 2019 03:45:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:51: #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 03:45:52: #1 tags after filtering in treatment: 23424126 INFO @ Fri, 05 Jul 2019 03:45:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:52: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:55: #2 number of paired peaks: 5919 INFO @ Fri, 05 Jul 2019 03:45:55: 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 37 bps INFO @ Fri, 05 Jul 2019 03:45:55: #2 alternative fragment length(s) may be 37,516 bps INFO @ Fri, 05 Jul 2019 03:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.05_model.r WARNING @ Fri, 05 Jul 2019 03:45:55: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:45:55: #2 You may need to consider one of the other alternative d(s): 37,516 WARNING @ Fri, 05 Jul 2019 03:45:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. 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 03:46:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:46:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.10_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.10_summits.bed INFO @ Fri, 05 Jul 2019 03:47:27: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (952 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.20_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.20_summits.bed INFO @ Fri, 05 Jul 2019 03:47:33: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.05_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008743/ERX008743.05_summits.bed INFO @ Fri, 05 Jul 2019 03:47:58: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (1817 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。