Job ID = 2001135 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:18:17 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' 2019-07-04T18:18:17 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/ERR022310/ERR022310.1' 2019-07-04T18:18:17 fasterq-dump.2.9.6 err: invalid accession 'ERR022310' 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-2/ERR022310/ERR022310.1' 2019-07-04T18:18:32 fasterq-dump.2.9.6 err: invalid accession 'ERR022310' spots read : 29,433,011 reads read : 29,433,011 reads written : 29,433,011 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR022310.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: 00:11:23 29433011 reads; of these: 29433011 (100.00%) were unpaired; of these: 729726 (2.48%) aligned 0 times 20191351 (68.60%) aligned exactly 1 time 8511934 (28.92%) aligned >1 times 97.52% overall alignment rate Time searching: 00:11:27 Overall time: 00:11:27 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] 1483541 / 28703285 = 0.0517 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 03:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.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 03:41:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.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 03:41:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.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 03:41:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:41:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:41:26: 1000000 INFO @ Fri, 05 Jul 2019 03:41:27: 1000000 INFO @ Fri, 05 Jul 2019 03:41:29: 1000000 INFO @ Fri, 05 Jul 2019 03:41:34: 2000000 INFO @ Fri, 05 Jul 2019 03:41:36: 2000000 INFO @ Fri, 05 Jul 2019 03:41:39: 2000000 INFO @ Fri, 05 Jul 2019 03:41:43: 3000000 INFO @ Fri, 05 Jul 2019 03:41:45: 3000000 INFO @ Fri, 05 Jul 2019 03:41:49: 3000000 INFO @ Fri, 05 Jul 2019 03:41:52: 4000000 INFO @ Fri, 05 Jul 2019 03:41:54: 4000000 INFO @ Fri, 05 Jul 2019 03:41:59: 4000000 INFO @ Fri, 05 Jul 2019 03:42:01: 5000000 INFO @ Fri, 05 Jul 2019 03:42:03: 5000000 INFO @ Fri, 05 Jul 2019 03:42:09: 5000000 INFO @ Fri, 05 Jul 2019 03:42:10: 6000000 INFO @ Fri, 05 Jul 2019 03:42:13: 6000000 INFO @ Fri, 05 Jul 2019 03:42:19: 7000000 INFO @ Fri, 05 Jul 2019 03:42:20: 6000000 INFO @ Fri, 05 Jul 2019 03:42:22: 7000000 INFO @ Fri, 05 Jul 2019 03:42:28: 8000000 INFO @ Fri, 05 Jul 2019 03:42:32: 8000000 INFO @ Fri, 05 Jul 2019 03:42:32: 7000000 INFO @ Fri, 05 Jul 2019 03:42:37: 9000000 INFO @ Fri, 05 Jul 2019 03:42:41: 9000000 INFO @ Fri, 05 Jul 2019 03:42:43: 8000000 INFO @ Fri, 05 Jul 2019 03:42:46: 10000000 INFO @ Fri, 05 Jul 2019 03:42:50: 10000000 INFO @ Fri, 05 Jul 2019 03:42:54: 9000000 INFO @ Fri, 05 Jul 2019 03:42:54: 11000000 INFO @ Fri, 05 Jul 2019 03:42:58: 11000000 INFO @ Fri, 05 Jul 2019 03:43:02: 12000000 INFO @ Fri, 05 Jul 2019 03:43:04: 10000000 INFO @ Fri, 05 Jul 2019 03:43:06: 12000000 INFO @ Fri, 05 Jul 2019 03:43:09: 13000000 INFO @ Fri, 05 Jul 2019 03:43:13: 13000000 INFO @ Fri, 05 Jul 2019 03:43:14: 11000000 INFO @ Fri, 05 Jul 2019 03:43:18: 14000000 INFO @ Fri, 05 Jul 2019 03:43:21: 14000000 INFO @ Fri, 05 Jul 2019 03:43:23: 12000000 INFO @ Fri, 05 Jul 2019 03:43:26: 15000000 INFO @ Fri, 05 Jul 2019 03:43:29: 15000000 INFO @ Fri, 05 Jul 2019 03:43:34: 13000000 INFO @ Fri, 05 Jul 2019 03:43:34: 16000000 INFO @ Fri, 05 Jul 2019 03:43:38: 16000000 INFO @ Fri, 05 Jul 2019 03:43:42: 17000000 INFO @ Fri, 05 Jul 2019 03:43:44: 14000000 INFO @ Fri, 05 Jul 2019 03:43:46: 17000000 INFO @ Fri, 05 Jul 2019 03:43:51: 18000000 INFO @ Fri, 05 Jul 2019 03:43:54: 18000000 INFO @ Fri, 05 Jul 2019 03:43:55: 15000000 INFO @ Fri, 05 Jul 2019 03:43:59: 19000000 INFO @ Fri, 05 Jul 2019 03:44:02: 19000000 INFO @ Fri, 05 Jul 2019 03:44:05: 16000000 INFO @ Fri, 05 Jul 2019 03:44:07: 20000000 INFO @ Fri, 05 Jul 2019 03:44:11: 20000000 INFO @ Fri, 05 Jul 2019 03:44:14: 17000000 INFO @ Fri, 05 Jul 2019 03:44:15: 21000000 INFO @ Fri, 05 Jul 2019 03:44:19: 21000000 INFO @ Fri, 05 Jul 2019 03:44:23: 22000000 INFO @ Fri, 05 Jul 2019 03:44:24: 18000000 INFO @ Fri, 05 Jul 2019 03:44:27: 22000000 INFO @ Fri, 05 Jul 2019 03:44:32: 23000000 INFO @ Fri, 05 Jul 2019 03:44:34: 19000000 INFO @ Fri, 05 Jul 2019 03:44:35: 23000000 INFO @ Fri, 05 Jul 2019 03:44:40: 24000000 INFO @ Fri, 05 Jul 2019 03:44:44: 24000000 INFO @ Fri, 05 Jul 2019 03:44:44: 20000000 INFO @ Fri, 05 Jul 2019 03:44:48: 25000000 INFO @ Fri, 05 Jul 2019 03:44:52: 25000000 INFO @ Fri, 05 Jul 2019 03:44:54: 21000000 INFO @ Fri, 05 Jul 2019 03:44:56: 26000000 INFO @ Fri, 05 Jul 2019 03:45:00: 26000000 INFO @ Fri, 05 Jul 2019 03:45:04: 27000000 INFO @ Fri, 05 Jul 2019 03:45:04: 22000000 INFO @ Fri, 05 Jul 2019 03:45:06: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:06: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:06: #1 total tags in treatment: 27219744 INFO @ Fri, 05 Jul 2019 03:45:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:06: #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 03:45:07: #1 tags after filtering in treatment: 27219647 INFO @ Fri, 05 Jul 2019 03:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:07: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:08: 27000000 INFO @ Fri, 05 Jul 2019 03:45:10: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:10: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:10: #1 total tags in treatment: 27219744 INFO @ Fri, 05 Jul 2019 03:45:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:10: #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 03:45:11: #1 tags after filtering in treatment: 27219647 INFO @ Fri, 05 Jul 2019 03:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:11: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:11: #2 number of paired peaks: 7965 INFO @ Fri, 05 Jul 2019 03:45:11: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:11: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:11: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:11: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:11: #2 predicted fragment length is 42 bps INFO @ Fri, 05 Jul 2019 03:45:11: #2 alternative fragment length(s) may be 42,77 bps INFO @ Fri, 05 Jul 2019 03:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.05_model.r WARNING @ Fri, 05 Jul 2019 03:45:11: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:45:11: #2 You may need to consider one of the other alternative d(s): 42,77 WARNING @ Fri, 05 Jul 2019 03:45:11: #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 03:45:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:14: 23000000 INFO @ Fri, 05 Jul 2019 03:45:14: #2 number of paired peaks: 7965 INFO @ Fri, 05 Jul 2019 03:45:14: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:15: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:15: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:15: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:15: #2 predicted fragment length is 42 bps INFO @ Fri, 05 Jul 2019 03:45:15: #2 alternative fragment length(s) may be 42,77 bps INFO @ Fri, 05 Jul 2019 03:45:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.10_model.r WARNING @ Fri, 05 Jul 2019 03:45:15: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:45:15: #2 You may need to consider one of the other alternative d(s): 42,77 WARNING @ Fri, 05 Jul 2019 03:45:15: #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 03:45:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:24: 24000000 INFO @ Fri, 05 Jul 2019 03:45:33: 25000000 INFO @ Fri, 05 Jul 2019 03:45:43: 26000000 INFO @ Fri, 05 Jul 2019 03:45:51: 27000000 INFO @ Fri, 05 Jul 2019 03:45:53: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:53: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:53: #1 total tags in treatment: 27219744 INFO @ Fri, 05 Jul 2019 03:45:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:53: #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 03:45:54: #1 tags after filtering in treatment: 27219647 INFO @ Fri, 05 Jul 2019 03:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:54: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:58: #2 number of paired peaks: 7965 INFO @ Fri, 05 Jul 2019 03:45:58: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:58: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:58: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:58: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:58: #2 predicted fragment length is 42 bps INFO @ Fri, 05 Jul 2019 03:45:58: #2 alternative fragment length(s) may be 42,77 bps INFO @ Fri, 05 Jul 2019 03:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.20_model.r WARNING @ Fri, 05 Jul 2019 03:45:58: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:45:58: #2 You may need to consider one of the other alternative d(s): 42,77 WARNING @ Fri, 05 Jul 2019 03:45:58: #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 03:45:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:46:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:46:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.05_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.05_summits.bed INFO @ Fri, 05 Jul 2019 03:47:24: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (2633 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:47:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.10_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.10_summits.bed INFO @ Fri, 05 Jul 2019 03:47:27: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1144 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.20_peaks.xls INFO @ Fri, 05 Jul 2019 03:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX008727/ERX008727.20_summits.bed INFO @ Fri, 05 Jul 2019 03:48:11: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (468 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。