Job ID = 1294982 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:00:21 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' 2019-06-03T02:00:21 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/sra11/SRR/000849/SRR870228' 2019-06-03T02:00:31 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR870228' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 17,355,751 reads read : 17,355,751 reads written : 17,355,751 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:52 17355751 reads; of these: 17355751 (100.00%) were unpaired; of these: 1036323 (5.97%) aligned 0 times 10820051 (62.34%) aligned exactly 1 time 5499377 (31.69%) aligned >1 times 94.03% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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 8 files... [bam_rmdupse_core] 2522607 / 16319428 = 0.1546 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 11:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.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 11:24:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:24:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.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 11:24:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:24:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.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 11:24:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:24:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:24:30: 1000000 INFO @ Mon, 03 Jun 2019 11:24:31: 1000000 INFO @ Mon, 03 Jun 2019 11:24:31: 1000000 INFO @ Mon, 03 Jun 2019 11:24:38: 2000000 INFO @ Mon, 03 Jun 2019 11:24:39: 2000000 INFO @ Mon, 03 Jun 2019 11:24:39: 2000000 INFO @ Mon, 03 Jun 2019 11:24:46: 3000000 INFO @ Mon, 03 Jun 2019 11:24:46: 3000000 INFO @ Mon, 03 Jun 2019 11:24:47: 3000000 INFO @ Mon, 03 Jun 2019 11:24:54: 4000000 INFO @ Mon, 03 Jun 2019 11:24:54: 4000000 INFO @ Mon, 03 Jun 2019 11:24:55: 4000000 INFO @ Mon, 03 Jun 2019 11:25:01: 5000000 INFO @ Mon, 03 Jun 2019 11:25:02: 5000000 INFO @ Mon, 03 Jun 2019 11:25:04: 5000000 INFO @ Mon, 03 Jun 2019 11:25:09: 6000000 INFO @ Mon, 03 Jun 2019 11:25:10: 6000000 INFO @ Mon, 03 Jun 2019 11:25:12: 6000000 INFO @ Mon, 03 Jun 2019 11:25:18: 7000000 INFO @ Mon, 03 Jun 2019 11:25:18: 7000000 INFO @ Mon, 03 Jun 2019 11:25:20: 7000000 INFO @ Mon, 03 Jun 2019 11:25:25: 8000000 INFO @ Mon, 03 Jun 2019 11:25:26: 8000000 INFO @ Mon, 03 Jun 2019 11:25:28: 8000000 INFO @ Mon, 03 Jun 2019 11:25:33: 9000000 INFO @ Mon, 03 Jun 2019 11:25:35: 9000000 INFO @ Mon, 03 Jun 2019 11:25:37: 9000000 INFO @ Mon, 03 Jun 2019 11:25:41: 10000000 INFO @ Mon, 03 Jun 2019 11:25:43: 10000000 INFO @ Mon, 03 Jun 2019 11:25:46: 10000000 INFO @ Mon, 03 Jun 2019 11:25:49: 11000000 INFO @ Mon, 03 Jun 2019 11:25:53: 11000000 INFO @ Mon, 03 Jun 2019 11:25:55: 11000000 INFO @ Mon, 03 Jun 2019 11:25:57: 12000000 INFO @ Mon, 03 Jun 2019 11:26:02: 12000000 INFO @ Mon, 03 Jun 2019 11:26:04: 12000000 INFO @ Mon, 03 Jun 2019 11:26:05: 13000000 INFO @ Mon, 03 Jun 2019 11:26:11: 13000000 INFO @ Mon, 03 Jun 2019 11:26:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:26:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:26:11: #1 total tags in treatment: 13796821 INFO @ Mon, 03 Jun 2019 11:26:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:26:11: #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 11:26:12: #1 tags after filtering in treatment: 13796821 INFO @ Mon, 03 Jun 2019 11:26:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:26:12: #1 finished! INFO @ Mon, 03 Jun 2019 11:26:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:26:13: #2 number of paired peaks: 294 WARNING @ Mon, 03 Jun 2019 11:26:13: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 03 Jun 2019 11:26:13: start model_add_line... INFO @ Mon, 03 Jun 2019 11:26:13: start X-correlation... INFO @ Mon, 03 Jun 2019 11:26:13: end of X-cor INFO @ Mon, 03 Jun 2019 11:26:13: #2 finished! INFO @ Mon, 03 Jun 2019 11:26:13: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:26:13: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:26:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.20_model.r WARNING @ Mon, 03 Jun 2019 11:26:13: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:26:13: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:26:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:26:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:26:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:26:13: 13000000 INFO @ Mon, 03 Jun 2019 11:26:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:26:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:26:18: #1 total tags in treatment: 13796821 INFO @ Mon, 03 Jun 2019 11:26:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:26:18: #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 11:26:18: #1 tags after filtering in treatment: 13796821 INFO @ Mon, 03 Jun 2019 11:26:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:26:18: #1 finished! INFO @ Mon, 03 Jun 2019 11:26:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:26:19: #2 number of paired peaks: 294 WARNING @ Mon, 03 Jun 2019 11:26:19: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 03 Jun 2019 11:26:19: start model_add_line... INFO @ Mon, 03 Jun 2019 11:26:19: start X-correlation... INFO @ Mon, 03 Jun 2019 11:26:19: end of X-cor INFO @ Mon, 03 Jun 2019 11:26:19: #2 finished! INFO @ Mon, 03 Jun 2019 11:26:19: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:26:19: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.05_model.r WARNING @ Mon, 03 Jun 2019 11:26:19: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:26:19: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:26:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:26:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:26:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:26:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:26:20: #1 total tags in treatment: 13796821 INFO @ Mon, 03 Jun 2019 11:26:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:26:20: #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 11:26:20: #1 tags after filtering in treatment: 13796821 INFO @ Mon, 03 Jun 2019 11:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:26:20: #1 finished! INFO @ Mon, 03 Jun 2019 11:26:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:26:21: #2 number of paired peaks: 294 WARNING @ Mon, 03 Jun 2019 11:26:21: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 03 Jun 2019 11:26:21: start model_add_line... INFO @ Mon, 03 Jun 2019 11:26:21: start X-correlation... INFO @ Mon, 03 Jun 2019 11:26:21: end of X-cor INFO @ Mon, 03 Jun 2019 11:26:21: #2 finished! INFO @ Mon, 03 Jun 2019 11:26:21: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:26:21: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.10_model.r WARNING @ Mon, 03 Jun 2019 11:26:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:26:21: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:26:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:26:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:26:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:26:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:26:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.20_summits.bed INFO @ Mon, 03 Jun 2019 11:27:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1293 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.05_summits.bed INFO @ Mon, 03 Jun 2019 11:27:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2138 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288039/SRX288039.10_summits.bed INFO @ Mon, 03 Jun 2019 11:27:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1779 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。