Job ID = 1295073 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:30:34 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' 2019-06-03T02:30:34 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/sra52/SRR/005873/SRR6014266' 2019-06-03T02:30:44 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR6014266' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T02:30:44 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 22,091,417 reads read : 22,091,417 reads written : 22,091,417 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:43 22091417 reads; of these: 22091417 (100.00%) were unpaired; of these: 1277499 (5.78%) aligned 0 times 15826163 (71.64%) aligned exactly 1 time 4987755 (22.58%) aligned >1 times 94.22% overall alignment rate Time searching: 00:07:44 Overall time: 00:07:44 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 12 files... [bam_rmdupse_core] 2358293 / 20813918 = 0.1133 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 12:11:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.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 12:11:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:11:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:11:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.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 12:11:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:11:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:11:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.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 12:11:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:11:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:11:56: 1000000 INFO @ Mon, 03 Jun 2019 12:11:57: 1000000 INFO @ Mon, 03 Jun 2019 12:11:58: 1000000 INFO @ Mon, 03 Jun 2019 12:12:04: 2000000 INFO @ Mon, 03 Jun 2019 12:12:06: 2000000 INFO @ Mon, 03 Jun 2019 12:12:09: 2000000 INFO @ Mon, 03 Jun 2019 12:12:12: 3000000 INFO @ Mon, 03 Jun 2019 12:12:14: 3000000 INFO @ Mon, 03 Jun 2019 12:12:19: 3000000 INFO @ Mon, 03 Jun 2019 12:12:19: 4000000 INFO @ Mon, 03 Jun 2019 12:12:23: 4000000 INFO @ Mon, 03 Jun 2019 12:12:27: 5000000 INFO @ Mon, 03 Jun 2019 12:12:29: 4000000 INFO @ Mon, 03 Jun 2019 12:12:31: 5000000 INFO @ Mon, 03 Jun 2019 12:12:35: 6000000 INFO @ Mon, 03 Jun 2019 12:12:40: 5000000 INFO @ Mon, 03 Jun 2019 12:12:41: 6000000 INFO @ Mon, 03 Jun 2019 12:12:43: 7000000 INFO @ Mon, 03 Jun 2019 12:12:50: 6000000 INFO @ Mon, 03 Jun 2019 12:12:51: 7000000 INFO @ Mon, 03 Jun 2019 12:12:52: 8000000 INFO @ Mon, 03 Jun 2019 12:12:59: 8000000 INFO @ Mon, 03 Jun 2019 12:12:59: 9000000 INFO @ Mon, 03 Jun 2019 12:13:00: 7000000 INFO @ Mon, 03 Jun 2019 12:13:07: 10000000 INFO @ Mon, 03 Jun 2019 12:13:07: 9000000 INFO @ Mon, 03 Jun 2019 12:13:10: 8000000 INFO @ Mon, 03 Jun 2019 12:13:14: 11000000 INFO @ Mon, 03 Jun 2019 12:13:16: 10000000 INFO @ Mon, 03 Jun 2019 12:13:20: 9000000 INFO @ Mon, 03 Jun 2019 12:13:22: 12000000 INFO @ Mon, 03 Jun 2019 12:13:24: 11000000 INFO @ Mon, 03 Jun 2019 12:13:29: 13000000 INFO @ Mon, 03 Jun 2019 12:13:30: 10000000 INFO @ Mon, 03 Jun 2019 12:13:32: 12000000 INFO @ Mon, 03 Jun 2019 12:13:37: 14000000 INFO @ Mon, 03 Jun 2019 12:13:40: 11000000 INFO @ Mon, 03 Jun 2019 12:13:41: 13000000 INFO @ Mon, 03 Jun 2019 12:13:44: 15000000 INFO @ Mon, 03 Jun 2019 12:13:49: 14000000 INFO @ Mon, 03 Jun 2019 12:13:50: 12000000 INFO @ Mon, 03 Jun 2019 12:13:52: 16000000 INFO @ Mon, 03 Jun 2019 12:13:58: 15000000 INFO @ Mon, 03 Jun 2019 12:13:59: 17000000 INFO @ Mon, 03 Jun 2019 12:14:00: 13000000 INFO @ Mon, 03 Jun 2019 12:14:06: 16000000 INFO @ Mon, 03 Jun 2019 12:14:07: 18000000 INFO @ Mon, 03 Jun 2019 12:14:10: 14000000 INFO @ Mon, 03 Jun 2019 12:14:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:14:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:14:10: #1 total tags in treatment: 18455625 INFO @ Mon, 03 Jun 2019 12:14:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:14:10: #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 12:14:11: #1 tags after filtering in treatment: 18455625 INFO @ Mon, 03 Jun 2019 12:14:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:14:11: #1 finished! INFO @ Mon, 03 Jun 2019 12:14:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:14:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:14:12: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 12:14:12: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 12:14:12: start model_add_line... INFO @ Mon, 03 Jun 2019 12:14:13: start X-correlation... INFO @ Mon, 03 Jun 2019 12:14:13: end of X-cor INFO @ Mon, 03 Jun 2019 12:14:13: #2 finished! INFO @ Mon, 03 Jun 2019 12:14:13: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 12:14:13: #2 alternative fragment length(s) may be 4,53,541 bps INFO @ Mon, 03 Jun 2019 12:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.10_model.r WARNING @ Mon, 03 Jun 2019 12:14:13: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:14:13: #2 You may need to consider one of the other alternative d(s): 4,53,541 WARNING @ Mon, 03 Jun 2019 12:14:13: #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 12:14:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:14:14: 17000000 INFO @ Mon, 03 Jun 2019 12:14:20: 15000000 INFO @ Mon, 03 Jun 2019 12:14:22: 18000000 INFO @ Mon, 03 Jun 2019 12:14:26: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:14:26: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:14:26: #1 total tags in treatment: 18455625 INFO @ Mon, 03 Jun 2019 12:14:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:14:26: #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 12:14:27: #1 tags after filtering in treatment: 18455625 INFO @ Mon, 03 Jun 2019 12:14:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:14:27: #1 finished! INFO @ Mon, 03 Jun 2019 12:14:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:14:28: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 12:14:28: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 12:14:28: start model_add_line... INFO @ Mon, 03 Jun 2019 12:14:28: start X-correlation... INFO @ Mon, 03 Jun 2019 12:14:28: end of X-cor INFO @ Mon, 03 Jun 2019 12:14:28: #2 finished! INFO @ Mon, 03 Jun 2019 12:14:28: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 12:14:28: #2 alternative fragment length(s) may be 4,53,541 bps INFO @ Mon, 03 Jun 2019 12:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.20_model.r WARNING @ Mon, 03 Jun 2019 12:14:28: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:14:28: #2 You may need to consider one of the other alternative d(s): 4,53,541 WARNING @ Mon, 03 Jun 2019 12:14:28: #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 12:14:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:14:30: 16000000 INFO @ Mon, 03 Jun 2019 12:14:40: 17000000 INFO @ Mon, 03 Jun 2019 12:14:50: 18000000 INFO @ Mon, 03 Jun 2019 12:14:54: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:14:54: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:14:54: #1 total tags in treatment: 18455625 INFO @ Mon, 03 Jun 2019 12:14:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:14:54: #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 12:14:54: #1 tags after filtering in treatment: 18455625 INFO @ Mon, 03 Jun 2019 12:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:14:54: #1 finished! INFO @ Mon, 03 Jun 2019 12:14:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:14:56: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 12:14:56: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 12:14:56: start model_add_line... INFO @ Mon, 03 Jun 2019 12:14:56: start X-correlation... INFO @ Mon, 03 Jun 2019 12:14:56: end of X-cor INFO @ Mon, 03 Jun 2019 12:14:56: #2 finished! INFO @ Mon, 03 Jun 2019 12:14:56: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 12:14:56: #2 alternative fragment length(s) may be 4,53,541 bps INFO @ Mon, 03 Jun 2019 12:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.05_model.r WARNING @ Mon, 03 Jun 2019 12:14:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:14:56: #2 You may need to consider one of the other alternative d(s): 4,53,541 WARNING @ Mon, 03 Jun 2019 12:14:56: #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 12:14:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:14:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:14:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:15:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.10_summits.bed INFO @ Mon, 03 Jun 2019 12:15:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (996 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.20_summits.bed INFO @ Mon, 03 Jun 2019 12:15:39: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (481 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:15:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:16:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167263/SRX3167263.05_summits.bed INFO @ Mon, 03 Jun 2019 12:16:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2035 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。