Job ID = 1294818 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:11:15 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' 2019-06-03T01:11:15 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/SRR870106' 2019-06-03T01:11:15 fasterq-dump.2.9.6 err: invalid accession 'SRR870106' spots read : 16,164,431 reads read : 16,164,431 reads written : 16,164,431 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:50 16164431 reads; of these: 16164431 (100.00%) were unpaired; of these: 1060874 (6.56%) aligned 0 times 11225980 (69.45%) aligned exactly 1 time 3877577 (23.99%) aligned >1 times 93.44% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 1317326 / 15103557 = 0.0872 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 10:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.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 10:32:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:32:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.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 10:32:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:32:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.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 10:32:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:32:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:32:25: 1000000 INFO @ Mon, 03 Jun 2019 10:32:27: 1000000 INFO @ Mon, 03 Jun 2019 10:32:27: 1000000 INFO @ Mon, 03 Jun 2019 10:32:32: 2000000 INFO @ Mon, 03 Jun 2019 10:32:35: 2000000 INFO @ Mon, 03 Jun 2019 10:32:36: 2000000 INFO @ Mon, 03 Jun 2019 10:32:39: 3000000 INFO @ Mon, 03 Jun 2019 10:32:42: 3000000 INFO @ Mon, 03 Jun 2019 10:32:44: 3000000 INFO @ Mon, 03 Jun 2019 10:32:46: 4000000 INFO @ Mon, 03 Jun 2019 10:32:50: 4000000 INFO @ Mon, 03 Jun 2019 10:32:52: 4000000 INFO @ Mon, 03 Jun 2019 10:32:53: 5000000 INFO @ Mon, 03 Jun 2019 10:32:58: 5000000 INFO @ Mon, 03 Jun 2019 10:32:59: 6000000 INFO @ Mon, 03 Jun 2019 10:33:01: 5000000 INFO @ Mon, 03 Jun 2019 10:33:06: 6000000 INFO @ Mon, 03 Jun 2019 10:33:07: 7000000 INFO @ Mon, 03 Jun 2019 10:33:09: 6000000 INFO @ Mon, 03 Jun 2019 10:33:13: 8000000 INFO @ Mon, 03 Jun 2019 10:33:14: 7000000 INFO @ Mon, 03 Jun 2019 10:33:17: 7000000 INFO @ Mon, 03 Jun 2019 10:33:20: 9000000 INFO @ Mon, 03 Jun 2019 10:33:22: 8000000 INFO @ Mon, 03 Jun 2019 10:33:25: 8000000 INFO @ Mon, 03 Jun 2019 10:33:27: 10000000 INFO @ Mon, 03 Jun 2019 10:33:30: 9000000 INFO @ Mon, 03 Jun 2019 10:33:34: 11000000 INFO @ Mon, 03 Jun 2019 10:33:34: 9000000 INFO @ Mon, 03 Jun 2019 10:33:37: 10000000 INFO @ Mon, 03 Jun 2019 10:33:40: 12000000 INFO @ Mon, 03 Jun 2019 10:33:43: 10000000 INFO @ Mon, 03 Jun 2019 10:33:45: 11000000 INFO @ Mon, 03 Jun 2019 10:33:47: 13000000 INFO @ Mon, 03 Jun 2019 10:33:51: 11000000 INFO @ Mon, 03 Jun 2019 10:33:52: 12000000 INFO @ Mon, 03 Jun 2019 10:33:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:33:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:33:52: #1 total tags in treatment: 13786231 INFO @ Mon, 03 Jun 2019 10:33:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:33:52: #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 10:33:53: #1 tags after filtering in treatment: 13786231 INFO @ Mon, 03 Jun 2019 10:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:33:53: #1 finished! INFO @ Mon, 03 Jun 2019 10:33:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:33:54: #2 number of paired peaks: 115 WARNING @ Mon, 03 Jun 2019 10:33:54: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 03 Jun 2019 10:33:54: start model_add_line... INFO @ Mon, 03 Jun 2019 10:33:54: start X-correlation... INFO @ Mon, 03 Jun 2019 10:33:54: end of X-cor INFO @ Mon, 03 Jun 2019 10:33:54: #2 finished! INFO @ Mon, 03 Jun 2019 10:33:54: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:33:54: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.05_model.r WARNING @ Mon, 03 Jun 2019 10:33:54: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:33:54: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:33:54: #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 10:33:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:33:59: 12000000 INFO @ Mon, 03 Jun 2019 10:34:00: 13000000 INFO @ Mon, 03 Jun 2019 10:34:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:34:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:34:06: #1 total tags in treatment: 13786231 INFO @ Mon, 03 Jun 2019 10:34:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:34:06: #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 10:34:06: #1 tags after filtering in treatment: 13786231 INFO @ Mon, 03 Jun 2019 10:34:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:34:06: #1 finished! INFO @ Mon, 03 Jun 2019 10:34:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:34:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:34:07: 13000000 INFO @ Mon, 03 Jun 2019 10:34:07: #2 number of paired peaks: 115 WARNING @ Mon, 03 Jun 2019 10:34:07: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 03 Jun 2019 10:34:07: start model_add_line... INFO @ Mon, 03 Jun 2019 10:34:07: start X-correlation... INFO @ Mon, 03 Jun 2019 10:34:07: end of X-cor INFO @ Mon, 03 Jun 2019 10:34:07: #2 finished! INFO @ Mon, 03 Jun 2019 10:34:07: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:34:07: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:34:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.20_model.r WARNING @ Mon, 03 Jun 2019 10:34:07: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:34:07: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:34:07: #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 10:34:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:34:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:34:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:34:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:34:13: #1 total tags in treatment: 13786231 INFO @ Mon, 03 Jun 2019 10:34:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:34:13: #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 10:34:13: #1 tags after filtering in treatment: 13786231 INFO @ Mon, 03 Jun 2019 10:34:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:34:13: #1 finished! INFO @ Mon, 03 Jun 2019 10:34:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:34:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:34:15: #2 number of paired peaks: 115 WARNING @ Mon, 03 Jun 2019 10:34:15: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 03 Jun 2019 10:34:15: start model_add_line... INFO @ Mon, 03 Jun 2019 10:34:15: start X-correlation... INFO @ Mon, 03 Jun 2019 10:34:15: end of X-cor INFO @ Mon, 03 Jun 2019 10:34:15: #2 finished! INFO @ Mon, 03 Jun 2019 10:34:15: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:34:15: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.10_model.r WARNING @ Mon, 03 Jun 2019 10:34:15: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:34:15: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:34:15: #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 10:34:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:34:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:34:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:34:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:34:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:34:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:34:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.05_summits.bed INFO @ Mon, 03 Jun 2019 10:34:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1927 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:34:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:35:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:35:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:35:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.20_summits.bed INFO @ Mon, 03 Jun 2019 10:35:03: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1170 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:35:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:35:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:35:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287917/SRX287917.10_summits.bed INFO @ Mon, 03 Jun 2019 10:35:11: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1652 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。