Job ID = 1303055 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,326,443 reads read : 21,326,443 reads written : 21,326,443 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: 00:00:01 Multiseed full-index search: 00:07:09 21326443 reads; of these: 21326443 (100.00%) were unpaired; of these: 4050741 (18.99%) aligned 0 times 12829328 (60.16%) aligned exactly 1 time 4446374 (20.85%) aligned >1 times 81.01% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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] 4479032 / 17275702 = 0.2593 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 20:39:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.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 20:39:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.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 20:39:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:39:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:39:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:39:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:39:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.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 20:39:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:39:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:39:11: 1000000 INFO @ Mon, 03 Jun 2019 20:39:11: 1000000 INFO @ Mon, 03 Jun 2019 20:39:13: 1000000 INFO @ Mon, 03 Jun 2019 20:39:21: 2000000 INFO @ Mon, 03 Jun 2019 20:39:21: 2000000 INFO @ Mon, 03 Jun 2019 20:39:26: 2000000 INFO @ Mon, 03 Jun 2019 20:39:31: 3000000 INFO @ Mon, 03 Jun 2019 20:39:31: 3000000 INFO @ Mon, 03 Jun 2019 20:39:39: 3000000 INFO @ Mon, 03 Jun 2019 20:39:41: 4000000 INFO @ Mon, 03 Jun 2019 20:39:41: 4000000 INFO @ Mon, 03 Jun 2019 20:39:51: 5000000 INFO @ Mon, 03 Jun 2019 20:39:51: 5000000 INFO @ Mon, 03 Jun 2019 20:39:51: 4000000 INFO @ Mon, 03 Jun 2019 20:40:01: 6000000 INFO @ Mon, 03 Jun 2019 20:40:01: 6000000 INFO @ Mon, 03 Jun 2019 20:40:03: 5000000 INFO @ Mon, 03 Jun 2019 20:40:11: 7000000 INFO @ Mon, 03 Jun 2019 20:40:11: 7000000 INFO @ Mon, 03 Jun 2019 20:40:16: 6000000 INFO @ Mon, 03 Jun 2019 20:40:21: 8000000 INFO @ Mon, 03 Jun 2019 20:40:21: 8000000 INFO @ Mon, 03 Jun 2019 20:40:28: 7000000 INFO @ Mon, 03 Jun 2019 20:40:30: 9000000 INFO @ Mon, 03 Jun 2019 20:40:30: 9000000 INFO @ Mon, 03 Jun 2019 20:40:40: 8000000 INFO @ Mon, 03 Jun 2019 20:40:40: 10000000 INFO @ Mon, 03 Jun 2019 20:40:40: 10000000 INFO @ Mon, 03 Jun 2019 20:40:50: 11000000 INFO @ Mon, 03 Jun 2019 20:40:50: 11000000 INFO @ Mon, 03 Jun 2019 20:40:52: 9000000 INFO @ Mon, 03 Jun 2019 20:41:00: 12000000 INFO @ Mon, 03 Jun 2019 20:41:00: 12000000 INFO @ Mon, 03 Jun 2019 20:41:04: 10000000 INFO @ Mon, 03 Jun 2019 20:41:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:41:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:41:08: #1 total tags in treatment: 12796670 INFO @ Mon, 03 Jun 2019 20:41:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:41:08: #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 20:41:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:41:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:41:08: #1 total tags in treatment: 12796670 INFO @ Mon, 03 Jun 2019 20:41:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:41:08: #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 20:41:08: #1 tags after filtering in treatment: 12796670 INFO @ Mon, 03 Jun 2019 20:41:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:41:08: #1 finished! INFO @ Mon, 03 Jun 2019 20:41:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:41:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:41:08: #1 tags after filtering in treatment: 12796670 INFO @ Mon, 03 Jun 2019 20:41:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:41:08: #1 finished! INFO @ Mon, 03 Jun 2019 20:41:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:41:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:41:09: #2 number of paired peaks: 209 WARNING @ Mon, 03 Jun 2019 20:41:09: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Mon, 03 Jun 2019 20:41:09: start model_add_line... INFO @ Mon, 03 Jun 2019 20:41:09: #2 number of paired peaks: 209 WARNING @ Mon, 03 Jun 2019 20:41:09: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Mon, 03 Jun 2019 20:41:09: start model_add_line... INFO @ Mon, 03 Jun 2019 20:41:10: start X-correlation... INFO @ Mon, 03 Jun 2019 20:41:10: start X-correlation... INFO @ Mon, 03 Jun 2019 20:41:10: end of X-cor INFO @ Mon, 03 Jun 2019 20:41:10: #2 finished! INFO @ Mon, 03 Jun 2019 20:41:10: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:41:10: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:41:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.20_model.r WARNING @ Mon, 03 Jun 2019 20:41:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:41:10: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:41:10: #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 20:41:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:41:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:41:10: end of X-cor INFO @ Mon, 03 Jun 2019 20:41:10: #2 finished! INFO @ Mon, 03 Jun 2019 20:41:10: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:41:10: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:41:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.10_model.r WARNING @ Mon, 03 Jun 2019 20:41:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:41:10: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:41:10: #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 20:41:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:41:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:41:16: 11000000 INFO @ Mon, 03 Jun 2019 20:41:28: 12000000 INFO @ Mon, 03 Jun 2019 20:41:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:41:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:41:37: #1 total tags in treatment: 12796670 INFO @ Mon, 03 Jun 2019 20:41:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:41:37: #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 20:41:38: #1 tags after filtering in treatment: 12796670 INFO @ Mon, 03 Jun 2019 20:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:41:38: #1 finished! INFO @ Mon, 03 Jun 2019 20:41:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:41:39: #2 number of paired peaks: 209 WARNING @ Mon, 03 Jun 2019 20:41:39: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Mon, 03 Jun 2019 20:41:39: start model_add_line... INFO @ Mon, 03 Jun 2019 20:41:39: start X-correlation... INFO @ Mon, 03 Jun 2019 20:41:39: end of X-cor INFO @ Mon, 03 Jun 2019 20:41:39: #2 finished! INFO @ Mon, 03 Jun 2019 20:41:39: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:41:39: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.05_model.r WARNING @ Mon, 03 Jun 2019 20:41:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:41:39: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:41:39: #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 20:41:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:41:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:41:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.20_summits.bed INFO @ Mon, 03 Jun 2019 20:42:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (784 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:42:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:42:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:42:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.10_summits.bed INFO @ Mon, 03 Jun 2019 20:42:03: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1218 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:42:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:42:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:42:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:42:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933898/SRX4933898.05_summits.bed INFO @ Mon, 03 Jun 2019 20:42:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1616 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。