Job ID = 1295708 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,198,671 reads read : 26,397,342 reads written : 13,198,671 reads 0-length : 13,198,671 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: 00:04:51 13198671 reads; of these: 13198671 (100.00%) were unpaired; of these: 622122 (4.71%) aligned 0 times 8912541 (67.53%) aligned exactly 1 time 3664008 (27.76%) aligned >1 times 95.29% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 3863355 / 12576549 = 0.3072 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 15:15:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.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 15:15:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:15:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:15:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.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 15:15:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:15:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:15:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.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 15:15:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:15:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:15:47: 1000000 INFO @ Mon, 03 Jun 2019 15:15:48: 1000000 INFO @ Mon, 03 Jun 2019 15:15:48: 1000000 INFO @ Mon, 03 Jun 2019 15:15:54: 2000000 INFO @ Mon, 03 Jun 2019 15:15:55: 2000000 INFO @ Mon, 03 Jun 2019 15:15:56: 2000000 INFO @ Mon, 03 Jun 2019 15:16:01: 3000000 INFO @ Mon, 03 Jun 2019 15:16:02: 3000000 INFO @ Mon, 03 Jun 2019 15:16:04: 3000000 INFO @ Mon, 03 Jun 2019 15:16:08: 4000000 INFO @ Mon, 03 Jun 2019 15:16:09: 4000000 INFO @ Mon, 03 Jun 2019 15:16:12: 4000000 INFO @ Mon, 03 Jun 2019 15:16:16: 5000000 INFO @ Mon, 03 Jun 2019 15:16:16: 5000000 INFO @ Mon, 03 Jun 2019 15:16:20: 5000000 INFO @ Mon, 03 Jun 2019 15:16:23: 6000000 INFO @ Mon, 03 Jun 2019 15:16:23: 6000000 INFO @ Mon, 03 Jun 2019 15:16:28: 6000000 INFO @ Mon, 03 Jun 2019 15:16:30: 7000000 INFO @ Mon, 03 Jun 2019 15:16:30: 7000000 INFO @ Mon, 03 Jun 2019 15:16:36: 7000000 INFO @ Mon, 03 Jun 2019 15:16:37: 8000000 INFO @ Mon, 03 Jun 2019 15:16:38: 8000000 INFO @ Mon, 03 Jun 2019 15:16:43: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 15:16:43: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 15:16:43: #1 total tags in treatment: 8713194 INFO @ Mon, 03 Jun 2019 15:16:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:16:43: #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 15:16:43: #1 tags after filtering in treatment: 8713194 INFO @ Mon, 03 Jun 2019 15:16:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:16:43: #1 finished! INFO @ Mon, 03 Jun 2019 15:16:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:16:43: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 15:16:43: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 15:16:43: #1 total tags in treatment: 8713194 INFO @ Mon, 03 Jun 2019 15:16:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:16:43: #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 15:16:43: #1 tags after filtering in treatment: 8713194 INFO @ Mon, 03 Jun 2019 15:16:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:16:43: #1 finished! INFO @ Mon, 03 Jun 2019 15:16:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:16:44: #2 number of paired peaks: 1762 INFO @ Mon, 03 Jun 2019 15:16:44: start model_add_line... INFO @ Mon, 03 Jun 2019 15:16:44: start X-correlation... INFO @ Mon, 03 Jun 2019 15:16:44: end of X-cor INFO @ Mon, 03 Jun 2019 15:16:44: #2 finished! INFO @ Mon, 03 Jun 2019 15:16:44: #2 predicted fragment length is 55 bps INFO @ Mon, 03 Jun 2019 15:16:44: #2 alternative fragment length(s) may be 3,55 bps INFO @ Mon, 03 Jun 2019 15:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.20_model.r WARNING @ Mon, 03 Jun 2019 15:16:44: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:16:44: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Mon, 03 Jun 2019 15:16:44: #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 15:16:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:16:44: #2 number of paired peaks: 1762 INFO @ Mon, 03 Jun 2019 15:16:44: start model_add_line... INFO @ Mon, 03 Jun 2019 15:16:44: 8000000 INFO @ Mon, 03 Jun 2019 15:16:44: start X-correlation... INFO @ Mon, 03 Jun 2019 15:16:44: end of X-cor INFO @ Mon, 03 Jun 2019 15:16:44: #2 finished! INFO @ Mon, 03 Jun 2019 15:16:44: #2 predicted fragment length is 55 bps INFO @ Mon, 03 Jun 2019 15:16:44: #2 alternative fragment length(s) may be 3,55 bps INFO @ Mon, 03 Jun 2019 15:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.10_model.r WARNING @ Mon, 03 Jun 2019 15:16:44: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:16:44: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Mon, 03 Jun 2019 15:16:44: #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 15:16:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:16:50: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 15:16:50: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 15:16:50: #1 total tags in treatment: 8713194 INFO @ Mon, 03 Jun 2019 15:16:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:16:50: #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 15:16:50: #1 tags after filtering in treatment: 8713194 INFO @ Mon, 03 Jun 2019 15:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:16:50: #1 finished! INFO @ Mon, 03 Jun 2019 15:16:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:16:51: #2 number of paired peaks: 1762 INFO @ Mon, 03 Jun 2019 15:16:51: start model_add_line... INFO @ Mon, 03 Jun 2019 15:16:51: start X-correlation... INFO @ Mon, 03 Jun 2019 15:16:51: end of X-cor INFO @ Mon, 03 Jun 2019 15:16:51: #2 finished! INFO @ Mon, 03 Jun 2019 15:16:51: #2 predicted fragment length is 55 bps INFO @ Mon, 03 Jun 2019 15:16:51: #2 alternative fragment length(s) may be 3,55 bps INFO @ Mon, 03 Jun 2019 15:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.05_model.r WARNING @ Mon, 03 Jun 2019 15:16:51: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:16:51: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Mon, 03 Jun 2019 15:16:51: #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 15:16:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:17:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:17:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:17:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.20_summits.bed INFO @ Mon, 03 Jun 2019 15:17:22: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.10_summits.bed INFO @ Mon, 03 Jun 2019 15:17:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1463 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:17:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:17:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:17:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370068/SRX4370068.05_summits.bed INFO @ Mon, 03 Jun 2019 15:17:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3266 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。