Job ID = 4178584 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 23,865,910 reads read : 47,731,820 reads written : 47,731,820 rm: cannot remove ‘[DSE]RR*’: 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: 01:02:24 23865910 reads; of these: 23865910 (100.00%) were paired; of these: 13315568 (55.79%) aligned concordantly 0 times 8508584 (35.65%) aligned concordantly exactly 1 time 2041758 (8.56%) aligned concordantly >1 times ---- 13315568 pairs aligned concordantly 0 times; of these: 2337109 (17.55%) aligned discordantly 1 time ---- 10978459 pairs aligned 0 times concordantly or discordantly; of these: 21956918 mates make up the pairs; of these: 20362116 (92.74%) aligned 0 times 657680 (3.00%) aligned exactly 1 time 937122 (4.27%) aligned >1 times 57.34% overall alignment rate Time searching: 01:02:24 Overall time: 01:02:24 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 12172517 / 12637516 = 0.9632 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 14:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.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 @ Thu, 05 Dec 2019 14:51:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:51:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:51:50: 1000000 INFO @ Thu, 05 Dec 2019 14:52:02: 2000000 INFO @ Thu, 05 Dec 2019 14:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.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 @ Thu, 05 Dec 2019 14:52:05: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:52:05: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:52:15: 3000000 INFO @ Thu, 05 Dec 2019 14:52:15: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 14:52:15: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 14:52:15: #1 total tags in treatment: 535045 INFO @ Thu, 05 Dec 2019 14:52:15: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:52:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:52:15: #1 tags after filtering in treatment: 273132 INFO @ Thu, 05 Dec 2019 14:52:15: #1 Redundant rate of treatment: 0.49 INFO @ Thu, 05 Dec 2019 14:52:15: #1 finished! INFO @ Thu, 05 Dec 2019 14:52:15: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:52:15: #2 number of paired peaks: 4575 INFO @ Thu, 05 Dec 2019 14:52:15: start model_add_line... INFO @ Thu, 05 Dec 2019 14:52:15: start X-correlation... INFO @ Thu, 05 Dec 2019 14:52:15: end of X-cor INFO @ Thu, 05 Dec 2019 14:52:15: #2 finished! INFO @ Thu, 05 Dec 2019 14:52:15: #2 predicted fragment length is 217 bps INFO @ Thu, 05 Dec 2019 14:52:15: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 05 Dec 2019 14:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.05_model.r WARNING @ Thu, 05 Dec 2019 14:52:15: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:52:15: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 05 Dec 2019 14:52:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 14:52:15: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:52:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.05_peaks.xls INFO @ Thu, 05 Dec 2019 14:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.05_summits.bed INFO @ Thu, 05 Dec 2019 14:52:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (754 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:52:17: 1000000 INFO @ Thu, 05 Dec 2019 14:52:27: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 14:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.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 @ Thu, 05 Dec 2019 14:52:35: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:52:35: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:52:37: 3000000 INFO @ Thu, 05 Dec 2019 14:52:37: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 14:52:37: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 14:52:37: #1 total tags in treatment: 535045 INFO @ Thu, 05 Dec 2019 14:52:37: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:52:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:52:37: #1 tags after filtering in treatment: 273132 INFO @ Thu, 05 Dec 2019 14:52:37: #1 Redundant rate of treatment: 0.49 INFO @ Thu, 05 Dec 2019 14:52:37: #1 finished! INFO @ Thu, 05 Dec 2019 14:52:37: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:52:38: #2 number of paired peaks: 4575 INFO @ Thu, 05 Dec 2019 14:52:38: start model_add_line... INFO @ Thu, 05 Dec 2019 14:52:38: start X-correlation... INFO @ Thu, 05 Dec 2019 14:52:38: end of X-cor INFO @ Thu, 05 Dec 2019 14:52:38: #2 finished! INFO @ Thu, 05 Dec 2019 14:52:38: #2 predicted fragment length is 217 bps INFO @ Thu, 05 Dec 2019 14:52:38: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 05 Dec 2019 14:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.10_model.r WARNING @ Thu, 05 Dec 2019 14:52:38: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:52:38: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 05 Dec 2019 14:52:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 14:52:38: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:52:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:52:39: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:52:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.10_peaks.xls INFO @ Thu, 05 Dec 2019 14:52:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:52:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.10_summits.bed INFO @ Thu, 05 Dec 2019 14:52:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:52:47: 1000000 INFO @ Thu, 05 Dec 2019 14:52:58: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Thu, 05 Dec 2019 14:53:10: 3000000 INFO @ Thu, 05 Dec 2019 14:53:10: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 14:53:10: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 14:53:10: #1 total tags in treatment: 535045 INFO @ Thu, 05 Dec 2019 14:53:10: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:53:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:53:10: #1 tags after filtering in treatment: 273132 INFO @ Thu, 05 Dec 2019 14:53:10: #1 Redundant rate of treatment: 0.49 INFO @ Thu, 05 Dec 2019 14:53:10: #1 finished! INFO @ Thu, 05 Dec 2019 14:53:10: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:53:11: #2 number of paired peaks: 4575 INFO @ Thu, 05 Dec 2019 14:53:11: start model_add_line... INFO @ Thu, 05 Dec 2019 14:53:11: start X-correlation... INFO @ Thu, 05 Dec 2019 14:53:11: end of X-cor INFO @ Thu, 05 Dec 2019 14:53:11: #2 finished! INFO @ Thu, 05 Dec 2019 14:53:11: #2 predicted fragment length is 217 bps INFO @ Thu, 05 Dec 2019 14:53:11: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 05 Dec 2019 14:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.20_model.r WARNING @ Thu, 05 Dec 2019 14:53:11: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:53:11: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 05 Dec 2019 14:53:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 14:53:11: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:53:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:53:12: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.20_peaks.xls INFO @ Thu, 05 Dec 2019 14:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827848/SRX5827848.20_summits.bed INFO @ Thu, 05 Dec 2019 14:53:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 2 millis CompletedMACS2peakCalling