Job ID = 4178488 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,409,634 reads read : 8,409,634 reads written : 8,409,634 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:03 8409634 reads; of these: 8409634 (100.00%) were unpaired; of these: 241446 (2.87%) aligned 0 times 5658345 (67.28%) aligned exactly 1 time 2509843 (29.84%) aligned >1 times 97.13% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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_rmdupse_core] 1181541 / 8168188 = 0.1447 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:35:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.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 12:35:12: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:35:12: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:35:22: 1000000 INFO @ Thu, 05 Dec 2019 12:35:33: 2000000 INFO @ Thu, 05 Dec 2019 12:35:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.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 12:35:42: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:35:42: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:35:44: 3000000 INFO @ Thu, 05 Dec 2019 12:35:54: 1000000 INFO @ Thu, 05 Dec 2019 12:35:56: 4000000 INFO @ Thu, 05 Dec 2019 12:36:07: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:36:09: 5000000 INFO @ Thu, 05 Dec 2019 12:36:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.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 12:36:11: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:36:11: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:36:19: 3000000 INFO @ Thu, 05 Dec 2019 12:36:20: 1000000 INFO @ Thu, 05 Dec 2019 12:36:22: 6000000 INFO @ Thu, 05 Dec 2019 12:36:28: 2000000 INFO @ Thu, 05 Dec 2019 12:36:32: 4000000 INFO @ Thu, 05 Dec 2019 12:36:34: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:36:34: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:36:34: #1 total tags in treatment: 6986647 INFO @ Thu, 05 Dec 2019 12:36:34: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:36:34: #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 12:36:35: #1 tags after filtering in treatment: 6986647 INFO @ Thu, 05 Dec 2019 12:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:36:35: #1 finished! INFO @ Thu, 05 Dec 2019 12:36:35: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:36:35: #2 number of paired peaks: 956 WARNING @ Thu, 05 Dec 2019 12:36:35: Fewer paired peaks (956) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 956 pairs to build model! INFO @ Thu, 05 Dec 2019 12:36:35: start model_add_line... INFO @ Thu, 05 Dec 2019 12:36:35: start X-correlation... INFO @ Thu, 05 Dec 2019 12:36:35: end of X-cor INFO @ Thu, 05 Dec 2019 12:36:35: #2 finished! INFO @ Thu, 05 Dec 2019 12:36:35: #2 predicted fragment length is 82 bps INFO @ Thu, 05 Dec 2019 12:36:35: #2 alternative fragment length(s) may be 2,65,82,578 bps INFO @ Thu, 05 Dec 2019 12:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.05_model.r WARNING @ Thu, 05 Dec 2019 12:36:35: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:36:35: #2 You may need to consider one of the other alternative d(s): 2,65,82,578 WARNING @ Thu, 05 Dec 2019 12:36:35: #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 12:36:35: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:36:36: 3000000 INFO @ Thu, 05 Dec 2019 12:36:45: 5000000 INFO @ Thu, 05 Dec 2019 12:36:45: 4000000 INFO @ Thu, 05 Dec 2019 12:36:53: 5000000 INFO @ Thu, 05 Dec 2019 12:36:56: 6000000 INFO @ Thu, 05 Dec 2019 12:36:59: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:37:01: 6000000 INFO @ Thu, 05 Dec 2019 12:37:07: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:37:07: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:37:07: #1 total tags in treatment: 6986647 INFO @ Thu, 05 Dec 2019 12:37:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:37:07: #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 12:37:07: #1 tags after filtering in treatment: 6986647 INFO @ Thu, 05 Dec 2019 12:37:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:37:07: #1 finished! INFO @ Thu, 05 Dec 2019 12:37:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:37:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:37:08: #2 number of paired peaks: 956 WARNING @ Thu, 05 Dec 2019 12:37:08: Fewer paired peaks (956) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 956 pairs to build model! INFO @ Thu, 05 Dec 2019 12:37:08: start model_add_line... INFO @ Thu, 05 Dec 2019 12:37:08: start X-correlation... INFO @ Thu, 05 Dec 2019 12:37:08: end of X-cor INFO @ Thu, 05 Dec 2019 12:37:08: #2 finished! INFO @ Thu, 05 Dec 2019 12:37:08: #2 predicted fragment length is 82 bps INFO @ Thu, 05 Dec 2019 12:37:08: #2 alternative fragment length(s) may be 2,65,82,578 bps INFO @ Thu, 05 Dec 2019 12:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.10_model.r WARNING @ Thu, 05 Dec 2019 12:37:08: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:37:08: #2 You may need to consider one of the other alternative d(s): 2,65,82,578 WARNING @ Thu, 05 Dec 2019 12:37:08: #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 12:37:08: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:37:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:37:09: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:37:09: #1 total tags in treatment: 6986647 INFO @ Thu, 05 Dec 2019 12:37:09: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:37:09: #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 12:37:09: #1 tags after filtering in treatment: 6986647 INFO @ Thu, 05 Dec 2019 12:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:37:09: #1 finished! INFO @ Thu, 05 Dec 2019 12:37:09: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:37:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:37:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:37:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.05_summits.bed INFO @ Thu, 05 Dec 2019 12:37:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2075 records, 4 fields): 240 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:37:10: #2 number of paired peaks: 956 WARNING @ Thu, 05 Dec 2019 12:37:10: Fewer paired peaks (956) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 956 pairs to build model! INFO @ Thu, 05 Dec 2019 12:37:10: start model_add_line... INFO @ Thu, 05 Dec 2019 12:37:10: start X-correlation... INFO @ Thu, 05 Dec 2019 12:37:10: end of X-cor INFO @ Thu, 05 Dec 2019 12:37:10: #2 finished! INFO @ Thu, 05 Dec 2019 12:37:10: #2 predicted fragment length is 82 bps INFO @ Thu, 05 Dec 2019 12:37:10: #2 alternative fragment length(s) may be 2,65,82,578 bps INFO @ Thu, 05 Dec 2019 12:37:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.20_model.r WARNING @ Thu, 05 Dec 2019 12:37:10: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:37:10: #2 You may need to consider one of the other alternative d(s): 2,65,82,578 WARNING @ Thu, 05 Dec 2019 12:37:10: #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 12:37:10: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:37:29: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:37:31: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:37:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:37:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:37:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.10_summits.bed INFO @ Thu, 05 Dec 2019 12:37:39: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1146 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535389/SRX5535389.20_summits.bed INFO @ Thu, 05 Dec 2019 12:37:41: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (265 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。