Job ID = 1295198 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,559,305 reads read : 21,559,305 reads written : 21,559,305 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: 00:09:06 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1335738 (6.20%) aligned 0 times 15428591 (71.56%) aligned exactly 1 time 4794976 (22.24%) aligned >1 times 93.80% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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 12 files... [bam_rmdupse_core] 1890353 / 20223567 = 0.0935 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 13:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.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 13:00:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.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 13:00:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.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 13:00:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:01:04: 1000000 INFO @ Mon, 03 Jun 2019 13:01:05: 1000000 INFO @ Mon, 03 Jun 2019 13:01:07: 1000000 INFO @ Mon, 03 Jun 2019 13:01:12: 2000000 INFO @ Mon, 03 Jun 2019 13:01:14: 2000000 INFO @ Mon, 03 Jun 2019 13:01:18: 2000000 INFO @ Mon, 03 Jun 2019 13:01:20: 3000000 INFO @ Mon, 03 Jun 2019 13:01:23: 3000000 INFO @ Mon, 03 Jun 2019 13:01:28: 4000000 INFO @ Mon, 03 Jun 2019 13:01:29: 3000000 INFO @ Mon, 03 Jun 2019 13:01:32: 4000000 INFO @ Mon, 03 Jun 2019 13:01:36: 5000000 INFO @ Mon, 03 Jun 2019 13:01:39: 4000000 INFO @ Mon, 03 Jun 2019 13:01:41: 5000000 INFO @ Mon, 03 Jun 2019 13:01:44: 6000000 INFO @ Mon, 03 Jun 2019 13:01:49: 6000000 INFO @ Mon, 03 Jun 2019 13:01:50: 5000000 INFO @ Mon, 03 Jun 2019 13:01:52: 7000000 INFO @ Mon, 03 Jun 2019 13:01:58: 7000000 INFO @ Mon, 03 Jun 2019 13:01:59: 8000000 INFO @ Mon, 03 Jun 2019 13:02:00: 6000000 INFO @ Mon, 03 Jun 2019 13:02:07: 8000000 INFO @ Mon, 03 Jun 2019 13:02:07: 9000000 INFO @ Mon, 03 Jun 2019 13:02:11: 7000000 INFO @ Mon, 03 Jun 2019 13:02:15: 10000000 INFO @ Mon, 03 Jun 2019 13:02:16: 9000000 INFO @ Mon, 03 Jun 2019 13:02:21: 8000000 INFO @ Mon, 03 Jun 2019 13:02:23: 11000000 INFO @ Mon, 03 Jun 2019 13:02:25: 10000000 INFO @ Mon, 03 Jun 2019 13:02:32: 12000000 INFO @ Mon, 03 Jun 2019 13:02:33: 9000000 INFO @ Mon, 03 Jun 2019 13:02:35: 11000000 INFO @ Mon, 03 Jun 2019 13:02:39: 13000000 INFO @ Mon, 03 Jun 2019 13:02:43: 12000000 INFO @ Mon, 03 Jun 2019 13:02:44: 10000000 INFO @ Mon, 03 Jun 2019 13:02:47: 14000000 INFO @ Mon, 03 Jun 2019 13:02:52: 13000000 INFO @ Mon, 03 Jun 2019 13:02:54: 11000000 INFO @ Mon, 03 Jun 2019 13:02:55: 15000000 INFO @ Mon, 03 Jun 2019 13:03:01: 14000000 INFO @ Mon, 03 Jun 2019 13:03:02: 16000000 INFO @ Mon, 03 Jun 2019 13:03:05: 12000000 INFO @ Mon, 03 Jun 2019 13:03:10: 15000000 INFO @ Mon, 03 Jun 2019 13:03:10: 17000000 INFO @ Mon, 03 Jun 2019 13:03:16: 13000000 INFO @ Mon, 03 Jun 2019 13:03:18: 18000000 INFO @ Mon, 03 Jun 2019 13:03:19: 16000000 INFO @ Mon, 03 Jun 2019 13:03:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:03:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:03:21: #1 total tags in treatment: 18333214 INFO @ Mon, 03 Jun 2019 13:03:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:03:21: #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 13:03:21: #1 tags after filtering in treatment: 18333214 INFO @ Mon, 03 Jun 2019 13:03:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:03:21: #1 finished! INFO @ Mon, 03 Jun 2019 13:03:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:03:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:03:23: #2 number of paired peaks: 149 WARNING @ Mon, 03 Jun 2019 13:03:23: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Mon, 03 Jun 2019 13:03:23: start model_add_line... INFO @ Mon, 03 Jun 2019 13:03:23: start X-correlation... INFO @ Mon, 03 Jun 2019 13:03:23: end of X-cor INFO @ Mon, 03 Jun 2019 13:03:23: #2 finished! INFO @ Mon, 03 Jun 2019 13:03:23: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 13:03:23: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 13:03:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.10_model.r WARNING @ Mon, 03 Jun 2019 13:03:23: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:03:23: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 13:03:23: #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 13:03:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:03:27: 14000000 INFO @ Mon, 03 Jun 2019 13:03:28: 17000000 INFO @ Mon, 03 Jun 2019 13:03:37: 18000000 INFO @ Mon, 03 Jun 2019 13:03:38: 15000000 INFO @ Mon, 03 Jun 2019 13:03:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:03:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:03:40: #1 total tags in treatment: 18333214 INFO @ Mon, 03 Jun 2019 13:03:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:03:40: #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 13:03:41: #1 tags after filtering in treatment: 18333214 INFO @ Mon, 03 Jun 2019 13:03:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:03:41: #1 finished! INFO @ Mon, 03 Jun 2019 13:03:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:03:42: #2 number of paired peaks: 149 WARNING @ Mon, 03 Jun 2019 13:03:42: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Mon, 03 Jun 2019 13:03:42: start model_add_line... INFO @ Mon, 03 Jun 2019 13:03:42: start X-correlation... INFO @ Mon, 03 Jun 2019 13:03:42: end of X-cor INFO @ Mon, 03 Jun 2019 13:03:42: #2 finished! INFO @ Mon, 03 Jun 2019 13:03:42: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 13:03:42: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 13:03:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.20_model.r WARNING @ Mon, 03 Jun 2019 13:03:42: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:03:42: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 13:03:42: #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 13:03:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:03:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:03:49: 16000000 INFO @ Mon, 03 Jun 2019 13:04:00: 17000000 INFO @ Mon, 03 Jun 2019 13:04:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:04:10: 18000000 INFO @ Mon, 03 Jun 2019 13:04:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:04:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:04:14: #1 total tags in treatment: 18333214 INFO @ Mon, 03 Jun 2019 13:04:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:04:14: #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 13:04:14: #1 tags after filtering in treatment: 18333214 INFO @ Mon, 03 Jun 2019 13:04:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:04:14: #1 finished! INFO @ Mon, 03 Jun 2019 13:04:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:04:16: #2 number of paired peaks: 149 WARNING @ Mon, 03 Jun 2019 13:04:16: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Mon, 03 Jun 2019 13:04:16: start model_add_line... INFO @ Mon, 03 Jun 2019 13:04:16: start X-correlation... INFO @ Mon, 03 Jun 2019 13:04:16: end of X-cor INFO @ Mon, 03 Jun 2019 13:04:16: #2 finished! INFO @ Mon, 03 Jun 2019 13:04:16: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 13:04:16: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 13:04:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.05_model.r WARNING @ Mon, 03 Jun 2019 13:04:16: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:04:16: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 13:04:16: #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 13:04:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:04:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:04:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:04:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.10_summits.bed INFO @ Mon, 03 Jun 2019 13:04:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1639 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:04:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.20_summits.bed INFO @ Mon, 03 Jun 2019 13:04:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:05:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331382/SRX331382.05_summits.bed INFO @ Mon, 03 Jun 2019 13:05:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2026 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。