Job ID = 2590950 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,576,945 reads read : 65,153,890 reads written : 32,576,945 reads 0-length : 32,576,945 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: 00:16:24 32576945 reads; of these: 32576945 (100.00%) were unpaired; of these: 912535 (2.80%) aligned 0 times 15087525 (46.31%) aligned exactly 1 time 16576885 (50.89%) aligned >1 times 97.20% overall alignment rate Time searching: 00:16:24 Overall time: 00:16:24 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 16 files... [bam_rmdupse_core] 8439989 / 31664410 = 0.2665 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 @ Tue, 13 Aug 2019 00:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.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 @ Tue, 13 Aug 2019 00:33:48: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:33:48: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.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 @ Tue, 13 Aug 2019 00:33:48: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:33:48: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.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 @ Tue, 13 Aug 2019 00:33:49: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:33:49: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:33:55: 1000000 INFO @ Tue, 13 Aug 2019 00:33:56: 1000000 INFO @ Tue, 13 Aug 2019 00:33:57: 1000000 INFO @ Tue, 13 Aug 2019 00:34:03: 2000000 INFO @ Tue, 13 Aug 2019 00:34:03: 2000000 INFO @ Tue, 13 Aug 2019 00:34:06: 2000000 INFO @ Tue, 13 Aug 2019 00:34:09: 3000000 INFO @ Tue, 13 Aug 2019 00:34:10: 3000000 INFO @ Tue, 13 Aug 2019 00:34:14: 3000000 INFO @ Tue, 13 Aug 2019 00:34:16: 4000000 INFO @ Tue, 13 Aug 2019 00:34:16: 4000000 INFO @ Tue, 13 Aug 2019 00:34:22: 4000000 INFO @ Tue, 13 Aug 2019 00:34:23: 5000000 INFO @ Tue, 13 Aug 2019 00:34:23: 5000000 INFO @ Tue, 13 Aug 2019 00:34:29: 6000000 INFO @ Tue, 13 Aug 2019 00:34:29: 6000000 INFO @ Tue, 13 Aug 2019 00:34:30: 5000000 INFO @ Tue, 13 Aug 2019 00:34:36: 7000000 INFO @ Tue, 13 Aug 2019 00:34:36: 7000000 INFO @ Tue, 13 Aug 2019 00:34:39: 6000000 INFO @ Tue, 13 Aug 2019 00:34:43: 8000000 INFO @ Tue, 13 Aug 2019 00:34:43: 8000000 INFO @ Tue, 13 Aug 2019 00:34:47: 7000000 INFO @ Tue, 13 Aug 2019 00:34:49: 9000000 INFO @ Tue, 13 Aug 2019 00:34:49: 9000000 INFO @ Tue, 13 Aug 2019 00:34:55: 8000000 INFO @ Tue, 13 Aug 2019 00:34:56: 10000000 INFO @ Tue, 13 Aug 2019 00:34:56: 10000000 INFO @ Tue, 13 Aug 2019 00:35:02: 11000000 INFO @ Tue, 13 Aug 2019 00:35:02: 11000000 INFO @ Tue, 13 Aug 2019 00:35:03: 9000000 INFO @ Tue, 13 Aug 2019 00:35:09: 12000000 INFO @ Tue, 13 Aug 2019 00:35:09: 12000000 INFO @ Tue, 13 Aug 2019 00:35:12: 10000000 INFO @ Tue, 13 Aug 2019 00:35:16: 13000000 INFO @ Tue, 13 Aug 2019 00:35:16: 13000000 INFO @ Tue, 13 Aug 2019 00:35:21: 11000000 INFO @ Tue, 13 Aug 2019 00:35:23: 14000000 INFO @ Tue, 13 Aug 2019 00:35:23: 14000000 INFO @ Tue, 13 Aug 2019 00:35:29: 12000000 INFO @ Tue, 13 Aug 2019 00:35:30: 15000000 INFO @ Tue, 13 Aug 2019 00:35:30: 15000000 INFO @ Tue, 13 Aug 2019 00:35:37: 16000000 INFO @ Tue, 13 Aug 2019 00:35:37: 16000000 INFO @ Tue, 13 Aug 2019 00:35:37: 13000000 INFO @ Tue, 13 Aug 2019 00:35:44: 17000000 INFO @ Tue, 13 Aug 2019 00:35:44: 17000000 INFO @ Tue, 13 Aug 2019 00:35:47: 14000000 INFO @ Tue, 13 Aug 2019 00:35:52: 18000000 INFO @ Tue, 13 Aug 2019 00:35:52: 18000000 INFO @ Tue, 13 Aug 2019 00:35:55: 15000000 INFO @ Tue, 13 Aug 2019 00:35:59: 19000000 INFO @ Tue, 13 Aug 2019 00:35:59: 19000000 INFO @ Tue, 13 Aug 2019 00:36:03: 16000000 INFO @ Tue, 13 Aug 2019 00:36:07: 20000000 INFO @ Tue, 13 Aug 2019 00:36:07: 20000000 INFO @ Tue, 13 Aug 2019 00:36:11: 17000000 INFO @ Tue, 13 Aug 2019 00:36:14: 21000000 INFO @ Tue, 13 Aug 2019 00:36:14: 21000000 INFO @ Tue, 13 Aug 2019 00:36:19: 18000000 INFO @ Tue, 13 Aug 2019 00:36:22: 22000000 INFO @ Tue, 13 Aug 2019 00:36:22: 22000000 INFO @ Tue, 13 Aug 2019 00:36:27: 19000000 INFO @ Tue, 13 Aug 2019 00:36:29: 23000000 INFO @ Tue, 13 Aug 2019 00:36:29: 23000000 INFO @ Tue, 13 Aug 2019 00:36:31: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:36:31: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:36:31: #1 total tags in treatment: 23224421 INFO @ Tue, 13 Aug 2019 00:36:31: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:36:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:36:31: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:36:31: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:36:31: #1 total tags in treatment: 23224421 INFO @ Tue, 13 Aug 2019 00:36:31: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:36:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:36:31: #1 tags after filtering in treatment: 23224421 INFO @ Tue, 13 Aug 2019 00:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:36:31: #1 finished! INFO @ Tue, 13 Aug 2019 00:36:31: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:36:31: #1 tags after filtering in treatment: 23224421 INFO @ Tue, 13 Aug 2019 00:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:36:31: #1 finished! INFO @ Tue, 13 Aug 2019 00:36:31: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:36:33: #2 number of paired peaks: 409 WARNING @ Tue, 13 Aug 2019 00:36:33: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Tue, 13 Aug 2019 00:36:33: start model_add_line... INFO @ Tue, 13 Aug 2019 00:36:33: #2 number of paired peaks: 409 WARNING @ Tue, 13 Aug 2019 00:36:33: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Tue, 13 Aug 2019 00:36:33: start model_add_line... INFO @ Tue, 13 Aug 2019 00:36:34: start X-correlation... INFO @ Tue, 13 Aug 2019 00:36:34: end of X-cor INFO @ Tue, 13 Aug 2019 00:36:34: #2 finished! INFO @ Tue, 13 Aug 2019 00:36:34: #2 predicted fragment length is 40 bps INFO @ Tue, 13 Aug 2019 00:36:34: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 13 Aug 2019 00:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.10_model.r WARNING @ Tue, 13 Aug 2019 00:36:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:36:34: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 13 Aug 2019 00:36:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:36:34: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:36:34: start X-correlation... INFO @ Tue, 13 Aug 2019 00:36:34: end of X-cor INFO @ Tue, 13 Aug 2019 00:36:34: #2 finished! INFO @ Tue, 13 Aug 2019 00:36:34: #2 predicted fragment length is 40 bps INFO @ Tue, 13 Aug 2019 00:36:34: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 13 Aug 2019 00:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.20_model.r WARNING @ Tue, 13 Aug 2019 00:36:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:36:34: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 13 Aug 2019 00:36:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:36:34: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:36:35: 20000000 INFO @ Tue, 13 Aug 2019 00:36:42: 21000000 INFO @ Tue, 13 Aug 2019 00:36:50: 22000000 INFO @ Tue, 13 Aug 2019 00:36:58: 23000000 INFO @ Tue, 13 Aug 2019 00:37:00: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:37:00: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:37:00: #1 total tags in treatment: 23224421 INFO @ Tue, 13 Aug 2019 00:37:00: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:37:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:37:01: #1 tags after filtering in treatment: 23224421 INFO @ Tue, 13 Aug 2019 00:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:37:01: #1 finished! INFO @ Tue, 13 Aug 2019 00:37:01: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:37:03: #2 number of paired peaks: 409 WARNING @ Tue, 13 Aug 2019 00:37:03: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Tue, 13 Aug 2019 00:37:03: start model_add_line... INFO @ Tue, 13 Aug 2019 00:37:03: start X-correlation... INFO @ Tue, 13 Aug 2019 00:37:03: end of X-cor INFO @ Tue, 13 Aug 2019 00:37:03: #2 finished! INFO @ Tue, 13 Aug 2019 00:37:03: #2 predicted fragment length is 40 bps INFO @ Tue, 13 Aug 2019 00:37:03: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 13 Aug 2019 00:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.05_model.r WARNING @ Tue, 13 Aug 2019 00:37:03: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:37:03: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 13 Aug 2019 00:37:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:37:03: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:37:30: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:37:31: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:37:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.10_summits.bed INFO @ Tue, 13 Aug 2019 00:38:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3951 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:38:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:38:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.20_summits.bed INFO @ Tue, 13 Aug 2019 00:38:01: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:38:02: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (892 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:38:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:38:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:38:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661488/SRX5661488.05_summits.bed INFO @ Tue, 13 Aug 2019 00:38:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12170 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。