Job ID = 1308210 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,105,087 reads read : 48,210,174 reads written : 24,105,087 reads 0-length : 24,105,087 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: 00:09:01 24105087 reads; of these: 24105087 (100.00%) were unpaired; of these: 7259953 (30.12%) aligned 0 times 13815473 (57.31%) aligned exactly 1 time 3029661 (12.57%) aligned >1 times 69.88% overall alignment rate Time searching: 00:09:01 Overall time: 00:09:01 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] 8268281 / 16845134 = 0.4908 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 23:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.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 23:05:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:05:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.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 23:05:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:05:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.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 23:05:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:05:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:05:59: 1000000 INFO @ Mon, 03 Jun 2019 23:06:00: 1000000 INFO @ Mon, 03 Jun 2019 23:06:00: 1000000 INFO @ Mon, 03 Jun 2019 23:06:06: 2000000 INFO @ Mon, 03 Jun 2019 23:06:07: 2000000 INFO @ Mon, 03 Jun 2019 23:06:08: 2000000 INFO @ Mon, 03 Jun 2019 23:06:14: 3000000 INFO @ Mon, 03 Jun 2019 23:06:15: 3000000 INFO @ Mon, 03 Jun 2019 23:06:16: 3000000 INFO @ Mon, 03 Jun 2019 23:06:21: 4000000 INFO @ Mon, 03 Jun 2019 23:06:22: 4000000 INFO @ Mon, 03 Jun 2019 23:06:24: 4000000 INFO @ Mon, 03 Jun 2019 23:06:28: 5000000 INFO @ Mon, 03 Jun 2019 23:06:29: 5000000 INFO @ Mon, 03 Jun 2019 23:06:31: 5000000 INFO @ Mon, 03 Jun 2019 23:06:35: 6000000 INFO @ Mon, 03 Jun 2019 23:06:37: 6000000 INFO @ Mon, 03 Jun 2019 23:06:39: 6000000 INFO @ Mon, 03 Jun 2019 23:06:43: 7000000 INFO @ Mon, 03 Jun 2019 23:06:44: 7000000 INFO @ Mon, 03 Jun 2019 23:06:47: 7000000 INFO @ Mon, 03 Jun 2019 23:06:50: 8000000 INFO @ Mon, 03 Jun 2019 23:06:51: 8000000 INFO @ Mon, 03 Jun 2019 23:06:54: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:06:54: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:06:54: #1 total tags in treatment: 8576853 INFO @ Mon, 03 Jun 2019 23:06:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:06:54: #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 23:06:54: #1 tags after filtering in treatment: 8576853 INFO @ Mon, 03 Jun 2019 23:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:06:54: #1 finished! INFO @ Mon, 03 Jun 2019 23:06:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:06:54: 8000000 INFO @ Mon, 03 Jun 2019 23:06:55: #2 number of paired peaks: 874 WARNING @ Mon, 03 Jun 2019 23:06:55: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Mon, 03 Jun 2019 23:06:55: start model_add_line... INFO @ Mon, 03 Jun 2019 23:06:55: start X-correlation... INFO @ Mon, 03 Jun 2019 23:06:55: end of X-cor INFO @ Mon, 03 Jun 2019 23:06:55: #2 finished! INFO @ Mon, 03 Jun 2019 23:06:55: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 23:06:55: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 03 Jun 2019 23:06:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.20_model.r WARNING @ Mon, 03 Jun 2019 23:06:55: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:06:55: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Mon, 03 Jun 2019 23:06:55: #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 23:06:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:06:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:06:55: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:06:55: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:06:55: #1 total tags in treatment: 8576853 INFO @ Mon, 03 Jun 2019 23:06:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:06:55: #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 23:06:56: #1 tags after filtering in treatment: 8576853 INFO @ Mon, 03 Jun 2019 23:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:06:56: #1 finished! INFO @ Mon, 03 Jun 2019 23:06:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:06:56: #2 number of paired peaks: 874 WARNING @ Mon, 03 Jun 2019 23:06:56: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Mon, 03 Jun 2019 23:06:56: start model_add_line... INFO @ Mon, 03 Jun 2019 23:06:56: start X-correlation... INFO @ Mon, 03 Jun 2019 23:06:56: end of X-cor INFO @ Mon, 03 Jun 2019 23:06:56: #2 finished! INFO @ Mon, 03 Jun 2019 23:06:56: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 23:06:56: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 03 Jun 2019 23:06:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.05_model.r WARNING @ Mon, 03 Jun 2019 23:06:56: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:06:56: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Mon, 03 Jun 2019 23:06:56: #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 23:06:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:06:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:06:59: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:06:59: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:06:59: #1 total tags in treatment: 8576853 INFO @ Mon, 03 Jun 2019 23:06:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:06:59: #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 23:06:59: #1 tags after filtering in treatment: 8576853 INFO @ Mon, 03 Jun 2019 23:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:06:59: #1 finished! INFO @ Mon, 03 Jun 2019 23:06:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:07:00: #2 number of paired peaks: 874 WARNING @ Mon, 03 Jun 2019 23:07:00: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Mon, 03 Jun 2019 23:07:00: start model_add_line... INFO @ Mon, 03 Jun 2019 23:07:00: start X-correlation... INFO @ Mon, 03 Jun 2019 23:07:00: end of X-cor INFO @ Mon, 03 Jun 2019 23:07:00: #2 finished! INFO @ Mon, 03 Jun 2019 23:07:00: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 23:07:00: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 03 Jun 2019 23:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.10_model.r WARNING @ Mon, 03 Jun 2019 23:07:00: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:07:00: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Mon, 03 Jun 2019 23:07:00: #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 23:07:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:07:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:07:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:07:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.20_summits.bed INFO @ Mon, 03 Jun 2019 23:07:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1004 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.05_summits.bed INFO @ Mon, 03 Jun 2019 23:07:34: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5682 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343138/SRX5343138.10_summits.bed INFO @ Mon, 03 Jun 2019 23:07:40: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2606 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。