Job ID = 1294168 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,186,260 reads read : 12,186,260 reads written : 12,186,260 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: 00:03:59 12186260 reads; of these: 12186260 (100.00%) were unpaired; of these: 2227319 (18.28%) aligned 0 times 7514100 (61.66%) aligned exactly 1 time 2444841 (20.06%) aligned >1 times 81.72% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 1474985 / 9958941 = 0.1481 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 05:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.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 05:19:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:19:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.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 05:19:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:19:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.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 05:19:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:19:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:20:05: 1000000 INFO @ Mon, 03 Jun 2019 05:20:05: 1000000 INFO @ Mon, 03 Jun 2019 05:20:06: 1000000 INFO @ Mon, 03 Jun 2019 05:20:12: 2000000 INFO @ Mon, 03 Jun 2019 05:20:12: 2000000 INFO @ Mon, 03 Jun 2019 05:20:13: 2000000 INFO @ Mon, 03 Jun 2019 05:20:18: 3000000 INFO @ Mon, 03 Jun 2019 05:20:19: 3000000 INFO @ Mon, 03 Jun 2019 05:20:20: 3000000 INFO @ Mon, 03 Jun 2019 05:20:25: 4000000 INFO @ Mon, 03 Jun 2019 05:20:26: 4000000 INFO @ Mon, 03 Jun 2019 05:20:27: 4000000 INFO @ Mon, 03 Jun 2019 05:20:32: 5000000 INFO @ Mon, 03 Jun 2019 05:20:33: 5000000 INFO @ Mon, 03 Jun 2019 05:20:34: 5000000 INFO @ Mon, 03 Jun 2019 05:20:38: 6000000 INFO @ Mon, 03 Jun 2019 05:20:40: 6000000 INFO @ Mon, 03 Jun 2019 05:20:41: 6000000 INFO @ Mon, 03 Jun 2019 05:20:45: 7000000 INFO @ Mon, 03 Jun 2019 05:20:47: 7000000 INFO @ Mon, 03 Jun 2019 05:20:49: 7000000 INFO @ Mon, 03 Jun 2019 05:20:51: 8000000 INFO @ Mon, 03 Jun 2019 05:20:53: 8000000 INFO @ Mon, 03 Jun 2019 05:20:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:20:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:20:55: #1 total tags in treatment: 8483956 INFO @ Mon, 03 Jun 2019 05:20:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:20:55: #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 05:20:55: #1 tags after filtering in treatment: 8483956 INFO @ Mon, 03 Jun 2019 05:20:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:20:55: #1 finished! INFO @ Mon, 03 Jun 2019 05:20:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:20:56: #2 number of paired peaks: 203 WARNING @ Mon, 03 Jun 2019 05:20:56: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Mon, 03 Jun 2019 05:20:56: start model_add_line... INFO @ Mon, 03 Jun 2019 05:20:56: start X-correlation... INFO @ Mon, 03 Jun 2019 05:20:56: end of X-cor INFO @ Mon, 03 Jun 2019 05:20:56: #2 finished! INFO @ Mon, 03 Jun 2019 05:20:56: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 05:20:56: #2 alternative fragment length(s) may be 90,113 bps INFO @ Mon, 03 Jun 2019 05:20:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.10_model.r WARNING @ Mon, 03 Jun 2019 05:20:56: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:20:56: #2 You may need to consider one of the other alternative d(s): 90,113 WARNING @ Mon, 03 Jun 2019 05:20:56: #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 05:20:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:20:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:20:56: 8000000 INFO @ Mon, 03 Jun 2019 05:20:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:20:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:20:57: #1 total tags in treatment: 8483956 INFO @ Mon, 03 Jun 2019 05:20:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:20:57: #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 05:20:57: #1 tags after filtering in treatment: 8483956 INFO @ Mon, 03 Jun 2019 05:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:20:57: #1 finished! INFO @ Mon, 03 Jun 2019 05:20:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:20:58: #2 number of paired peaks: 203 WARNING @ Mon, 03 Jun 2019 05:20:58: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Mon, 03 Jun 2019 05:20:58: start model_add_line... INFO @ Mon, 03 Jun 2019 05:20:58: start X-correlation... INFO @ Mon, 03 Jun 2019 05:20:58: end of X-cor INFO @ Mon, 03 Jun 2019 05:20:58: #2 finished! INFO @ Mon, 03 Jun 2019 05:20:58: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 05:20:58: #2 alternative fragment length(s) may be 90,113 bps INFO @ Mon, 03 Jun 2019 05:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.05_model.r WARNING @ Mon, 03 Jun 2019 05:20:58: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:20:58: #2 You may need to consider one of the other alternative d(s): 90,113 WARNING @ Mon, 03 Jun 2019 05:20:58: #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 05:20:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:20:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:20:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:20:59: #1 total tags in treatment: 8483956 INFO @ Mon, 03 Jun 2019 05:20:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:20:59: #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 05:21:00: #1 tags after filtering in treatment: 8483956 INFO @ Mon, 03 Jun 2019 05:21:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:21:00: #1 finished! INFO @ Mon, 03 Jun 2019 05:21:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:21:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:21:00: #2 number of paired peaks: 203 WARNING @ Mon, 03 Jun 2019 05:21:00: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Mon, 03 Jun 2019 05:21:00: start model_add_line... INFO @ Mon, 03 Jun 2019 05:21:00: start X-correlation... INFO @ Mon, 03 Jun 2019 05:21:00: end of X-cor INFO @ Mon, 03 Jun 2019 05:21:00: #2 finished! INFO @ Mon, 03 Jun 2019 05:21:00: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 05:21:00: #2 alternative fragment length(s) may be 90,113 bps INFO @ Mon, 03 Jun 2019 05:21:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.20_model.r WARNING @ Mon, 03 Jun 2019 05:21:00: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:21:00: #2 You may need to consider one of the other alternative d(s): 90,113 WARNING @ Mon, 03 Jun 2019 05:21:00: #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 05:21:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:21:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:21:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:21:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:21:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:21:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:21:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:21:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.10_summits.bed INFO @ Mon, 03 Jun 2019 05:21:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.05_summits.bed INFO @ Mon, 03 Jun 2019 05:21:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1540 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193628/SRX193628.20_summits.bed INFO @ Mon, 03 Jun 2019 05:21:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (190 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。