Job ID = 1295121 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,523,111 reads read : 18,523,111 reads written : 18,523,111 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:44 18523111 reads; of these: 18523111 (100.00%) were unpaired; of these: 1520028 (8.21%) aligned 0 times 13586440 (73.35%) aligned exactly 1 time 3416643 (18.45%) aligned >1 times 91.79% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:50 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] 2767524 / 17003083 = 0.1628 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 12:15:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.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 12:15:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.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 12:15:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:15:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:15:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:15:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:15:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.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 12:15:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:15:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:15:11: 1000000 INFO @ Mon, 03 Jun 2019 12:15:11: 1000000 INFO @ Mon, 03 Jun 2019 12:15:16: 1000000 INFO @ Mon, 03 Jun 2019 12:15:16: 2000000 INFO @ Mon, 03 Jun 2019 12:15:16: 2000000 INFO @ Mon, 03 Jun 2019 12:15:21: 2000000 INFO @ Mon, 03 Jun 2019 12:15:21: 3000000 INFO @ Mon, 03 Jun 2019 12:15:22: 3000000 INFO @ Mon, 03 Jun 2019 12:15:27: 3000000 INFO @ Mon, 03 Jun 2019 12:15:27: 4000000 INFO @ Mon, 03 Jun 2019 12:15:27: 4000000 INFO @ Mon, 03 Jun 2019 12:15:32: 5000000 INFO @ Mon, 03 Jun 2019 12:15:32: 5000000 INFO @ Mon, 03 Jun 2019 12:15:32: 4000000 INFO @ Mon, 03 Jun 2019 12:15:37: 6000000 INFO @ Mon, 03 Jun 2019 12:15:38: 6000000 INFO @ Mon, 03 Jun 2019 12:15:38: 5000000 INFO @ Mon, 03 Jun 2019 12:15:43: 7000000 INFO @ Mon, 03 Jun 2019 12:15:43: 7000000 INFO @ Mon, 03 Jun 2019 12:15:43: 6000000 INFO @ Mon, 03 Jun 2019 12:15:48: 8000000 INFO @ Mon, 03 Jun 2019 12:15:48: 8000000 INFO @ Mon, 03 Jun 2019 12:15:49: 7000000 INFO @ Mon, 03 Jun 2019 12:15:53: 9000000 INFO @ Mon, 03 Jun 2019 12:15:54: 9000000 INFO @ Mon, 03 Jun 2019 12:15:54: 8000000 INFO @ Mon, 03 Jun 2019 12:15:59: 10000000 INFO @ Mon, 03 Jun 2019 12:15:59: 10000000 INFO @ Mon, 03 Jun 2019 12:16:00: 9000000 INFO @ Mon, 03 Jun 2019 12:16:04: 11000000 INFO @ Mon, 03 Jun 2019 12:16:04: 11000000 INFO @ Mon, 03 Jun 2019 12:16:05: 10000000 INFO @ Mon, 03 Jun 2019 12:16:10: 12000000 INFO @ Mon, 03 Jun 2019 12:16:10: 12000000 INFO @ Mon, 03 Jun 2019 12:16:11: 11000000 INFO @ Mon, 03 Jun 2019 12:16:15: 13000000 INFO @ Mon, 03 Jun 2019 12:16:15: 13000000 INFO @ Mon, 03 Jun 2019 12:16:16: 12000000 INFO @ Mon, 03 Jun 2019 12:16:20: 14000000 INFO @ Mon, 03 Jun 2019 12:16:20: 14000000 INFO @ Mon, 03 Jun 2019 12:16:22: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:16:22: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:16:22: #1 total tags in treatment: 14235559 INFO @ Mon, 03 Jun 2019 12:16:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:16:22: #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 12:16:22: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:16:22: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:16:22: #1 total tags in treatment: 14235559 INFO @ Mon, 03 Jun 2019 12:16:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:16:22: #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 12:16:22: #1 tags after filtering in treatment: 14235559 INFO @ Mon, 03 Jun 2019 12:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:16:22: #1 finished! INFO @ Mon, 03 Jun 2019 12:16:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:16:22: 13000000 INFO @ Mon, 03 Jun 2019 12:16:22: #1 tags after filtering in treatment: 14235559 INFO @ Mon, 03 Jun 2019 12:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:16:22: #1 finished! INFO @ Mon, 03 Jun 2019 12:16:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:16:23: #2 number of paired peaks: 213 WARNING @ Mon, 03 Jun 2019 12:16:23: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 03 Jun 2019 12:16:23: start model_add_line... INFO @ Mon, 03 Jun 2019 12:16:23: start X-correlation... INFO @ Mon, 03 Jun 2019 12:16:23: #2 number of paired peaks: 213 WARNING @ Mon, 03 Jun 2019 12:16:23: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 03 Jun 2019 12:16:23: start model_add_line... INFO @ Mon, 03 Jun 2019 12:16:23: end of X-cor INFO @ Mon, 03 Jun 2019 12:16:23: #2 finished! INFO @ Mon, 03 Jun 2019 12:16:23: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 12:16:23: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 12:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.20_model.r WARNING @ Mon, 03 Jun 2019 12:16:23: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:16:23: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 12:16:23: #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 12:16:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:16:23: start X-correlation... INFO @ Mon, 03 Jun 2019 12:16:23: end of X-cor INFO @ Mon, 03 Jun 2019 12:16:23: #2 finished! INFO @ Mon, 03 Jun 2019 12:16:23: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 12:16:23: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 12:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.10_model.r WARNING @ Mon, 03 Jun 2019 12:16:23: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:16:23: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 12:16:23: #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 12:16:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:16:27: 14000000 INFO @ Mon, 03 Jun 2019 12:16:28: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:16:28: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:16:28: #1 total tags in treatment: 14235559 INFO @ Mon, 03 Jun 2019 12:16:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:16:28: #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 12:16:28: #1 tags after filtering in treatment: 14235559 INFO @ Mon, 03 Jun 2019 12:16:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:16:28: #1 finished! INFO @ Mon, 03 Jun 2019 12:16:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:16:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:16:29: #2 number of paired peaks: 213 WARNING @ Mon, 03 Jun 2019 12:16:29: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 03 Jun 2019 12:16:29: start model_add_line... INFO @ Mon, 03 Jun 2019 12:16:29: start X-correlation... INFO @ Mon, 03 Jun 2019 12:16:29: end of X-cor INFO @ Mon, 03 Jun 2019 12:16:29: #2 finished! INFO @ Mon, 03 Jun 2019 12:16:29: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 12:16:29: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 12:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.05_model.r WARNING @ Mon, 03 Jun 2019 12:16:29: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:16:29: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 12:16:29: #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 12:16:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:16:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:16:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:16:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.20_summits.bed INFO @ Mon, 03 Jun 2019 12:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.10_summits.bed INFO @ Mon, 03 Jun 2019 12:17:03: Done! INFO @ Mon, 03 Jun 2019 12:17:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1692 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (909 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320157/SRX320157.05_summits.bed INFO @ Mon, 03 Jun 2019 12:17:09: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4737 records, 4 fields): 1754 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。