Job ID = 1294489 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,363,085 reads read : 11,363,085 reads written : 11,363,085 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: 00:05:04 11363085 reads; of these: 11363085 (100.00%) were unpaired; of these: 662092 (5.83%) aligned 0 times 7157281 (62.99%) aligned exactly 1 time 3543712 (31.19%) aligned >1 times 94.17% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 1421935 / 10700993 = 0.1329 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 08:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.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 08:34:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:34:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.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 08:34:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:34:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.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 08:34:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:34:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:34:16: 1000000 INFO @ Mon, 03 Jun 2019 08:34:17: 1000000 INFO @ Mon, 03 Jun 2019 08:34:18: 1000000 INFO @ Mon, 03 Jun 2019 08:34:25: 2000000 INFO @ Mon, 03 Jun 2019 08:34:27: 2000000 INFO @ Mon, 03 Jun 2019 08:34:28: 2000000 INFO @ Mon, 03 Jun 2019 08:34:34: 3000000 INFO @ Mon, 03 Jun 2019 08:34:37: 3000000 INFO @ Mon, 03 Jun 2019 08:34:38: 3000000 INFO @ Mon, 03 Jun 2019 08:34:42: 4000000 INFO @ Mon, 03 Jun 2019 08:34:46: 4000000 INFO @ Mon, 03 Jun 2019 08:34:47: 4000000 INFO @ Mon, 03 Jun 2019 08:34:51: 5000000 INFO @ Mon, 03 Jun 2019 08:34:55: 5000000 INFO @ Mon, 03 Jun 2019 08:34:57: 5000000 INFO @ Mon, 03 Jun 2019 08:34:59: 6000000 INFO @ Mon, 03 Jun 2019 08:35:05: 6000000 INFO @ Mon, 03 Jun 2019 08:35:06: 6000000 INFO @ Mon, 03 Jun 2019 08:35:08: 7000000 INFO @ Mon, 03 Jun 2019 08:35:14: 7000000 INFO @ Mon, 03 Jun 2019 08:35:16: 8000000 INFO @ Mon, 03 Jun 2019 08:35:16: 7000000 INFO @ Mon, 03 Jun 2019 08:35:23: 8000000 INFO @ Mon, 03 Jun 2019 08:35:24: 9000000 INFO @ Mon, 03 Jun 2019 08:35:25: 8000000 INFO @ Mon, 03 Jun 2019 08:35:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:35:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:35:27: #1 total tags in treatment: 9279058 INFO @ Mon, 03 Jun 2019 08:35:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:35:27: #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 08:35:27: #1 tags after filtering in treatment: 9279058 INFO @ Mon, 03 Jun 2019 08:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:35:27: #1 finished! INFO @ Mon, 03 Jun 2019 08:35:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:35:28: #2 number of paired peaks: 457 WARNING @ Mon, 03 Jun 2019 08:35:28: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Mon, 03 Jun 2019 08:35:28: start model_add_line... INFO @ Mon, 03 Jun 2019 08:35:28: start X-correlation... INFO @ Mon, 03 Jun 2019 08:35:28: end of X-cor INFO @ Mon, 03 Jun 2019 08:35:28: #2 finished! INFO @ Mon, 03 Jun 2019 08:35:28: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:35:28: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.20_model.r WARNING @ Mon, 03 Jun 2019 08:35:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:35:28: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:35:28: #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 08:35:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:35:33: 9000000 INFO @ Mon, 03 Jun 2019 08:35:35: 9000000 INFO @ Mon, 03 Jun 2019 08:35:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:35:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:35:35: #1 total tags in treatment: 9279058 INFO @ Mon, 03 Jun 2019 08:35:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:35:35: #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 08:35:36: #1 tags after filtering in treatment: 9279058 INFO @ Mon, 03 Jun 2019 08:35:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:35:36: #1 finished! INFO @ Mon, 03 Jun 2019 08:35:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:35:37: #2 number of paired peaks: 457 WARNING @ Mon, 03 Jun 2019 08:35:37: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Mon, 03 Jun 2019 08:35:37: start model_add_line... INFO @ Mon, 03 Jun 2019 08:35:37: start X-correlation... INFO @ Mon, 03 Jun 2019 08:35:37: end of X-cor INFO @ Mon, 03 Jun 2019 08:35:37: #2 finished! INFO @ Mon, 03 Jun 2019 08:35:37: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:35:37: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:35:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.05_model.r WARNING @ Mon, 03 Jun 2019 08:35:37: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:35:37: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:35:37: #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 08:35:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:35:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:35:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:35:37: #1 total tags in treatment: 9279058 INFO @ Mon, 03 Jun 2019 08:35:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:35:37: #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 08:35:38: #1 tags after filtering in treatment: 9279058 INFO @ Mon, 03 Jun 2019 08:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:35:38: #1 finished! INFO @ Mon, 03 Jun 2019 08:35:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:35:39: #2 number of paired peaks: 457 WARNING @ Mon, 03 Jun 2019 08:35:39: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Mon, 03 Jun 2019 08:35:39: start model_add_line... INFO @ Mon, 03 Jun 2019 08:35:39: start X-correlation... INFO @ Mon, 03 Jun 2019 08:35:39: end of X-cor INFO @ Mon, 03 Jun 2019 08:35:39: #2 finished! INFO @ Mon, 03 Jun 2019 08:35:39: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:35:39: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.10_model.r WARNING @ Mon, 03 Jun 2019 08:35:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:35:39: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:35:39: #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 08:35:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:35:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:36:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:36:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:36:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:36:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.20_summits.bed INFO @ Mon, 03 Jun 2019 08:36:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1108 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.05_summits.bed INFO @ Mon, 03 Jun 2019 08:36:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1884 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:36:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:36:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:36:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287689/SRX287689.10_summits.bed INFO @ Mon, 03 Jun 2019 08:36:19: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1570 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。