Job ID = 1295748 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,799,313 reads read : 27,598,626 reads written : 27,598,626 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: 01:19:39 13799313 reads; of these: 13799313 (100.00%) were paired; of these: 3725926 (27.00%) aligned concordantly 0 times 6960914 (50.44%) aligned concordantly exactly 1 time 3112473 (22.56%) aligned concordantly >1 times ---- 3725926 pairs aligned concordantly 0 times; of these: 109512 (2.94%) aligned discordantly 1 time ---- 3616414 pairs aligned 0 times concordantly or discordantly; of these: 7232828 mates make up the pairs; of these: 6160905 (85.18%) aligned 0 times 266033 (3.68%) aligned exactly 1 time 805890 (11.14%) aligned >1 times 77.68% overall alignment rate Time searching: 01:19:39 Overall time: 01:19:39 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 5384340 / 5618488 = 0.9583 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 17:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.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 17:11:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:11:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.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 17:11:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:11:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.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 17:11:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:11:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:11:36: 1000000 INFO @ Mon, 03 Jun 2019 17:11:38: 1000000 INFO @ Mon, 03 Jun 2019 17:11:41: 1000000 INFO @ Mon, 03 Jun 2019 17:11:45: 2000000 INFO @ Mon, 03 Jun 2019 17:11:48: 2000000 INFO @ Mon, 03 Jun 2019 17:11:54: 3000000 INFO @ Mon, 03 Jun 2019 17:11:54: 2000000 INFO @ Mon, 03 Jun 2019 17:11:59: 3000000 INFO @ Mon, 03 Jun 2019 17:12:03: 4000000 INFO @ Mon, 03 Jun 2019 17:12:08: 3000000 INFO @ Mon, 03 Jun 2019 17:12:09: 4000000 INFO @ Mon, 03 Jun 2019 17:12:11: 5000000 INFO @ Mon, 03 Jun 2019 17:12:19: 5000000 INFO @ Mon, 03 Jun 2019 17:12:20: 6000000 INFO @ Mon, 03 Jun 2019 17:12:21: 4000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 17:12:29: 7000000 INFO @ Mon, 03 Jun 2019 17:12:29: 6000000 INFO @ Mon, 03 Jun 2019 17:12:34: 5000000 INFO @ Mon, 03 Jun 2019 17:12:38: 8000000 INFO @ Mon, 03 Jun 2019 17:12:39: 7000000 INFO @ Mon, 03 Jun 2019 17:12:47: 6000000 INFO @ Mon, 03 Jun 2019 17:12:48: 9000000 INFO @ Mon, 03 Jun 2019 17:12:50: 8000000 INFO @ Mon, 03 Jun 2019 17:12:57: 10000000 INFO @ Mon, 03 Jun 2019 17:13:00: 7000000 INFO @ Mon, 03 Jun 2019 17:13:01: 9000000 INFO @ Mon, 03 Jun 2019 17:13:03: #1 tag size is determined as 150 bps INFO @ Mon, 03 Jun 2019 17:13:03: #1 tag size = 150 INFO @ Mon, 03 Jun 2019 17:13:03: #1 total tags in treatment: 4727914 INFO @ Mon, 03 Jun 2019 17:13:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:13:03: #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 17:13:03: #1 tags after filtering in treatment: 319072 INFO @ Mon, 03 Jun 2019 17:13:03: #1 Redundant rate of treatment: 0.93 INFO @ Mon, 03 Jun 2019 17:13:03: #1 finished! INFO @ Mon, 03 Jun 2019 17:13:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:13:03: #2 number of paired peaks: 5863 INFO @ Mon, 03 Jun 2019 17:13:03: start model_add_line... INFO @ Mon, 03 Jun 2019 17:13:03: start X-correlation... INFO @ Mon, 03 Jun 2019 17:13:03: end of X-cor INFO @ Mon, 03 Jun 2019 17:13:03: #2 finished! INFO @ Mon, 03 Jun 2019 17:13:03: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 17:13:03: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 17:13:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.20_model.r WARNING @ Mon, 03 Jun 2019 17:13:03: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:13:03: #2 You may need to consider one of the other alternative d(s): 153 WARNING @ Mon, 03 Jun 2019 17:13:03: #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 17:13:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:13:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.20_summits.bed INFO @ Mon, 03 Jun 2019 17:13:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (331 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:13:12: 10000000 INFO @ Mon, 03 Jun 2019 17:13:13: 8000000 INFO @ Mon, 03 Jun 2019 17:13:18: #1 tag size is determined as 150 bps INFO @ Mon, 03 Jun 2019 17:13:18: #1 tag size = 150 INFO @ Mon, 03 Jun 2019 17:13:18: #1 total tags in treatment: 4727914 INFO @ Mon, 03 Jun 2019 17:13:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:13:18: #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 17:13:18: #1 tags after filtering in treatment: 319072 INFO @ Mon, 03 Jun 2019 17:13:18: #1 Redundant rate of treatment: 0.93 INFO @ Mon, 03 Jun 2019 17:13:18: #1 finished! INFO @ Mon, 03 Jun 2019 17:13:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:13:18: #2 number of paired peaks: 5863 INFO @ Mon, 03 Jun 2019 17:13:18: start model_add_line... INFO @ Mon, 03 Jun 2019 17:13:18: start X-correlation... INFO @ Mon, 03 Jun 2019 17:13:18: end of X-cor INFO @ Mon, 03 Jun 2019 17:13:18: #2 finished! INFO @ Mon, 03 Jun 2019 17:13:18: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 17:13:18: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 17:13:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.10_model.r WARNING @ Mon, 03 Jun 2019 17:13:18: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:13:18: #2 You may need to consider one of the other alternative d(s): 153 WARNING @ Mon, 03 Jun 2019 17:13:18: #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 17:13:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:13:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:13:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:13:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:13:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:13:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.10_summits.bed INFO @ Mon, 03 Jun 2019 17:13:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1009 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:13:27: 9000000 INFO @ Mon, 03 Jun 2019 17:13:41: 10000000 INFO @ Mon, 03 Jun 2019 17:13:49: #1 tag size is determined as 150 bps INFO @ Mon, 03 Jun 2019 17:13:49: #1 tag size = 150 INFO @ Mon, 03 Jun 2019 17:13:49: #1 total tags in treatment: 4727914 INFO @ Mon, 03 Jun 2019 17:13:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:13:49: #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 17:13:49: #1 tags after filtering in treatment: 319072 INFO @ Mon, 03 Jun 2019 17:13:49: #1 Redundant rate of treatment: 0.93 INFO @ Mon, 03 Jun 2019 17:13:49: #1 finished! INFO @ Mon, 03 Jun 2019 17:13:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:13:49: #2 number of paired peaks: 5863 INFO @ Mon, 03 Jun 2019 17:13:49: start model_add_line... INFO @ Mon, 03 Jun 2019 17:13:49: start X-correlation... INFO @ Mon, 03 Jun 2019 17:13:49: end of X-cor INFO @ Mon, 03 Jun 2019 17:13:49: #2 finished! INFO @ Mon, 03 Jun 2019 17:13:49: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 17:13:49: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 17:13:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.05_model.r WARNING @ Mon, 03 Jun 2019 17:13:49: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:13:49: #2 You may need to consider one of the other alternative d(s): 153 WARNING @ Mon, 03 Jun 2019 17:13:49: #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 17:13:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:13:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:13:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453999/SRX4453999.05_summits.bed INFO @ Mon, 03 Jun 2019 17:13:51: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2375 records, 4 fields): 6 millis CompletedMACS2peakCalling