Job ID = 1303186 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,971,456 reads read : 21,971,456 reads written : 21,971,456 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: 00:06:41 21971456 reads; of these: 21971456 (100.00%) were unpaired; of these: 4545302 (20.69%) aligned 0 times 14750272 (67.13%) aligned exactly 1 time 2675882 (12.18%) aligned >1 times 79.31% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 12728832 / 17426154 = 0.7304 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 20:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.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 20:37:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:37:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.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 20:37:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:37:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.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 20:37:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:37:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:37:31: 1000000 INFO @ Mon, 03 Jun 2019 20:37:31: 1000000 INFO @ Mon, 03 Jun 2019 20:37:31: 1000000 INFO @ Mon, 03 Jun 2019 20:37:39: 2000000 INFO @ Mon, 03 Jun 2019 20:37:39: 2000000 INFO @ Mon, 03 Jun 2019 20:37:40: 2000000 INFO @ Mon, 03 Jun 2019 20:37:47: 3000000 INFO @ Mon, 03 Jun 2019 20:37:48: 3000000 INFO @ Mon, 03 Jun 2019 20:37:49: 3000000 INFO @ Mon, 03 Jun 2019 20:37:55: 4000000 INFO @ Mon, 03 Jun 2019 20:37:58: 4000000 INFO @ Mon, 03 Jun 2019 20:37:58: 4000000 INFO @ Mon, 03 Jun 2019 20:38:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:38:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:38:01: #1 total tags in treatment: 4697322 INFO @ Mon, 03 Jun 2019 20:38:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:38:01: #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 20:38:01: #1 tags after filtering in treatment: 4697322 INFO @ Mon, 03 Jun 2019 20:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:38:01: #1 finished! INFO @ Mon, 03 Jun 2019 20:38:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:38:02: #2 number of paired peaks: 2533 INFO @ Mon, 03 Jun 2019 20:38:02: start model_add_line... INFO @ Mon, 03 Jun 2019 20:38:02: start X-correlation... INFO @ Mon, 03 Jun 2019 20:38:02: end of X-cor INFO @ Mon, 03 Jun 2019 20:38:02: #2 finished! INFO @ Mon, 03 Jun 2019 20:38:02: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 20:38:02: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 20:38:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.20_model.r WARNING @ Mon, 03 Jun 2019 20:38:02: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:38:02: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 20:38:02: #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 20:38:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:38:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:38:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:38:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:38:03: #1 total tags in treatment: 4697322 INFO @ Mon, 03 Jun 2019 20:38:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:38:03: #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 20:38:04: #1 tags after filtering in treatment: 4697322 INFO @ Mon, 03 Jun 2019 20:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:38:04: #1 finished! INFO @ Mon, 03 Jun 2019 20:38:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:38:04: #2 number of paired peaks: 2533 INFO @ Mon, 03 Jun 2019 20:38:04: start model_add_line... INFO @ Mon, 03 Jun 2019 20:38:04: start X-correlation... INFO @ Mon, 03 Jun 2019 20:38:04: end of X-cor INFO @ Mon, 03 Jun 2019 20:38:04: #2 finished! INFO @ Mon, 03 Jun 2019 20:38:04: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 20:38:04: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 20:38:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.05_model.r WARNING @ Mon, 03 Jun 2019 20:38:04: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:38:04: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 20:38:04: #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 20:38:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:38:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:38:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:38:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:38:04: #1 total tags in treatment: 4697322 INFO @ Mon, 03 Jun 2019 20:38:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:38:04: #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 20:38:04: #1 tags after filtering in treatment: 4697322 INFO @ Mon, 03 Jun 2019 20:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:38:04: #1 finished! INFO @ Mon, 03 Jun 2019 20:38:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:38:05: #2 number of paired peaks: 2533 INFO @ Mon, 03 Jun 2019 20:38:05: start model_add_line... INFO @ Mon, 03 Jun 2019 20:38:05: start X-correlation... INFO @ Mon, 03 Jun 2019 20:38:05: end of X-cor INFO @ Mon, 03 Jun 2019 20:38:05: #2 finished! INFO @ Mon, 03 Jun 2019 20:38:05: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 20:38:05: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 20:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.10_model.r WARNING @ Mon, 03 Jun 2019 20:38:05: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:38:05: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 20:38:05: #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 20:38:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:38:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:38:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:38:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:38:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:38:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:38:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.20_summits.bed INFO @ Mon, 03 Jun 2019 20:38:23: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2123 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:38:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:38:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:38:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.05_summits.bed INFO @ Mon, 03 Jun 2019 20:38:26: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7508 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:38:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:38:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:38:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933900/SRX4933900.10_summits.bed INFO @ Mon, 03 Jun 2019 20:38:27: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4468 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。