Job ID = 1294279 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,087,614 reads read : 24,087,614 reads written : 24,087,614 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: 00:06:54 24087614 reads; of these: 24087614 (100.00%) were unpaired; of these: 3403886 (14.13%) aligned 0 times 16349513 (67.88%) aligned exactly 1 time 4334215 (17.99%) aligned >1 times 85.87% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 6285467 / 20683728 = 0.3039 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 06:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.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 06:32:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:32:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.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 06:32:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:32:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.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 06:32:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:32:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:32:28: 1000000 INFO @ Mon, 03 Jun 2019 06:32:30: 1000000 INFO @ Mon, 03 Jun 2019 06:32:30: 1000000 INFO @ Mon, 03 Jun 2019 06:32:36: 2000000 INFO @ Mon, 03 Jun 2019 06:32:39: 2000000 INFO @ Mon, 03 Jun 2019 06:32:39: 2000000 INFO @ Mon, 03 Jun 2019 06:32:43: 3000000 INFO @ Mon, 03 Jun 2019 06:32:47: 3000000 INFO @ Mon, 03 Jun 2019 06:32:48: 3000000 INFO @ Mon, 03 Jun 2019 06:32:50: 4000000 INFO @ Mon, 03 Jun 2019 06:32:56: 4000000 INFO @ Mon, 03 Jun 2019 06:32:56: 4000000 INFO @ Mon, 03 Jun 2019 06:32:57: 5000000 INFO @ Mon, 03 Jun 2019 06:33:04: 6000000 INFO @ Mon, 03 Jun 2019 06:33:05: 5000000 INFO @ Mon, 03 Jun 2019 06:33:05: 5000000 INFO @ Mon, 03 Jun 2019 06:33:11: 7000000 INFO @ Mon, 03 Jun 2019 06:33:13: 6000000 INFO @ Mon, 03 Jun 2019 06:33:14: 6000000 INFO @ Mon, 03 Jun 2019 06:33:18: 8000000 INFO @ Mon, 03 Jun 2019 06:33:23: 7000000 INFO @ Mon, 03 Jun 2019 06:33:23: 7000000 INFO @ Mon, 03 Jun 2019 06:33:27: 9000000 INFO @ Mon, 03 Jun 2019 06:33:32: 8000000 INFO @ Mon, 03 Jun 2019 06:33:32: 8000000 INFO @ Mon, 03 Jun 2019 06:33:35: 10000000 INFO @ Mon, 03 Jun 2019 06:33:40: 9000000 INFO @ Mon, 03 Jun 2019 06:33:40: 9000000 INFO @ Mon, 03 Jun 2019 06:33:42: 11000000 INFO @ Mon, 03 Jun 2019 06:33:49: 12000000 INFO @ Mon, 03 Jun 2019 06:33:49: 10000000 INFO @ Mon, 03 Jun 2019 06:33:50: 10000000 INFO @ Mon, 03 Jun 2019 06:33:56: 13000000 INFO @ Mon, 03 Jun 2019 06:33:58: 11000000 INFO @ Mon, 03 Jun 2019 06:33:59: 11000000 INFO @ Mon, 03 Jun 2019 06:34:03: 14000000 INFO @ Mon, 03 Jun 2019 06:34:06: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:34:06: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:34:06: #1 total tags in treatment: 14398261 INFO @ Mon, 03 Jun 2019 06:34:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:34:06: #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 06:34:06: #1 tags after filtering in treatment: 14398261 INFO @ Mon, 03 Jun 2019 06:34:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:34:06: #1 finished! INFO @ Mon, 03 Jun 2019 06:34:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:34:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:34:07: #2 number of paired peaks: 361 WARNING @ Mon, 03 Jun 2019 06:34:07: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Mon, 03 Jun 2019 06:34:07: start model_add_line... INFO @ Mon, 03 Jun 2019 06:34:07: start X-correlation... INFO @ Mon, 03 Jun 2019 06:34:07: end of X-cor INFO @ Mon, 03 Jun 2019 06:34:07: #2 finished! INFO @ Mon, 03 Jun 2019 06:34:07: #2 predicted fragment length is 59 bps INFO @ Mon, 03 Jun 2019 06:34:07: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 03 Jun 2019 06:34:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.20_model.r WARNING @ Mon, 03 Jun 2019 06:34:07: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:34:07: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 03 Jun 2019 06:34:07: #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 06:34:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:34:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:34:08: 12000000 INFO @ Mon, 03 Jun 2019 06:34:08: 12000000 INFO @ Mon, 03 Jun 2019 06:34:16: 13000000 INFO @ Mon, 03 Jun 2019 06:34:17: 13000000 INFO @ Mon, 03 Jun 2019 06:34:24: 14000000 INFO @ Mon, 03 Jun 2019 06:34:25: 14000000 INFO @ Mon, 03 Jun 2019 06:34:27: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:34:27: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:34:27: #1 total tags in treatment: 14398261 INFO @ Mon, 03 Jun 2019 06:34:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:34:27: #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 06:34:28: #1 tags after filtering in treatment: 14398261 INFO @ Mon, 03 Jun 2019 06:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:34:28: #1 finished! INFO @ Mon, 03 Jun 2019 06:34:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:34:29: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:34:29: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:34:29: #1 total tags in treatment: 14398261 INFO @ Mon, 03 Jun 2019 06:34:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:34:29: #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 06:34:29: #1 tags after filtering in treatment: 14398261 INFO @ Mon, 03 Jun 2019 06:34:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:34:29: #1 finished! INFO @ Mon, 03 Jun 2019 06:34:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:34:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:34:29: #2 number of paired peaks: 361 WARNING @ Mon, 03 Jun 2019 06:34:29: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Mon, 03 Jun 2019 06:34:29: start model_add_line... INFO @ Mon, 03 Jun 2019 06:34:29: start X-correlation... INFO @ Mon, 03 Jun 2019 06:34:29: end of X-cor INFO @ Mon, 03 Jun 2019 06:34:29: #2 finished! INFO @ Mon, 03 Jun 2019 06:34:29: #2 predicted fragment length is 59 bps INFO @ Mon, 03 Jun 2019 06:34:29: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 03 Jun 2019 06:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.05_model.r WARNING @ Mon, 03 Jun 2019 06:34:29: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:34:29: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 03 Jun 2019 06:34:29: #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 06:34:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:34:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:34:30: #2 number of paired peaks: 361 WARNING @ Mon, 03 Jun 2019 06:34:30: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Mon, 03 Jun 2019 06:34:30: start model_add_line... INFO @ Mon, 03 Jun 2019 06:34:30: start X-correlation... INFO @ Mon, 03 Jun 2019 06:34:30: end of X-cor INFO @ Mon, 03 Jun 2019 06:34:30: #2 finished! INFO @ Mon, 03 Jun 2019 06:34:30: #2 predicted fragment length is 59 bps INFO @ Mon, 03 Jun 2019 06:34:30: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 03 Jun 2019 06:34:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.10_model.r WARNING @ Mon, 03 Jun 2019 06:34:30: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:34:30: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 03 Jun 2019 06:34:30: #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 06:34:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:34:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:34:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.20_summits.bed INFO @ Mon, 03 Jun 2019 06:35:06: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1071 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:35:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:35:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:35:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:35:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:35:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.05_summits.bed INFO @ Mon, 03 Jun 2019 06:35:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5508 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX220305/SRX220305.10_summits.bed INFO @ Mon, 03 Jun 2019 06:35:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2073 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。