Job ID = 1294838 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,616,808 reads read : 14,616,808 reads written : 14,616,808 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: 00:06:27 14616808 reads; of these: 14616808 (100.00%) were unpaired; of these: 855495 (5.85%) aligned 0 times 9702599 (66.38%) aligned exactly 1 time 4058714 (27.77%) aligned >1 times 94.15% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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] 3729556 / 13761313 = 0.2710 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 10:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.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 10:40:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:40:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.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 10:40:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:40:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.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 10:40:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:40:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:40:16: 1000000 INFO @ Mon, 03 Jun 2019 10:40:16: 1000000 INFO @ Mon, 03 Jun 2019 10:40:17: 1000000 INFO @ Mon, 03 Jun 2019 10:40:23: 2000000 INFO @ Mon, 03 Jun 2019 10:40:24: 2000000 INFO @ Mon, 03 Jun 2019 10:40:26: 2000000 INFO @ Mon, 03 Jun 2019 10:40:30: 3000000 INFO @ Mon, 03 Jun 2019 10:40:31: 3000000 INFO @ Mon, 03 Jun 2019 10:40:35: 3000000 INFO @ Mon, 03 Jun 2019 10:40:37: 4000000 INFO @ Mon, 03 Jun 2019 10:40:38: 4000000 INFO @ Mon, 03 Jun 2019 10:40:44: 5000000 INFO @ Mon, 03 Jun 2019 10:40:44: 4000000 INFO @ Mon, 03 Jun 2019 10:40:46: 5000000 INFO @ Mon, 03 Jun 2019 10:40:51: 6000000 INFO @ Mon, 03 Jun 2019 10:40:54: 5000000 INFO @ Mon, 03 Jun 2019 10:40:55: 6000000 INFO @ Mon, 03 Jun 2019 10:40:59: 7000000 INFO @ Mon, 03 Jun 2019 10:41:02: 7000000 INFO @ Mon, 03 Jun 2019 10:41:04: 6000000 INFO @ Mon, 03 Jun 2019 10:41:06: 8000000 INFO @ Mon, 03 Jun 2019 10:41:10: 8000000 INFO @ Mon, 03 Jun 2019 10:41:13: 7000000 INFO @ Mon, 03 Jun 2019 10:41:13: 9000000 INFO @ Mon, 03 Jun 2019 10:41:16: 9000000 INFO @ Mon, 03 Jun 2019 10:41:20: 10000000 INFO @ Mon, 03 Jun 2019 10:41:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:41:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:41:21: #1 total tags in treatment: 10031757 INFO @ Mon, 03 Jun 2019 10:41:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:41:21: #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 10:41:21: #1 tags after filtering in treatment: 10031757 INFO @ Mon, 03 Jun 2019 10:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:41:21: #1 finished! INFO @ Mon, 03 Jun 2019 10:41:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:41:22: 8000000 INFO @ Mon, 03 Jun 2019 10:41:22: #2 number of paired peaks: 324 WARNING @ Mon, 03 Jun 2019 10:41:22: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Mon, 03 Jun 2019 10:41:22: start model_add_line... INFO @ Mon, 03 Jun 2019 10:41:22: start X-correlation... INFO @ Mon, 03 Jun 2019 10:41:22: end of X-cor INFO @ Mon, 03 Jun 2019 10:41:22: #2 finished! INFO @ Mon, 03 Jun 2019 10:41:22: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 10:41:22: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 10:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.10_model.r WARNING @ Mon, 03 Jun 2019 10:41:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:41:22: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 10:41:22: #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 10:41:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:41:23: 10000000 INFO @ Mon, 03 Jun 2019 10:41:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:41:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:41:24: #1 total tags in treatment: 10031757 INFO @ Mon, 03 Jun 2019 10:41:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:41:24: #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 10:41:24: #1 tags after filtering in treatment: 10031757 INFO @ Mon, 03 Jun 2019 10:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:41:24: #1 finished! INFO @ Mon, 03 Jun 2019 10:41:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:41:25: #2 number of paired peaks: 324 WARNING @ Mon, 03 Jun 2019 10:41:25: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Mon, 03 Jun 2019 10:41:25: start model_add_line... INFO @ Mon, 03 Jun 2019 10:41:25: start X-correlation... INFO @ Mon, 03 Jun 2019 10:41:25: end of X-cor INFO @ Mon, 03 Jun 2019 10:41:25: #2 finished! INFO @ Mon, 03 Jun 2019 10:41:25: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 10:41:25: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 10:41:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.05_model.r WARNING @ Mon, 03 Jun 2019 10:41:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:41:25: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 10:41:25: #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 10:41:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:41:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:41:30: 9000000 INFO @ Mon, 03 Jun 2019 10:41:39: 10000000 INFO @ Mon, 03 Jun 2019 10:41:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:41:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:41:39: #1 total tags in treatment: 10031757 INFO @ Mon, 03 Jun 2019 10:41:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:41:39: #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 10:41:39: #1 tags after filtering in treatment: 10031757 INFO @ Mon, 03 Jun 2019 10:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:41:39: #1 finished! INFO @ Mon, 03 Jun 2019 10:41:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:41:40: #2 number of paired peaks: 324 WARNING @ Mon, 03 Jun 2019 10:41:40: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Mon, 03 Jun 2019 10:41:40: start model_add_line... INFO @ Mon, 03 Jun 2019 10:41:40: start X-correlation... INFO @ Mon, 03 Jun 2019 10:41:40: end of X-cor INFO @ Mon, 03 Jun 2019 10:41:40: #2 finished! INFO @ Mon, 03 Jun 2019 10:41:40: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 10:41:40: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 10:41:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.20_model.r WARNING @ Mon, 03 Jun 2019 10:41:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:41:40: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 10:41:40: #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 10:41:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:41:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:41:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:41:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.10_summits.bed INFO @ Mon, 03 Jun 2019 10:42:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1528 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:42:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:42:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.05_summits.bed INFO @ Mon, 03 Jun 2019 10:42:07: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1999 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:42:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287937/SRX287937.20_summits.bed INFO @ Mon, 03 Jun 2019 10:42:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1176 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。