Job ID = 11170889 sra ファイルのダウンロード中... Completed: 125729K bytes transferred in 21 seconds (47423K bits/sec), in 1 file. Completed: 123834K bytes transferred in 8 seconds (114463K bits/sec), in 1 file. Completed: 121800K bytes transferred in 5 seconds (172152K bits/sec), in 1 file. Completed: 120088K bytes transferred in 4 seconds (204690K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 5362760 spots for /home/okishinya/chipatlas/results/dm3/SRX1078887/SRR2084575.sra Written 5362760 spots for /home/okishinya/chipatlas/results/dm3/SRX1078887/SRR2084575.sra Read 5450510 spots for /home/okishinya/chipatlas/results/dm3/SRX1078887/SRR2084574.sra Written 5450510 spots for /home/okishinya/chipatlas/results/dm3/SRX1078887/SRR2084574.sra Read 5507098 spots for /home/okishinya/chipatlas/results/dm3/SRX1078887/SRR2084573.sra Written 5507098 spots for /home/okishinya/chipatlas/results/dm3/SRX1078887/SRR2084573.sra Read 5566758 spots for /home/okishinya/chipatlas/results/dm3/SRX1078887/SRR2084572.sra Written 5566758 spots for /home/okishinya/chipatlas/results/dm3/SRX1078887/SRR2084572.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:53 21887126 reads; of these: 21887126 (100.00%) were unpaired; of these: 1917710 (8.76%) aligned 0 times 13199071 (60.31%) aligned exactly 1 time 6770345 (30.93%) aligned >1 times 91.24% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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 12 files... [bam_rmdupse_core] 2602332 / 19969416 = 0.1303 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 @ Sat, 08 Sep 2018 11:40:49: # Command line: callpeak -t SRX1078887.bam -f BAM -g dm -n SRX1078887.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1078887.05 # format = BAM # ChIP-seq file = ['SRX1078887.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 @ Sat, 08 Sep 2018 11:40:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:40:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:40:49: # Command line: callpeak -t SRX1078887.bam -f BAM -g dm -n SRX1078887.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1078887.10 # format = BAM # ChIP-seq file = ['SRX1078887.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 @ Sat, 08 Sep 2018 11:40:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:40:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:40:49: # Command line: callpeak -t SRX1078887.bam -f BAM -g dm -n SRX1078887.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1078887.20 # format = BAM # ChIP-seq file = ['SRX1078887.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 @ Sat, 08 Sep 2018 11:40:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:40:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:40:55: 1000000 INFO @ Sat, 08 Sep 2018 11:40:55: 1000000 INFO @ Sat, 08 Sep 2018 11:40:55: 1000000 INFO @ Sat, 08 Sep 2018 11:41:02: 2000000 INFO @ Sat, 08 Sep 2018 11:41:02: 2000000 INFO @ Sat, 08 Sep 2018 11:41:02: 2000000 INFO @ Sat, 08 Sep 2018 11:41:09: 3000000 INFO @ Sat, 08 Sep 2018 11:41:09: 3000000 INFO @ Sat, 08 Sep 2018 11:41:09: 3000000 INFO @ Sat, 08 Sep 2018 11:41:16: 4000000 INFO @ Sat, 08 Sep 2018 11:41:16: 4000000 INFO @ Sat, 08 Sep 2018 11:41:16: 4000000 INFO @ Sat, 08 Sep 2018 11:41:23: 5000000 INFO @ Sat, 08 Sep 2018 11:41:23: 5000000 INFO @ Sat, 08 Sep 2018 11:41:23: 5000000 INFO @ Sat, 08 Sep 2018 11:41:30: 6000000 INFO @ Sat, 08 Sep 2018 11:41:30: 6000000 INFO @ Sat, 08 Sep 2018 11:41:30: 6000000 INFO @ Sat, 08 Sep 2018 11:41:37: 7000000 INFO @ Sat, 08 Sep 2018 11:41:37: 7000000 INFO @ Sat, 08 Sep 2018 11:41:37: 7000000 INFO @ Sat, 08 Sep 2018 11:41:44: 8000000 INFO @ Sat, 08 Sep 2018 11:41:44: 8000000 INFO @ Sat, 08 Sep 2018 11:41:44: 8000000 INFO @ Sat, 08 Sep 2018 11:41:51: 9000000 INFO @ Sat, 08 Sep 2018 11:41:51: 9000000 INFO @ Sat, 08 Sep 2018 11:41:51: 9000000 INFO @ Sat, 08 Sep 2018 11:41:57: 10000000 INFO @ Sat, 08 Sep 2018 11:41:57: 10000000 INFO @ Sat, 08 Sep 2018 11:41:57: 10000000 INFO @ Sat, 08 Sep 2018 11:42:04: 11000000 INFO @ Sat, 08 Sep 2018 11:42:04: 11000000 INFO @ Sat, 08 Sep 2018 11:42:04: 11000000 INFO @ Sat, 08 Sep 2018 11:42:11: 12000000 INFO @ Sat, 08 Sep 2018 11:42:11: 12000000 INFO @ Sat, 08 Sep 2018 11:42:11: 12000000 INFO @ Sat, 08 Sep 2018 11:42:19: 13000000 INFO @ Sat, 08 Sep 2018 11:42:19: 13000000 INFO @ Sat, 08 Sep 2018 11:42:19: 13000000 INFO @ Sat, 08 Sep 2018 11:42:27: 14000000 INFO @ Sat, 08 Sep 2018 11:42:27: 14000000 INFO @ Sat, 08 Sep 2018 11:42:27: 14000000 INFO @ Sat, 08 Sep 2018 11:42:35: 15000000 INFO @ Sat, 08 Sep 2018 11:42:35: 15000000 INFO @ Sat, 08 Sep 2018 11:42:35: 15000000 INFO @ Sat, 08 Sep 2018 11:42:43: 16000000 INFO @ Sat, 08 Sep 2018 11:42:43: 16000000 INFO @ Sat, 08 Sep 2018 11:42:43: 16000000 INFO @ Sat, 08 Sep 2018 11:42:51: 17000000 INFO @ Sat, 08 Sep 2018 11:42:51: 17000000 INFO @ Sat, 08 Sep 2018 11:42:51: 17000000 INFO @ Sat, 08 Sep 2018 11:42:55: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:42:55: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:42:55: #1 total tags in treatment: 17367084 INFO @ Sat, 08 Sep 2018 11:42:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:42:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:42:55: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:42:55: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:42:55: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:42:55: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:42:55: #1 total tags in treatment: 17367084 INFO @ Sat, 08 Sep 2018 11:42:55: #1 total tags in treatment: 17367084 INFO @ Sat, 08 Sep 2018 11:42:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:42:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:42:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:42:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:42:55: #1 tags after filtering in treatment: 17367084 INFO @ Sat, 08 Sep 2018 11:42:55: #1 tags after filtering in treatment: 17367084 INFO @ Sat, 08 Sep 2018 11:42:55: #1 tags after filtering in treatment: 17367084 INFO @ Sat, 08 Sep 2018 11:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:42:55: #1 finished! INFO @ Sat, 08 Sep 2018 11:42:55: #1 finished! INFO @ Sat, 08 Sep 2018 11:42:55: #1 finished! INFO @ Sat, 08 Sep 2018 11:42:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:42:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:42:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:42:56: #2 number of paired peaks: 594 WARNING @ Sat, 08 Sep 2018 11:42:56: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 08 Sep 2018 11:42:56: start model_add_line... INFO @ Sat, 08 Sep 2018 11:42:56: #2 number of paired peaks: 594 WARNING @ Sat, 08 Sep 2018 11:42:56: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 08 Sep 2018 11:42:56: start model_add_line... INFO @ Sat, 08 Sep 2018 11:42:56: #2 number of paired peaks: 594 WARNING @ Sat, 08 Sep 2018 11:42:56: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 08 Sep 2018 11:42:56: start model_add_line... INFO @ Sat, 08 Sep 2018 11:42:56: start X-correlation... INFO @ Sat, 08 Sep 2018 11:42:56: end of X-cor INFO @ Sat, 08 Sep 2018 11:42:56: #2 finished! INFO @ Sat, 08 Sep 2018 11:42:56: #2 predicted fragment length is 54 bps INFO @ Sat, 08 Sep 2018 11:42:56: #2 alternative fragment length(s) may be 2,54,543 bps INFO @ Sat, 08 Sep 2018 11:42:56: #2.2 Generate R script for model : SRX1078887.10_model.r WARNING @ Sat, 08 Sep 2018 11:42:56: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:42:56: #2 You may need to consider one of the other alternative d(s): 2,54,543 WARNING @ Sat, 08 Sep 2018 11:42:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:42:56: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:42:56: start X-correlation... INFO @ Sat, 08 Sep 2018 11:42:56: end of X-cor INFO @ Sat, 08 Sep 2018 11:42:56: #2 finished! INFO @ Sat, 08 Sep 2018 11:42:56: #2 predicted fragment length is 54 bps INFO @ Sat, 08 Sep 2018 11:42:56: #2 alternative fragment length(s) may be 2,54,543 bps INFO @ Sat, 08 Sep 2018 11:42:56: #2.2 Generate R script for model : SRX1078887.05_model.r WARNING @ Sat, 08 Sep 2018 11:42:56: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:42:56: #2 You may need to consider one of the other alternative d(s): 2,54,543 WARNING @ Sat, 08 Sep 2018 11:42:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:42:56: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:42:57: start X-correlation... INFO @ Sat, 08 Sep 2018 11:42:57: end of X-cor INFO @ Sat, 08 Sep 2018 11:42:57: #2 finished! INFO @ Sat, 08 Sep 2018 11:42:57: #2 predicted fragment length is 54 bps INFO @ Sat, 08 Sep 2018 11:42:57: #2 alternative fragment length(s) may be 2,54,543 bps INFO @ Sat, 08 Sep 2018 11:42:57: #2.2 Generate R script for model : SRX1078887.20_model.r WARNING @ Sat, 08 Sep 2018 11:42:57: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:42:57: #2 You may need to consider one of the other alternative d(s): 2,54,543 WARNING @ Sat, 08 Sep 2018 11:42:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:42:57: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:42:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:43:32: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:43:32: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:43:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:43:51: #4 Write output xls file... SRX1078887.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:43:51: #4 Write peak in narrowPeak format file... SRX1078887.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:43:51: #4 Write summits bed file... SRX1078887.20_summits.bed INFO @ Sat, 08 Sep 2018 11:43:51: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (701 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:43:51: #4 Write output xls file... SRX1078887.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:43:51: #4 Write peak in narrowPeak format file... SRX1078887.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:43:51: #4 Write summits bed file... SRX1078887.10_summits.bed INFO @ Sat, 08 Sep 2018 11:43:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2044 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:43:55: #4 Write output xls file... SRX1078887.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:43:55: #4 Write peak in narrowPeak format file... SRX1078887.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:43:55: #4 Write summits bed file... SRX1078887.05_summits.bed INFO @ Sat, 08 Sep 2018 11:43:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3195 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。