Job ID = 9028940 sra ファイルのダウンロード中... Completed: 767145K bytes transferred in 10 seconds (619368K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1946 0 --:--:-- 0:00:07 --:--:-- 14936 100 51114 0 51114 0 0 6241 0 --:--:-- 0:00:08 --:--:-- 28587 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... Written 36880923 spots for /home/okishinya/chipatlas/results/ce10/SRX997752/SRR1977499.sra Written 36880923 spots total rm: cannot remove `[DSE]RR*.fastq': 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:25 36880923 reads; of these: 36880923 (100.00%) were unpaired; of these: 7917359 (21.47%) aligned 0 times 22900395 (62.09%) aligned exactly 1 time 6063169 (16.44%) aligned >1 times 78.53% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 25610269 / 28963564 = 0.8842 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, 03 Jun 2017 12:38:50: # Command line: callpeak -t SRX997752.bam -f BAM -g ce -n SRX997752.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997752.10 # format = BAM # ChIP-seq file = ['SRX997752.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 12:38:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:38:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:38:50: # Command line: callpeak -t SRX997752.bam -f BAM -g ce -n SRX997752.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997752.05 # format = BAM # ChIP-seq file = ['SRX997752.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 12:38:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:38:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:38:50: # Command line: callpeak -t SRX997752.bam -f BAM -g ce -n SRX997752.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997752.20 # format = BAM # ChIP-seq file = ['SRX997752.bam'] # control file = None # effective genome size = 9.00e+07 # 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 INFO @ Sat, 03 Jun 2017 12:38:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:38:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:38:56: 1000000 INFO @ Sat, 03 Jun 2017 12:38:56: 1000000 INFO @ Sat, 03 Jun 2017 12:38:56: 1000000 INFO @ Sat, 03 Jun 2017 12:39:02: 2000000 INFO @ Sat, 03 Jun 2017 12:39:02: 2000000 INFO @ Sat, 03 Jun 2017 12:39:02: 2000000 INFO @ Sat, 03 Jun 2017 12:39:08: 3000000 INFO @ Sat, 03 Jun 2017 12:39:08: 3000000 INFO @ Sat, 03 Jun 2017 12:39:08: 3000000 INFO @ Sat, 03 Jun 2017 12:39:09: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:39:09: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:39:09: #1 total tags in treatment: 3353295 INFO @ Sat, 03 Jun 2017 12:39:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:39:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 12:39:09: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:39:09: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:39:09: #1 total tags in treatment: 3353295 INFO @ Sat, 03 Jun 2017 12:39:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:39:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 12:39:10: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:39:10: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:39:10: #1 total tags in treatment: 3353295 INFO @ Sat, 03 Jun 2017 12:39:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:39:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 12:39:10: #1 tags after filtering in treatment: 3352925 INFO @ Sat, 03 Jun 2017 12:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:39:10: #1 finished! INFO @ Sat, 03 Jun 2017 12:39:10: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:39:10: #1 tags after filtering in treatment: 3352925 INFO @ Sat, 03 Jun 2017 12:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:39:10: #1 finished! INFO @ Sat, 03 Jun 2017 12:39:10: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:39:11: #1 tags after filtering in treatment: 3352925 INFO @ Sat, 03 Jun 2017 12:39:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:39:11: #1 finished! INFO @ Sat, 03 Jun 2017 12:39:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:39:11: #2 number of paired peaks: 992 WARNING @ Sat, 03 Jun 2017 12:39:11: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Sat, 03 Jun 2017 12:39:11: start model_add_line... INFO @ Sat, 03 Jun 2017 12:39:11: #2 number of paired peaks: 992 WARNING @ Sat, 03 Jun 2017 12:39:11: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Sat, 03 Jun 2017 12:39:11: start model_add_line... INFO @ Sat, 03 Jun 2017 12:39:11: #2 number of paired peaks: 992 WARNING @ Sat, 03 Jun 2017 12:39:11: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Sat, 03 Jun 2017 12:39:11: start model_add_line... INFO @ Sat, 03 Jun 2017 12:39:17: start X-correlation... INFO @ Sat, 03 Jun 2017 12:39:17: end of X-cor INFO @ Sat, 03 Jun 2017 12:39:17: #2 finished! INFO @ Sat, 03 Jun 2017 12:39:17: #2 predicted fragment length is 38 bps INFO @ Sat, 03 Jun 2017 12:39:17: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sat, 03 Jun 2017 12:39:17: #2.2 Generate R script for model : SRX997752.20_model.r INFO @ Sat, 03 Jun 2017 12:39:17: start X-correlation... WARNING @ Sat, 03 Jun 2017 12:39:17: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:39:17: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sat, 03 Jun 2017 12:39:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 12:39:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:39:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:39:17: end of X-cor INFO @ Sat, 03 Jun 2017 12:39:17: #2 finished! INFO @ Sat, 03 Jun 2017 12:39:17: #2 predicted fragment length is 38 bps INFO @ Sat, 03 Jun 2017 12:39:17: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sat, 03 Jun 2017 12:39:17: #2.2 Generate R script for model : SRX997752.10_model.r WARNING @ Sat, 03 Jun 2017 12:39:17: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:39:17: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sat, 03 Jun 2017 12:39:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 12:39:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:39:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:39:18: start X-correlation... INFO @ Sat, 03 Jun 2017 12:39:18: end of X-cor INFO @ Sat, 03 Jun 2017 12:39:18: #2 finished! INFO @ Sat, 03 Jun 2017 12:39:18: #2 predicted fragment length is 38 bps INFO @ Sat, 03 Jun 2017 12:39:18: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sat, 03 Jun 2017 12:39:18: #2.2 Generate R script for model : SRX997752.05_model.r WARNING @ Sat, 03 Jun 2017 12:39:18: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:39:18: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sat, 03 Jun 2017 12:39:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 12:39:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:39:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:39:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:39:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:39:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:39:50: #4 Write output xls file... SRX997752.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:39:50: #4 Write peak in narrowPeak format file... SRX997752.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:39:50: #4 Write summits bed file... SRX997752.20_summits.bed INFO @ Sat, 03 Jun 2017 12:39:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (267 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:39:51: #4 Write output xls file... SRX997752.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:39:51: #4 Write peak in narrowPeak format file... SRX997752.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:39:51: #4 Write summits bed file... SRX997752.10_summits.bed INFO @ Sat, 03 Jun 2017 12:39:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (901 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:39:52: #4 Write output xls file... SRX997752.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:39:52: #4 Write peak in narrowPeak format file... SRX997752.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:39:52: #4 Write summits bed file... SRX997752.05_summits.bed INFO @ Sat, 03 Jun 2017 12:39:52: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2606 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。