Job ID = 9029584 sra ファイルのダウンロード中... Completed: 1411504K bytes transferred in 16 seconds (710785K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 14324 0 14324 0 0 1859 0 --:--:-- 0:00:07 --:--:-- 12835 100 62318 0 62318 0 0 7164 0 --:--:-- 0:00:08 --:--:-- 29492 100 65433 0 65433 0 0 7521 0 --:--:-- 0:00:08 --:--:-- 30952 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 25208995 spots for /home/okishinya/chipatlas/results/dm3/SRX1850480/SRR3675037.sra Written 25208995 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: 00:17:00 25208995 reads; of these: 25208995 (100.00%) were unpaired; of these: 1867540 (7.41%) aligned 0 times 19978564 (79.25%) aligned exactly 1 time 3362891 (13.34%) aligned >1 times 92.59% overall alignment rate Time searching: 00:17:00 Overall time: 00:17:00 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] 21590235 / 23341455 = 0.9250 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 14:37:25: # Command line: callpeak -t SRX1850480.bam -f BAM -g dm -n SRX1850480.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1850480.05 # format = BAM # ChIP-seq file = ['SRX1850480.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 INFO @ Sat, 03 Jun 2017 14:37:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:37:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:37:25: # Command line: callpeak -t SRX1850480.bam -f BAM -g dm -n SRX1850480.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1850480.20 # format = BAM # ChIP-seq file = ['SRX1850480.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 INFO @ Sat, 03 Jun 2017 14:37:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:37:25: # Command line: callpeak -t SRX1850480.bam -f BAM -g dm -n SRX1850480.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1850480.10 # format = BAM # ChIP-seq file = ['SRX1850480.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 INFO @ Sat, 03 Jun 2017 14:37:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:37:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:37:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:37:33: 1000000 INFO @ Sat, 03 Jun 2017 14:37:36: 1000000 INFO @ Sat, 03 Jun 2017 14:37:36: 1000000 INFO @ Sat, 03 Jun 2017 14:37:38: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:37:38: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:37:38: #1 total tags in treatment: 1751220 INFO @ Sat, 03 Jun 2017 14:37:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:37:38: #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 14:37:39: #1 tags after filtering in treatment: 1746210 INFO @ Sat, 03 Jun 2017 14:37:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:37:39: #1 finished! INFO @ Sat, 03 Jun 2017 14:37:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:37:39: #2 number of paired peaks: 3335 INFO @ Sat, 03 Jun 2017 14:37:39: start model_add_line... INFO @ Sat, 03 Jun 2017 14:37:43: start X-correlation... INFO @ Sat, 03 Jun 2017 14:37:43: end of X-cor INFO @ Sat, 03 Jun 2017 14:37:43: #2 finished! INFO @ Sat, 03 Jun 2017 14:37:43: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Jun 2017 14:37:43: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 03 Jun 2017 14:37:43: #2.2 Generate R script for model : SRX1850480.05_model.r WARNING @ Sat, 03 Jun 2017 14:37:43: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:37:43: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 03 Jun 2017 14:37:43: #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 14:37:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:37:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:37:45: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:37:45: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:37:45: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:37:45: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:37:45: #1 total tags in treatment: 1751220 INFO @ Sat, 03 Jun 2017 14:37:45: #1 total tags in treatment: 1751220 INFO @ Sat, 03 Jun 2017 14:37:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:37:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:37:45: #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 14:37:45: #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 14:37:46: #1 tags after filtering in treatment: 1746210 INFO @ Sat, 03 Jun 2017 14:37:46: #1 tags after filtering in treatment: 1746210 INFO @ Sat, 03 Jun 2017 14:37:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:37:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:37:46: #1 finished! INFO @ Sat, 03 Jun 2017 14:37:46: #1 finished! INFO @ Sat, 03 Jun 2017 14:37:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:37:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:37:46: #2 number of paired peaks: 3335 INFO @ Sat, 03 Jun 2017 14:37:46: start model_add_line... INFO @ Sat, 03 Jun 2017 14:37:46: #2 number of paired peaks: 3335 INFO @ Sat, 03 Jun 2017 14:37:46: start model_add_line... INFO @ Sat, 03 Jun 2017 14:37:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:37:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:37:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:37:50: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Jun 2017 14:37:50: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 03 Jun 2017 14:37:50: #2.2 Generate R script for model : SRX1850480.20_model.r INFO @ Sat, 03 Jun 2017 14:37:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:37:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:37:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:37:50: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Jun 2017 14:37:50: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 03 Jun 2017 14:37:50: #2.2 Generate R script for model : SRX1850480.10_model.r WARNING @ Sat, 03 Jun 2017 14:37:50: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:37:50: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 03 Jun 2017 14:37:50: #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 14:37:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:37:50: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 03 Jun 2017 14:37:50: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:37:50: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 03 Jun 2017 14:37:50: #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 14:37:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:37:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:37:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:38:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:38:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:38:03: #4 Write output xls file... SRX1850480.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:38:03: #4 Write peak in narrowPeak format file... SRX1850480.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:38:03: #4 Write summits bed file... SRX1850480.05_summits.bed INFO @ Sat, 03 Jun 2017 14:38:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2885 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write output xls file... SRX1850480.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write peak in narrowPeak format file... SRX1850480.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write summits bed file... SRX1850480.10_summits.bed INFO @ Sat, 03 Jun 2017 14:38:09: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (781 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write output xls file... SRX1850480.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write peak in narrowPeak format file... SRX1850480.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write summits bed file... SRX1850480.20_summits.bed INFO @ Sat, 03 Jun 2017 14:38:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (337 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。