Job ID = 9029298 sra ファイルのダウンロード中... Completed: 388523K bytes transferred in 6 seconds (484503K 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 12007 0 12007 0 0 1560 0 --:--:-- 0:00:07 --:--:-- 10866 100 34589 0 34589 0 0 4056 0 --:--:-- 0:00:08 --:--:-- 17866 100 82373 0 82373 0 0 8651 0 --:--:-- 0:00:09 --:--:-- 28094 100 146k 0 146k 0 0 14510 0 --:--:-- 0:00:10 --:--:-- 39948 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 11768628 spots for /home/okishinya/chipatlas/results/dm3/SRX1537619/SRR3109314.sra Written 11768628 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: 00:04:31 11768628 reads; of these: 11768628 (100.00%) were unpaired; of these: 3932640 (33.42%) aligned 0 times 4700755 (39.94%) aligned exactly 1 time 3135233 (26.64%) aligned >1 times 66.58% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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_rmdupse_core] 2914246 / 7835988 = 0.3719 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 13:12:29: # Command line: callpeak -t SRX1537619.bam -f BAM -g dm -n SRX1537619.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1537619.20 # format = BAM # ChIP-seq file = ['SRX1537619.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 13:12:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:29: # Command line: callpeak -t SRX1537619.bam -f BAM -g dm -n SRX1537619.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1537619.05 # format = BAM # ChIP-seq file = ['SRX1537619.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 13:12:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:29: # Command line: callpeak -t SRX1537619.bam -f BAM -g dm -n SRX1537619.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1537619.10 # format = BAM # ChIP-seq file = ['SRX1537619.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 13:12:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:35: 1000000 INFO @ Sat, 03 Jun 2017 13:12:35: 1000000 INFO @ Sat, 03 Jun 2017 13:12:35: 1000000 INFO @ Sat, 03 Jun 2017 13:12:41: 2000000 INFO @ Sat, 03 Jun 2017 13:12:41: 2000000 INFO @ Sat, 03 Jun 2017 13:12:41: 2000000 INFO @ Sat, 03 Jun 2017 13:12:47: 3000000 INFO @ Sat, 03 Jun 2017 13:12:47: 3000000 INFO @ Sat, 03 Jun 2017 13:12:47: 3000000 INFO @ Sat, 03 Jun 2017 13:12:53: 4000000 INFO @ Sat, 03 Jun 2017 13:12:53: 4000000 INFO @ Sat, 03 Jun 2017 13:12:53: 4000000 INFO @ Sat, 03 Jun 2017 13:12:58: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:12:58: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:12:58: #1 total tags in treatment: 4921742 INFO @ Sat, 03 Jun 2017 13:12:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:12:58: #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 13:12:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:12:59: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:12:59: #1 total tags in treatment: 4921742 INFO @ Sat, 03 Jun 2017 13:12:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:12:59: #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 13:12:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:12:59: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:12:59: #1 total tags in treatment: 4921742 INFO @ Sat, 03 Jun 2017 13:12:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:12:59: #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 13:12:59: #1 tags after filtering in treatment: 4920833 INFO @ Sat, 03 Jun 2017 13:12:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:12:59: #1 finished! INFO @ Sat, 03 Jun 2017 13:12:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:00: #1 tags after filtering in treatment: 4920833 INFO @ Sat, 03 Jun 2017 13:13:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:00: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:00: #1 tags after filtering in treatment: 4920833 INFO @ Sat, 03 Jun 2017 13:13:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:00: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:00: #2 number of paired peaks: 2173 INFO @ Sat, 03 Jun 2017 13:13:00: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:01: #2 number of paired peaks: 2173 INFO @ Sat, 03 Jun 2017 13:13:01: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:01: #2 number of paired peaks: 2173 INFO @ Sat, 03 Jun 2017 13:13:01: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:08: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:08: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:08: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:08: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:13:08: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Jun 2017 13:13:08: #2.2 Generate R script for model : SRX1537619.10_model.r WARNING @ Sat, 03 Jun 2017 13:13:08: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:13:08: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Jun 2017 13:13:08: #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 13:13:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:09: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:09: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:09: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:09: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:13:09: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Jun 2017 13:13:09: #2.2 Generate R script for model : SRX1537619.05_model.r WARNING @ Sat, 03 Jun 2017 13:13:09: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:13:09: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Jun 2017 13:13:09: #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 13:13:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:09: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:09: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:09: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:09: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:13:09: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Jun 2017 13:13:09: #2.2 Generate R script for model : SRX1537619.20_model.r WARNING @ Sat, 03 Jun 2017 13:13:09: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:13:09: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Jun 2017 13:13:09: #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 13:13:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:58: #4 Write output xls file... SRX1537619.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:13:58: #4 Write peak in narrowPeak format file... SRX1537619.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:13:58: #4 Write summits bed file... SRX1537619.10_summits.bed INFO @ Sat, 03 Jun 2017 13:13:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2144 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:13:59: #4 Write output xls file... SRX1537619.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:13:59: #4 Write peak in narrowPeak format file... SRX1537619.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:13:59: #4 Write summits bed file... SRX1537619.05_summits.bed INFO @ Sat, 03 Jun 2017 13:13:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3527 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:00: #4 Write output xls file... SRX1537619.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:00: #4 Write peak in narrowPeak format file... SRX1537619.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:00: #4 Write summits bed file... SRX1537619.20_summits.bed INFO @ Sat, 03 Jun 2017 13:14:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1098 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。