Job ID = 9029864 sra ファイルのダウンロード中... Completed: 436236K bytes transferred in 6 seconds (522421K 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 --:--:-- 0 101 5455 0 5455 0 0 766 0 --:--:-- 0:00:07 --:--:-- 10490 100 30318 0 30318 0 0 3663 0 --:--:-- 0:00:08 --:--:-- 18035 100 53182 0 53182 0 0 5948 0 --:--:-- 0:00:08 --:--:-- 22688 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 18686024 spots for /home/okishinya/chipatlas/results/dm3/SRX2417580/SRR5101092.sra Written 18686024 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: 00:10:39 18686024 reads; of these: 18686024 (100.00%) were unpaired; of these: 2708035 (14.49%) aligned 0 times 7467789 (39.96%) aligned exactly 1 time 8510200 (45.54%) aligned >1 times 85.51% overall alignment rate Time searching: 00:10:39 Overall time: 00:10:39 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] 2098453 / 15977989 = 0.1313 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 15:47:42: # Command line: callpeak -t SRX2417580.bam -f BAM -g dm -n SRX2417580.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2417580.05 # format = BAM # ChIP-seq file = ['SRX2417580.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 15:47:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:42: # Command line: callpeak -t SRX2417580.bam -f BAM -g dm -n SRX2417580.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2417580.10 # format = BAM # ChIP-seq file = ['SRX2417580.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 15:47:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:42: # Command line: callpeak -t SRX2417580.bam -f BAM -g dm -n SRX2417580.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2417580.20 # format = BAM # ChIP-seq file = ['SRX2417580.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 15:47:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:49: 1000000 INFO @ Sat, 03 Jun 2017 15:47:49: 1000000 INFO @ Sat, 03 Jun 2017 15:47:49: 1000000 INFO @ Sat, 03 Jun 2017 15:47:56: 2000000 INFO @ Sat, 03 Jun 2017 15:47:56: 2000000 INFO @ Sat, 03 Jun 2017 15:47:56: 2000000 INFO @ Sat, 03 Jun 2017 15:48:02: 3000000 INFO @ Sat, 03 Jun 2017 15:48:03: 3000000 INFO @ Sat, 03 Jun 2017 15:48:03: 3000000 INFO @ Sat, 03 Jun 2017 15:48:09: 4000000 INFO @ Sat, 03 Jun 2017 15:48:10: 4000000 INFO @ Sat, 03 Jun 2017 15:48:10: 4000000 INFO @ Sat, 03 Jun 2017 15:48:15: 5000000 INFO @ Sat, 03 Jun 2017 15:48:17: 5000000 INFO @ Sat, 03 Jun 2017 15:48:17: 5000000 INFO @ Sat, 03 Jun 2017 15:48:22: 6000000 INFO @ Sat, 03 Jun 2017 15:48:24: 6000000 INFO @ Sat, 03 Jun 2017 15:48:25: 6000000 INFO @ Sat, 03 Jun 2017 15:48:28: 7000000 INFO @ Sat, 03 Jun 2017 15:48:31: 7000000 INFO @ Sat, 03 Jun 2017 15:48:33: 7000000 INFO @ Sat, 03 Jun 2017 15:48:34: 8000000 INFO @ Sat, 03 Jun 2017 15:48:38: 8000000 INFO @ Sat, 03 Jun 2017 15:48:41: 8000000 INFO @ Sat, 03 Jun 2017 15:48:41: 9000000 INFO @ Sat, 03 Jun 2017 15:48:45: 9000000 INFO @ Sat, 03 Jun 2017 15:48:47: 10000000 INFO @ Sat, 03 Jun 2017 15:48:48: 9000000 INFO @ Sat, 03 Jun 2017 15:48:53: 10000000 INFO @ Sat, 03 Jun 2017 15:48:54: 11000000 INFO @ Sat, 03 Jun 2017 15:48:56: 10000000 INFO @ Sat, 03 Jun 2017 15:49:00: 11000000 INFO @ Sat, 03 Jun 2017 15:49:00: 12000000 INFO @ Sat, 03 Jun 2017 15:49:04: 11000000 INFO @ Sat, 03 Jun 2017 15:49:06: 13000000 INFO @ Sat, 03 Jun 2017 15:49:07: 12000000 INFO @ Sat, 03 Jun 2017 15:49:12: 12000000 INFO @ Sat, 03 Jun 2017 15:49:12: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:49:12: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:49:12: #1 total tags in treatment: 13879536 INFO @ Sat, 03 Jun 2017 15:49:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:49:12: #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 15:49:14: 13000000 INFO @ Sat, 03 Jun 2017 15:49:15: #1 tags after filtering in treatment: 13877070 INFO @ Sat, 03 Jun 2017 15:49:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:49:15: #1 finished! INFO @ Sat, 03 Jun 2017 15:49:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:49:17: #2 number of paired peaks: 1123 INFO @ Sat, 03 Jun 2017 15:49:17: start model_add_line... INFO @ Sat, 03 Jun 2017 15:49:19: 13000000 INFO @ Sat, 03 Jun 2017 15:49:21: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:49:21: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:49:21: #1 total tags in treatment: 13879536 INFO @ Sat, 03 Jun 2017 15:49:21: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:49:21: #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 15:49:23: #1 tags after filtering in treatment: 13877070 INFO @ Sat, 03 Jun 2017 15:49:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:49:23: #1 finished! INFO @ Sat, 03 Jun 2017 15:49:23: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:49:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:49:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:49:25: #1 total tags in treatment: 13879536 INFO @ Sat, 03 Jun 2017 15:49:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:49:25: #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 15:49:25: #2 number of paired peaks: 1123 INFO @ Sat, 03 Jun 2017 15:49:25: start model_add_line... INFO @ Sat, 03 Jun 2017 15:49:27: start X-correlation... INFO @ Sat, 03 Jun 2017 15:49:27: end of X-cor INFO @ Sat, 03 Jun 2017 15:49:27: #2 finished! INFO @ Sat, 03 Jun 2017 15:49:27: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:49:27: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:49:27: #2.2 Generate R script for model : SRX2417580.10_model.r WARNING @ Sat, 03 Jun 2017 15:49:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:49:27: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:49:27: #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 15:49:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:49:28: #1 tags after filtering in treatment: 13877070 INFO @ Sat, 03 Jun 2017 15:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:49:28: #1 finished! INFO @ Sat, 03 Jun 2017 15:49:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:49:31: #2 number of paired peaks: 1123 INFO @ Sat, 03 Jun 2017 15:49:31: start model_add_line... INFO @ Sat, 03 Jun 2017 15:49:35: start X-correlation... INFO @ Sat, 03 Jun 2017 15:49:35: end of X-cor INFO @ Sat, 03 Jun 2017 15:49:35: #2 finished! INFO @ Sat, 03 Jun 2017 15:49:35: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:49:35: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:49:35: #2.2 Generate R script for model : SRX2417580.20_model.r WARNING @ Sat, 03 Jun 2017 15:49:35: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:49:35: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:49:35: #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 15:49:35: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:49:40: start X-correlation... INFO @ Sat, 03 Jun 2017 15:49:40: end of X-cor INFO @ Sat, 03 Jun 2017 15:49:40: #2 finished! INFO @ Sat, 03 Jun 2017 15:49:40: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:49:40: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:49:40: #2.2 Generate R script for model : SRX2417580.05_model.r WARNING @ Sat, 03 Jun 2017 15:49:40: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:49:40: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:49:40: #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 15:49:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:49:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:50:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:50:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:50:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:51:28: #4 Write output xls file... SRX2417580.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:51:28: #4 Write peak in narrowPeak format file... SRX2417580.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:51:28: #4 Write summits bed file... SRX2417580.10_summits.bed INFO @ Sat, 03 Jun 2017 15:51:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2503 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:51:43: #4 Write output xls file... SRX2417580.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:51:43: #4 Write peak in narrowPeak format file... SRX2417580.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:51:43: #4 Write summits bed file... SRX2417580.20_summits.bed INFO @ Sat, 03 Jun 2017 15:51:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1361 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:51:49: #4 Write output xls file... SRX2417580.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:51:49: #4 Write peak in narrowPeak format file... SRX2417580.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:51:49: #4 Write summits bed file... SRX2417580.05_summits.bed INFO @ Sat, 03 Jun 2017 15:51:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4515 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。