Job ID = 9031596 sra ファイルのダウンロード中... Completed: 1581045K bytes transferred in 26 seconds (487430K bits/sec), in 13 files, 14 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 7663 0 7663 0 0 1042 0 --:--:-- 0:00:07 --:--:-- 10355 100 30318 0 30318 0 0 3707 0 --:--:-- 0:00:08 --:--:-- 19310 100 76121 0 76121 0 0 8608 0 --:--:-- 0:00:08 --:--:-- 34089 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 500916 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175616.sra Written 500916 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175623.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175612.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175618.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175615.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175614.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175622.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175624.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175621.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175613.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175620.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175617.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475422/SRR1175619.sra Written 4000000 spots total 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: 00:17:18 48500916 reads; of these: 48500916 (100.00%) were unpaired; of these: 18066999 (37.25%) aligned 0 times 19706931 (40.63%) aligned exactly 1 time 10726986 (22.12%) aligned >1 times 62.75% overall alignment rate Time searching: 00:17:18 Overall time: 00:17:18 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 16 files... [bam_rmdupse_core] 21327145 / 30433917 = 0.7008 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 20:44:03: # Command line: callpeak -t SRX475422.bam -f BAM -g dm -n SRX475422.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX475422.05 # format = BAM # ChIP-seq file = ['SRX475422.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 20:44:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:44:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:44:03: # Command line: callpeak -t SRX475422.bam -f BAM -g dm -n SRX475422.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX475422.20 # format = BAM # ChIP-seq file = ['SRX475422.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 20:44:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:44:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:44:03: # Command line: callpeak -t SRX475422.bam -f BAM -g dm -n SRX475422.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX475422.10 # format = BAM # ChIP-seq file = ['SRX475422.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 20:44:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:44:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:44:09: 1000000 INFO @ Sat, 03 Jun 2017 20:44:09: 1000000 INFO @ Sat, 03 Jun 2017 20:44:09: 1000000 INFO @ Sat, 03 Jun 2017 20:44:15: 2000000 INFO @ Sat, 03 Jun 2017 20:44:16: 2000000 INFO @ Sat, 03 Jun 2017 20:44:16: 2000000 INFO @ Sat, 03 Jun 2017 20:44:21: 3000000 INFO @ Sat, 03 Jun 2017 20:44:23: 3000000 INFO @ Sat, 03 Jun 2017 20:44:23: 3000000 INFO @ Sat, 03 Jun 2017 20:44:27: 4000000 INFO @ Sat, 03 Jun 2017 20:44:29: 4000000 INFO @ Sat, 03 Jun 2017 20:44:29: 4000000 INFO @ Sat, 03 Jun 2017 20:44:33: 5000000 INFO @ Sat, 03 Jun 2017 20:44:36: 5000000 INFO @ Sat, 03 Jun 2017 20:44:36: 5000000 INFO @ Sat, 03 Jun 2017 20:44:40: 6000000 INFO @ Sat, 03 Jun 2017 20:44:43: 6000000 INFO @ Sat, 03 Jun 2017 20:44:43: 6000000 INFO @ Sat, 03 Jun 2017 20:44:46: 7000000 INFO @ Sat, 03 Jun 2017 20:44:49: 7000000 INFO @ Sat, 03 Jun 2017 20:44:49: 7000000 INFO @ Sat, 03 Jun 2017 20:44:52: 8000000 INFO @ Sat, 03 Jun 2017 20:44:56: 8000000 INFO @ Sat, 03 Jun 2017 20:44:56: 8000000 INFO @ Sat, 03 Jun 2017 20:44:58: 9000000 INFO @ Sat, 03 Jun 2017 20:44:59: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:44:59: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:44:59: #1 total tags in treatment: 9106772 INFO @ Sat, 03 Jun 2017 20:44:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:44:59: #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 20:45:01: #1 tags after filtering in treatment: 9102921 INFO @ Sat, 03 Jun 2017 20:45:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:45:01: #1 finished! INFO @ Sat, 03 Jun 2017 20:45:01: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:45:03: 9000000 INFO @ Sat, 03 Jun 2017 20:45:03: #2 number of paired peaks: 3410 INFO @ Sat, 03 Jun 2017 20:45:03: start model_add_line... INFO @ Sat, 03 Jun 2017 20:45:03: 9000000 INFO @ Sat, 03 Jun 2017 20:45:03: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:45:03: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:45:03: #1 total tags in treatment: 9106772 INFO @ Sat, 03 Jun 2017 20:45:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:45:03: #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 20:45:04: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:45:04: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:45:04: #1 total tags in treatment: 9106772 INFO @ Sat, 03 Jun 2017 20:45:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:45:04: #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 20:45:05: #1 tags after filtering in treatment: 9102921 INFO @ Sat, 03 Jun 2017 20:45:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:45:05: #1 finished! INFO @ Sat, 03 Jun 2017 20:45:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:45:05: #1 tags after filtering in treatment: 9102921 INFO @ Sat, 03 Jun 2017 20:45:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:45:05: #1 finished! INFO @ Sat, 03 Jun 2017 20:45:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:45:07: #2 number of paired peaks: 3410 INFO @ Sat, 03 Jun 2017 20:45:07: start model_add_line... INFO @ Sat, 03 Jun 2017 20:45:08: #2 number of paired peaks: 3410 INFO @ Sat, 03 Jun 2017 20:45:08: start model_add_line... INFO @ Sat, 03 Jun 2017 20:45:28: start X-correlation... INFO @ Sat, 03 Jun 2017 20:45:28: end of X-cor INFO @ Sat, 03 Jun 2017 20:45:28: #2 finished! INFO @ Sat, 03 Jun 2017 20:45:28: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Jun 2017 20:45:28: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 03 Jun 2017 20:45:28: #2.2 Generate R script for model : SRX475422.10_model.r WARNING @ Sat, 03 Jun 2017 20:45:28: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:45:28: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 03 Jun 2017 20:45:28: #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 20:45:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:45:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:45:34: start X-correlation... INFO @ Sat, 03 Jun 2017 20:45:34: end of X-cor INFO @ Sat, 03 Jun 2017 20:45:34: #2 finished! INFO @ Sat, 03 Jun 2017 20:45:34: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Jun 2017 20:45:34: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 03 Jun 2017 20:45:34: #2.2 Generate R script for model : SRX475422.20_model.r WARNING @ Sat, 03 Jun 2017 20:45:34: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:45:34: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 03 Jun 2017 20:45:34: #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 20:45:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:45:34: start X-correlation... INFO @ Sat, 03 Jun 2017 20:45:34: end of X-cor INFO @ Sat, 03 Jun 2017 20:45:34: #2 finished! INFO @ Sat, 03 Jun 2017 20:45:34: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Jun 2017 20:45:34: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 03 Jun 2017 20:45:34: #2.2 Generate R script for model : SRX475422.05_model.r WARNING @ Sat, 03 Jun 2017 20:45:34: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:45:34: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 03 Jun 2017 20:45:34: #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 20:45:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:46:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:46:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:46:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:46:55: #4 Write output xls file... SRX475422.10_peaks.xls INFO @ Sat, 03 Jun 2017 20:46:55: #4 Write peak in narrowPeak format file... SRX475422.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:46:55: #4 Write summits bed file... SRX475422.10_summits.bed INFO @ Sat, 03 Jun 2017 20:46:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4547 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 20:47:04: #4 Write output xls file... SRX475422.20_peaks.xls INFO @ Sat, 03 Jun 2017 20:47:04: #4 Write peak in narrowPeak format file... SRX475422.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:47:04: #4 Write summits bed file... SRX475422.20_summits.bed INFO @ Sat, 03 Jun 2017 20:47:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2849 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 20:47:04: #4 Write output xls file... SRX475422.05_peaks.xls INFO @ Sat, 03 Jun 2017 20:47:04: #4 Write peak in narrowPeak format file... SRX475422.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:47:04: #4 Write summits bed file... SRX475422.05_summits.bed INFO @ Sat, 03 Jun 2017 20:47:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7367 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。