Job ID = 9028835 sra ファイルのダウンロード中... Completed: 636730K bytes transferred in 8 seconds (597569K bits/sec), in 2 files, 3 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 7663 0 7663 0 0 928 0 --:--:-- 0:00:08 --:--:-- 4669 100 28798 0 28798 0 0 3168 0 --:--:-- 0:00:09 --:--:-- 11654 100 59679 0 59679 0 0 6226 0 --:--:-- 0:00:09 --:--:-- 20100 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 8742686 spots for /home/okishinya/chipatlas/results/ce10/SRX982069/SRR1956545.sra Written 8742686 spots total Written 11619841 spots for /home/okishinya/chipatlas/results/ce10/SRX982069/SRR1956546.sra Written 11619841 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: 00:06:07 20362527 reads; of these: 20362527 (100.00%) were unpaired; of these: 1953700 (9.59%) aligned 0 times 15189424 (74.59%) aligned exactly 1 time 3219403 (15.81%) aligned >1 times 90.41% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 2665518 / 18408827 = 0.1448 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 12:08:51: # Command line: callpeak -t SRX982069.bam -f BAM -g ce -n SRX982069.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982069.10 # format = BAM # ChIP-seq file = ['SRX982069.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 12:08:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:51: # Command line: callpeak -t SRX982069.bam -f BAM -g ce -n SRX982069.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982069.20 # format = BAM # ChIP-seq file = ['SRX982069.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 12:08:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:51: # Command line: callpeak -t SRX982069.bam -f BAM -g ce -n SRX982069.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982069.05 # format = BAM # ChIP-seq file = ['SRX982069.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 12:08:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:57: 1000000 INFO @ Sat, 03 Jun 2017 12:08:57: 1000000 INFO @ Sat, 03 Jun 2017 12:08:57: 1000000 INFO @ Sat, 03 Jun 2017 12:09:03: 2000000 INFO @ Sat, 03 Jun 2017 12:09:04: 2000000 INFO @ Sat, 03 Jun 2017 12:09:04: 2000000 INFO @ Sat, 03 Jun 2017 12:09:09: 3000000 INFO @ Sat, 03 Jun 2017 12:09:11: 3000000 INFO @ Sat, 03 Jun 2017 12:09:11: 3000000 INFO @ Sat, 03 Jun 2017 12:09:15: 4000000 INFO @ Sat, 03 Jun 2017 12:09:18: 4000000 INFO @ Sat, 03 Jun 2017 12:09:18: 4000000 INFO @ Sat, 03 Jun 2017 12:09:21: 5000000 INFO @ Sat, 03 Jun 2017 12:09:24: 5000000 INFO @ Sat, 03 Jun 2017 12:09:24: 5000000 INFO @ Sat, 03 Jun 2017 12:09:26: 6000000 INFO @ Sat, 03 Jun 2017 12:09:31: 6000000 INFO @ Sat, 03 Jun 2017 12:09:31: 6000000 INFO @ Sat, 03 Jun 2017 12:09:32: 7000000 INFO @ Sat, 03 Jun 2017 12:09:37: 7000000 INFO @ Sat, 03 Jun 2017 12:09:38: 7000000 INFO @ Sat, 03 Jun 2017 12:09:38: 8000000 INFO @ Sat, 03 Jun 2017 12:09:44: 8000000 INFO @ Sat, 03 Jun 2017 12:09:44: 8000000 INFO @ Sat, 03 Jun 2017 12:09:44: 9000000 INFO @ Sat, 03 Jun 2017 12:09:50: 10000000 INFO @ Sat, 03 Jun 2017 12:09:51: 9000000 INFO @ Sat, 03 Jun 2017 12:09:51: 9000000 INFO @ Sat, 03 Jun 2017 12:09:56: 11000000 INFO @ Sat, 03 Jun 2017 12:09:58: 10000000 INFO @ Sat, 03 Jun 2017 12:09:58: 10000000 INFO @ Sat, 03 Jun 2017 12:10:02: 12000000 INFO @ Sat, 03 Jun 2017 12:10:04: 11000000 INFO @ Sat, 03 Jun 2017 12:10:04: 11000000 INFO @ Sat, 03 Jun 2017 12:10:08: 13000000 INFO @ Sat, 03 Jun 2017 12:10:11: 12000000 INFO @ Sat, 03 Jun 2017 12:10:11: 12000000 INFO @ Sat, 03 Jun 2017 12:10:14: 14000000 INFO @ Sat, 03 Jun 2017 12:10:17: 13000000 INFO @ Sat, 03 Jun 2017 12:10:17: 13000000 INFO @ Sat, 03 Jun 2017 12:10:20: 15000000 INFO @ Sat, 03 Jun 2017 12:10:24: 14000000 INFO @ Sat, 03 Jun 2017 12:10:24: 14000000 INFO @ Sat, 03 Jun 2017 12:10:25: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:25: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:25: #1 total tags in treatment: 15743309 INFO @ Sat, 03 Jun 2017 12:10:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:25: #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 12:10:28: #1 tags after filtering in treatment: 15740671 INFO @ Sat, 03 Jun 2017 12:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:28: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:31: 15000000 INFO @ Sat, 03 Jun 2017 12:10:31: 15000000 INFO @ Sat, 03 Jun 2017 12:10:31: #2 number of paired peaks: 275 WARNING @ Sat, 03 Jun 2017 12:10:31: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Sat, 03 Jun 2017 12:10:31: start model_add_line... INFO @ Sat, 03 Jun 2017 12:10:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:36: #1 total tags in treatment: 15743309 INFO @ Sat, 03 Jun 2017 12:10:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:36: #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 12:10:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:36: #1 total tags in treatment: 15743309 INFO @ Sat, 03 Jun 2017 12:10:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:36: #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 12:10:36: start X-correlation... INFO @ Sat, 03 Jun 2017 12:10:36: end of X-cor INFO @ Sat, 03 Jun 2017 12:10:36: #2 finished! INFO @ Sat, 03 Jun 2017 12:10:36: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 12:10:36: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sat, 03 Jun 2017 12:10:36: #2.2 Generate R script for model : SRX982069.10_model.r WARNING @ Sat, 03 Jun 2017 12:10:36: #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 12:10:36: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sat, 03 Jun 2017 12:10:36: #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 12:10:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:10:39: #1 tags after filtering in treatment: 15740671 INFO @ Sat, 03 Jun 2017 12:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:39: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:39: #1 tags after filtering in treatment: 15740671 INFO @ Sat, 03 Jun 2017 12:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:39: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:41: #2 number of paired peaks: 275 WARNING @ Sat, 03 Jun 2017 12:10:41: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Sat, 03 Jun 2017 12:10:41: start model_add_line... INFO @ Sat, 03 Jun 2017 12:10:41: #2 number of paired peaks: 275 WARNING @ Sat, 03 Jun 2017 12:10:41: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Sat, 03 Jun 2017 12:10:41: start model_add_line... INFO @ Sat, 03 Jun 2017 12:10:46: start X-correlation... INFO @ Sat, 03 Jun 2017 12:10:46: end of X-cor INFO @ Sat, 03 Jun 2017 12:10:46: #2 finished! INFO @ Sat, 03 Jun 2017 12:10:46: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 12:10:46: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sat, 03 Jun 2017 12:10:46: #2.2 Generate R script for model : SRX982069.20_model.r WARNING @ Sat, 03 Jun 2017 12:10:46: #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 12:10:46: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sat, 03 Jun 2017 12:10:46: #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 12:10:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:10:47: start X-correlation... INFO @ Sat, 03 Jun 2017 12:10:47: end of X-cor INFO @ Sat, 03 Jun 2017 12:10:47: #2 finished! INFO @ Sat, 03 Jun 2017 12:10:47: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 12:10:47: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sat, 03 Jun 2017 12:10:47: #2.2 Generate R script for model : SRX982069.05_model.r WARNING @ Sat, 03 Jun 2017 12:10:47: #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 12:10:47: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sat, 03 Jun 2017 12:10:47: #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 12:10:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:11:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:11:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:12:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:12:52: #4 Write output xls file... SRX982069.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:12:52: #4 Write peak in narrowPeak format file... SRX982069.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:12:52: #4 Write summits bed file... SRX982069.10_summits.bed INFO @ Sat, 03 Jun 2017 12:12:52: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (470 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:13:01: #4 Write output xls file... SRX982069.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:13:01: #4 Write peak in narrowPeak format file... SRX982069.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:13:01: #4 Write summits bed file... SRX982069.20_summits.bed INFO @ Sat, 03 Jun 2017 12:13:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:13:07: #4 Write output xls file... SRX982069.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:13:07: #4 Write peak in narrowPeak format file... SRX982069.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:13:07: #4 Write summits bed file... SRX982069.05_summits.bed INFO @ Sat, 03 Jun 2017 12:13:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (804 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。