Job ID = 9028851 sra ファイルのダウンロード中... Completed: 250820K bytes transferred in 6 seconds (340881K 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 --:--:-- 0 100 10559 0 10559 0 0 1404 0 --:--:-- 0:00:07 --:--:-- 11378 100 28798 0 28798 0 0 3450 0 --:--:-- 0:00:08 --:--:-- 16390 100 50145 0 50145 0 0 5566 0 --:--:-- 0:00:09 --:--:-- 20729 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 4118030 spots for /home/okishinya/chipatlas/results/ce10/SRX982077/SRR1956557.sra Written 4118030 spots total Written 5093036 spots for /home/okishinya/chipatlas/results/ce10/SRX982077/SRR1956558.sra Written 5093036 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: 00:02:42 9211066 reads; of these: 9211066 (100.00%) were unpaired; of these: 470647 (5.11%) aligned 0 times 7046666 (76.50%) aligned exactly 1 time 1693753 (18.39%) aligned >1 times 94.89% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:43 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_rmdupse_core] 921112 / 8740419 = 0.1054 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 12:07:10: # Command line: callpeak -t SRX982077.bam -f BAM -g ce -n SRX982077.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982077.05 # format = BAM # ChIP-seq file = ['SRX982077.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 12:07:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:07:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:07:10: # Command line: callpeak -t SRX982077.bam -f BAM -g ce -n SRX982077.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982077.20 # format = BAM # ChIP-seq file = ['SRX982077.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 12:07:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:07:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:07:10: # Command line: callpeak -t SRX982077.bam -f BAM -g ce -n SRX982077.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982077.10 # format = BAM # ChIP-seq file = ['SRX982077.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 12:07:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:07:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:07:16: 1000000 INFO @ Sat, 03 Jun 2017 12:07:16: 1000000 INFO @ Sat, 03 Jun 2017 12:07:17: 1000000 INFO @ Sat, 03 Jun 2017 12:07:23: 2000000 INFO @ Sat, 03 Jun 2017 12:07:23: 2000000 INFO @ Sat, 03 Jun 2017 12:07:23: 2000000 INFO @ Sat, 03 Jun 2017 12:07:30: 3000000 INFO @ Sat, 03 Jun 2017 12:07:30: 3000000 INFO @ Sat, 03 Jun 2017 12:07:30: 3000000 INFO @ Sat, 03 Jun 2017 12:07:37: 4000000 INFO @ Sat, 03 Jun 2017 12:07:37: 4000000 INFO @ Sat, 03 Jun 2017 12:07:37: 4000000 INFO @ Sat, 03 Jun 2017 12:07:43: 5000000 INFO @ Sat, 03 Jun 2017 12:07:43: 5000000 INFO @ Sat, 03 Jun 2017 12:07:44: 5000000 INFO @ Sat, 03 Jun 2017 12:07:49: 6000000 INFO @ Sat, 03 Jun 2017 12:07:50: 6000000 INFO @ Sat, 03 Jun 2017 12:07:51: 6000000 INFO @ Sat, 03 Jun 2017 12:07:55: 7000000 INFO @ Sat, 03 Jun 2017 12:07:56: 7000000 INFO @ Sat, 03 Jun 2017 12:07:58: 7000000 INFO @ Sat, 03 Jun 2017 12:08:00: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:08:00: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:08:00: #1 total tags in treatment: 7819307 INFO @ Sat, 03 Jun 2017 12:08:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:08:00: #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 12:08:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:08:01: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:08:01: #1 total tags in treatment: 7819307 INFO @ Sat, 03 Jun 2017 12:08:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:08:01: #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 12:08:02: #1 tags after filtering in treatment: 7816860 INFO @ Sat, 03 Jun 2017 12:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:08:02: #1 finished! INFO @ Sat, 03 Jun 2017 12:08:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:08:03: #1 tags after filtering in treatment: 7816860 INFO @ Sat, 03 Jun 2017 12:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:08:03: #1 finished! INFO @ Sat, 03 Jun 2017 12:08:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:08:03: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:08:03: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:08:03: #1 total tags in treatment: 7819307 INFO @ Sat, 03 Jun 2017 12:08:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:08:03: #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 12:08:03: #2 number of paired peaks: 468 WARNING @ Sat, 03 Jun 2017 12:08:03: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 03 Jun 2017 12:08:03: start model_add_line... INFO @ Sat, 03 Jun 2017 12:08:04: #2 number of paired peaks: 468 WARNING @ Sat, 03 Jun 2017 12:08:04: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 03 Jun 2017 12:08:04: start model_add_line... INFO @ Sat, 03 Jun 2017 12:08:04: #1 tags after filtering in treatment: 7816860 INFO @ Sat, 03 Jun 2017 12:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:08:04: #1 finished! INFO @ Sat, 03 Jun 2017 12:08:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:08:06: #2 number of paired peaks: 468 WARNING @ Sat, 03 Jun 2017 12:08:06: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 03 Jun 2017 12:08:06: start model_add_line... INFO @ Sat, 03 Jun 2017 12:08:09: start X-correlation... INFO @ Sat, 03 Jun 2017 12:08:09: end of X-cor INFO @ Sat, 03 Jun 2017 12:08:09: #2 finished! INFO @ Sat, 03 Jun 2017 12:08:09: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Jun 2017 12:08:09: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 03 Jun 2017 12:08:09: #2.2 Generate R script for model : SRX982077.10_model.r WARNING @ Sat, 03 Jun 2017 12:08:09: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:08:09: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 03 Jun 2017 12:08:09: #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 12:08:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:08:09: start X-correlation... INFO @ Sat, 03 Jun 2017 12:08:09: end of X-cor INFO @ Sat, 03 Jun 2017 12:08:09: #2 finished! INFO @ Sat, 03 Jun 2017 12:08:09: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Jun 2017 12:08:09: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 03 Jun 2017 12:08:09: #2.2 Generate R script for model : SRX982077.05_model.r WARNING @ Sat, 03 Jun 2017 12:08:09: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:08:09: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 03 Jun 2017 12:08:09: #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 12:08:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:08:11: start X-correlation... INFO @ Sat, 03 Jun 2017 12:08:11: end of X-cor INFO @ Sat, 03 Jun 2017 12:08:11: #2 finished! INFO @ Sat, 03 Jun 2017 12:08:11: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Jun 2017 12:08:11: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 03 Jun 2017 12:08:11: #2.2 Generate R script for model : SRX982077.20_model.r WARNING @ Sat, 03 Jun 2017 12:08:11: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:08:11: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 03 Jun 2017 12:08:11: #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 12:08:11: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:08:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:08:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:08:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:08:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:09:19: #4 Write output xls file... SRX982077.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:19: #4 Write peak in narrowPeak format file... SRX982077.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:19: #4 Write summits bed file... SRX982077.10_summits.bed INFO @ Sat, 03 Jun 2017 12:09:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:09:24: #4 Write output xls file... SRX982077.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:24: #4 Write peak in narrowPeak format file... SRX982077.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:24: #4 Write summits bed file... SRX982077.20_summits.bed INFO @ Sat, 03 Jun 2017 12:09:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:09:28: #4 Write output xls file... SRX982077.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:28: #4 Write peak in narrowPeak format file... SRX982077.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:28: #4 Write summits bed file... SRX982077.05_summits.bed INFO @ Sat, 03 Jun 2017 12:09:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1247 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。