Job ID = 9028930 sra ファイルのダウンロード中... Completed: 786981K bytes transferred in 9 seconds (688354K 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 14324 0 14324 0 0 1909 0 --:--:-- 0:00:07 --:--:-- 14936 100 38317 0 38317 0 0 4508 0 --:--:-- 0:00:08 --:--:-- 19589 100 86317 0 86317 0 0 9090 0 --:--:-- 0:00:09 --:--:-- 29240 100 95329 0 95329 0 0 9997 0 --:--:-- 0:00:09 --:--:-- 31850 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 37008414 spots for /home/okishinya/chipatlas/results/ce10/SRX997749/SRR1977496.sra Written 37008414 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:56 37008414 reads; of these: 37008414 (100.00%) were unpaired; of these: 13224769 (35.73%) aligned 0 times 18507406 (50.01%) aligned exactly 1 time 5276239 (14.26%) aligned >1 times 64.27% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 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] 21195791 / 23783645 = 0.8912 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 12:37:02: # Command line: callpeak -t SRX997749.bam -f BAM -g ce -n SRX997749.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997749.05 # format = BAM # ChIP-seq file = ['SRX997749.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 12:37:02: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:37:02: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:37:02: # Command line: callpeak -t SRX997749.bam -f BAM -g ce -n SRX997749.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997749.10 # format = BAM # ChIP-seq file = ['SRX997749.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 12:37:02: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:37:02: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:37:02: # Command line: callpeak -t SRX997749.bam -f BAM -g ce -n SRX997749.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997749.20 # format = BAM # ChIP-seq file = ['SRX997749.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 12:37:02: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:37:02: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:37:07: 1000000 INFO @ Sat, 03 Jun 2017 12:37:07: 1000000 INFO @ Sat, 03 Jun 2017 12:37:07: 1000000 INFO @ Sat, 03 Jun 2017 12:37:13: 2000000 INFO @ Sat, 03 Jun 2017 12:37:13: 2000000 INFO @ Sat, 03 Jun 2017 12:37:13: 2000000 INFO @ Sat, 03 Jun 2017 12:37:16: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:37:16: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:37:16: #1 total tags in treatment: 2587854 INFO @ Sat, 03 Jun 2017 12:37:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:37:16: #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 12:37:16: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:37:16: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:37:16: #1 total tags in treatment: 2587854 INFO @ Sat, 03 Jun 2017 12:37:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:37:16: #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 12:37:16: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:37:16: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:37:16: #1 total tags in treatment: 2587854 INFO @ Sat, 03 Jun 2017 12:37:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:37:16: #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 12:37:16: #1 tags after filtering in treatment: 2586359 INFO @ Sat, 03 Jun 2017 12:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:37:16: #1 finished! INFO @ Sat, 03 Jun 2017 12:37:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:37:16: #1 tags after filtering in treatment: 2586359 INFO @ Sat, 03 Jun 2017 12:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:37:16: #1 finished! INFO @ Sat, 03 Jun 2017 12:37:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:37:16: #1 tags after filtering in treatment: 2586359 INFO @ Sat, 03 Jun 2017 12:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:37:16: #1 finished! INFO @ Sat, 03 Jun 2017 12:37:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:37:17: #2 number of paired peaks: 1046 INFO @ Sat, 03 Jun 2017 12:37:17: start model_add_line... INFO @ Sat, 03 Jun 2017 12:37:17: #2 number of paired peaks: 1046 INFO @ Sat, 03 Jun 2017 12:37:17: start model_add_line... INFO @ Sat, 03 Jun 2017 12:37:17: #2 number of paired peaks: 1046 INFO @ Sat, 03 Jun 2017 12:37:17: start model_add_line... INFO @ Sat, 03 Jun 2017 12:37:21: start X-correlation... INFO @ Sat, 03 Jun 2017 12:37:21: end of X-cor INFO @ Sat, 03 Jun 2017 12:37:21: #2 finished! INFO @ Sat, 03 Jun 2017 12:37:21: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 12:37:21: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 03 Jun 2017 12:37:21: #2.2 Generate R script for model : SRX997749.20_model.r WARNING @ Sat, 03 Jun 2017 12:37:21: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:37:21: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 03 Jun 2017 12:37:21: #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 12:37:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:37:21: start X-correlation... INFO @ Sat, 03 Jun 2017 12:37:21: end of X-cor INFO @ Sat, 03 Jun 2017 12:37:21: #2 finished! INFO @ Sat, 03 Jun 2017 12:37:21: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 12:37:21: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 03 Jun 2017 12:37:21: #2.2 Generate R script for model : SRX997749.10_model.r WARNING @ Sat, 03 Jun 2017 12:37:21: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:37:21: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 03 Jun 2017 12:37:21: #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 12:37:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:37:21: start X-correlation... INFO @ Sat, 03 Jun 2017 12:37:21: end of X-cor INFO @ Sat, 03 Jun 2017 12:37:21: #2 finished! INFO @ Sat, 03 Jun 2017 12:37:21: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 12:37:21: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 03 Jun 2017 12:37:21: #2.2 Generate R script for model : SRX997749.05_model.r WARNING @ Sat, 03 Jun 2017 12:37:21: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:37:21: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 03 Jun 2017 12:37:21: #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 12:37:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:37:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:37:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:37:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write output xls file... SRX997749.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write peak in narrowPeak format file... SRX997749.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write summits bed file... SRX997749.20_summits.bed INFO @ Sat, 03 Jun 2017 12:37:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write output xls file... SRX997749.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write peak in narrowPeak format file... SRX997749.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write summits bed file... SRX997749.05_summits.bed INFO @ Sat, 03 Jun 2017 12:37:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2575 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write output xls file... SRX997749.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write peak in narrowPeak format file... SRX997749.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:37:48: #4 Write summits bed file... SRX997749.10_summits.bed INFO @ Sat, 03 Jun 2017 12:37:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (971 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。