Job ID = 9025525 sra ファイルのダウンロード中... Completed: 75846K bytes transferred in 4 seconds (155235K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2834 0 --:--:-- 0:00:07 --:--:-- 16705 100 42716 0 42716 0 0 5101 0 --:--:-- 0:00:08 --:--:-- 23278 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 3261040 spots for /home/okishinya/chipatlas/results/ce10/SRX1388774/SRR2832490.sra Written 3261040 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:53 3261040 reads; of these: 3261040 (100.00%) were unpaired; of these: 104406 (3.20%) aligned 0 times 2444385 (74.96%) aligned exactly 1 time 712249 (21.84%) aligned >1 times 96.80% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 192660 / 3156634 = 0.0610 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 04:15:38: # Command line: callpeak -t SRX1388774.bam -f BAM -g ce -n SRX1388774.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388774.20 # format = BAM # ChIP-seq file = ['SRX1388774.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 04:15:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:38: # Command line: callpeak -t SRX1388774.bam -f BAM -g ce -n SRX1388774.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388774.05 # format = BAM # ChIP-seq file = ['SRX1388774.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 04:15:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:38: # Command line: callpeak -t SRX1388774.bam -f BAM -g ce -n SRX1388774.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388774.10 # format = BAM # ChIP-seq file = ['SRX1388774.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 04:15:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:15:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:15:44: 1000000 INFO @ Sat, 03 Jun 2017 04:15:44: 1000000 INFO @ Sat, 03 Jun 2017 04:15:44: 1000000 INFO @ Sat, 03 Jun 2017 04:15:51: 2000000 INFO @ Sat, 03 Jun 2017 04:15:51: 2000000 INFO @ Sat, 03 Jun 2017 04:15:51: 2000000 INFO @ Sat, 03 Jun 2017 04:15:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:57: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:57: #1 total tags in treatment: 2963974 INFO @ Sat, 03 Jun 2017 04:15:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:57: #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 04:15:58: #1 tags after filtering in treatment: 2963594 INFO @ Sat, 03 Jun 2017 04:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:58: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:58: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:58: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:58: #1 total tags in treatment: 2963974 INFO @ Sat, 03 Jun 2017 04:15:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:58: #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 04:15:58: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:15:58: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:15:58: #1 total tags in treatment: 2963974 INFO @ Sat, 03 Jun 2017 04:15:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:15:58: #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 04:15:58: #2 number of paired peaks: 504 WARNING @ Sat, 03 Jun 2017 04:15:58: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sat, 03 Jun 2017 04:15:58: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:58: #1 tags after filtering in treatment: 2963594 INFO @ Sat, 03 Jun 2017 04:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:58: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:59: #1 tags after filtering in treatment: 2963594 INFO @ Sat, 03 Jun 2017 04:15:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:15:59: #1 finished! INFO @ Sat, 03 Jun 2017 04:15:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:15:59: #2 number of paired peaks: 504 WARNING @ Sat, 03 Jun 2017 04:15:59: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sat, 03 Jun 2017 04:15:59: start model_add_line... INFO @ Sat, 03 Jun 2017 04:15:59: #2 number of paired peaks: 504 WARNING @ Sat, 03 Jun 2017 04:15:59: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sat, 03 Jun 2017 04:15:59: start model_add_line... INFO @ Sat, 03 Jun 2017 04:16:01: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:01: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:01: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:01: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:16:01: #2 alternative fragment length(s) may be 50,573 bps INFO @ Sat, 03 Jun 2017 04:16:01: #2.2 Generate R script for model : SRX1388774.20_model.r WARNING @ Sat, 03 Jun 2017 04:16:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:16:01: #2 You may need to consider one of the other alternative d(s): 50,573 WARNING @ Sat, 03 Jun 2017 04:16:01: #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 04:16:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:16:02: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:02: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:02: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:02: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:16:02: #2 alternative fragment length(s) may be 50,573 bps INFO @ Sat, 03 Jun 2017 04:16:02: #2.2 Generate R script for model : SRX1388774.10_model.r WARNING @ Sat, 03 Jun 2017 04:16:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:16:02: #2 You may need to consider one of the other alternative d(s): 50,573 WARNING @ Sat, 03 Jun 2017 04:16:02: #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 04:16:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:16:02: start X-correlation... INFO @ Sat, 03 Jun 2017 04:16:02: end of X-cor INFO @ Sat, 03 Jun 2017 04:16:02: #2 finished! INFO @ Sat, 03 Jun 2017 04:16:02: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:16:02: #2 alternative fragment length(s) may be 50,573 bps INFO @ Sat, 03 Jun 2017 04:16:02: #2.2 Generate R script for model : SRX1388774.05_model.r WARNING @ Sat, 03 Jun 2017 04:16:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:16:02: #2 You may need to consider one of the other alternative d(s): 50,573 WARNING @ Sat, 03 Jun 2017 04:16:02: #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 04:16:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:16:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:16:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:16:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:16:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:16:31: #4 Write output xls file... SRX1388774.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:16:31: #4 Write peak in narrowPeak format file... SRX1388774.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:16:31: #4 Write summits bed file... SRX1388774.20_summits.bed INFO @ Sat, 03 Jun 2017 04:16:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (115 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:16:32: #4 Write output xls file... SRX1388774.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:16:32: #4 Write peak in narrowPeak format file... SRX1388774.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:16:32: #4 Write summits bed file... SRX1388774.10_summits.bed INFO @ Sat, 03 Jun 2017 04:16:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (276 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:16:36: #4 Write output xls file... SRX1388774.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:16:36: #4 Write peak in narrowPeak format file... SRX1388774.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:16:36: #4 Write summits bed file... SRX1388774.05_summits.bed INFO @ Sat, 03 Jun 2017 04:16:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 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。