Job ID = 9028914 sra ファイルのダウンロード中... Completed: 318556K bytes transferred in 6 seconds (427755K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 100 7663 0 7663 0 0 764 0 --:--:-- 0:00:10 --:--:-- 2113 100 36038 0 36038 0 0 3269 0 --:--:-- 0:00:11 --:--:-- 7798 100 56857 0 56857 0 0 5007 0 --:--:-- 0:00:11 --:--:-- 14394 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 5368560 spots for /home/okishinya/chipatlas/results/ce10/SRX982106/SRR1956595.sra Written 5368560 spots total Written 6347799 spots for /home/okishinya/chipatlas/results/ce10/SRX982106/SRR1956596.sra Written 6347799 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: 00:03:13 11716359 reads; of these: 11716359 (100.00%) were unpaired; of these: 1287216 (10.99%) aligned 0 times 8733758 (74.54%) aligned exactly 1 time 1695385 (14.47%) aligned >1 times 89.01% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 818399 / 10429143 = 0.0785 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 12:27:30: # Command line: callpeak -t SRX982106.bam -f BAM -g ce -n SRX982106.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982106.10 # format = BAM # ChIP-seq file = ['SRX982106.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 12:27:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:30: # Command line: callpeak -t SRX982106.bam -f BAM -g ce -n SRX982106.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982106.20 # format = BAM # ChIP-seq file = ['SRX982106.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 12:27:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:30: # Command line: callpeak -t SRX982106.bam -f BAM -g ce -n SRX982106.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982106.05 # format = BAM # ChIP-seq file = ['SRX982106.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 12:27:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:38: 1000000 INFO @ Sat, 03 Jun 2017 12:27:38: 1000000 INFO @ Sat, 03 Jun 2017 12:27:38: 1000000 INFO @ Sat, 03 Jun 2017 12:27:45: 2000000 INFO @ Sat, 03 Jun 2017 12:27:46: 2000000 INFO @ Sat, 03 Jun 2017 12:27:47: 2000000 INFO @ Sat, 03 Jun 2017 12:27:52: 3000000 INFO @ Sat, 03 Jun 2017 12:27:54: 3000000 INFO @ Sat, 03 Jun 2017 12:27:56: 3000000 INFO @ Sat, 03 Jun 2017 12:27:59: 4000000 INFO @ Sat, 03 Jun 2017 12:28:02: 4000000 INFO @ Sat, 03 Jun 2017 12:28:04: 4000000 INFO @ Sat, 03 Jun 2017 12:28:07: 5000000 INFO @ Sat, 03 Jun 2017 12:28:10: 5000000 INFO @ Sat, 03 Jun 2017 12:28:13: 5000000 INFO @ Sat, 03 Jun 2017 12:28:14: 6000000 INFO @ Sat, 03 Jun 2017 12:28:18: 6000000 INFO @ Sat, 03 Jun 2017 12:28:22: 6000000 INFO @ Sat, 03 Jun 2017 12:28:22: 7000000 INFO @ Sat, 03 Jun 2017 12:28:26: 7000000 INFO @ Sat, 03 Jun 2017 12:28:29: 8000000 INFO @ Sat, 03 Jun 2017 12:28:30: 7000000 INFO @ Sat, 03 Jun 2017 12:28:34: 8000000 INFO @ Sat, 03 Jun 2017 12:28:37: 9000000 INFO @ Sat, 03 Jun 2017 12:28:39: 8000000 INFO @ Sat, 03 Jun 2017 12:28:41: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:41: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:41: #1 total tags in treatment: 9610744 INFO @ Sat, 03 Jun 2017 12:28:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:41: #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 12:28:42: 9000000 INFO @ Sat, 03 Jun 2017 12:28:43: #1 tags after filtering in treatment: 9608444 INFO @ Sat, 03 Jun 2017 12:28:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:43: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:45: #2 number of paired peaks: 320 WARNING @ Sat, 03 Jun 2017 12:28:45: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sat, 03 Jun 2017 12:28:45: start model_add_line... INFO @ Sat, 03 Jun 2017 12:28:47: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:47: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:47: #1 total tags in treatment: 9610744 INFO @ Sat, 03 Jun 2017 12:28:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:47: #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 12:28:47: 9000000 INFO @ Sat, 03 Jun 2017 12:28:49: #1 tags after filtering in treatment: 9608444 INFO @ Sat, 03 Jun 2017 12:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:49: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:49: start X-correlation... INFO @ Sat, 03 Jun 2017 12:28:49: end of X-cor INFO @ Sat, 03 Jun 2017 12:28:49: #2 finished! INFO @ Sat, 03 Jun 2017 12:28:49: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 12:28:49: #2 alternative fragment length(s) may be 3,48,569 bps INFO @ Sat, 03 Jun 2017 12:28:49: #2.2 Generate R script for model : SRX982106.10_model.r WARNING @ Sat, 03 Jun 2017 12:28:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:28:49: #2 You may need to consider one of the other alternative d(s): 3,48,569 WARNING @ Sat, 03 Jun 2017 12:28:49: #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 12:28:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:28:50: #2 number of paired peaks: 320 WARNING @ Sat, 03 Jun 2017 12:28:50: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sat, 03 Jun 2017 12:28:50: start model_add_line... INFO @ Sat, 03 Jun 2017 12:28:52: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:52: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:52: #1 total tags in treatment: 9610744 INFO @ Sat, 03 Jun 2017 12:28:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:52: #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 12:28:54: #1 tags after filtering in treatment: 9608444 INFO @ Sat, 03 Jun 2017 12:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:54: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:55: start X-correlation... INFO @ Sat, 03 Jun 2017 12:28:55: end of X-cor INFO @ Sat, 03 Jun 2017 12:28:55: #2 finished! INFO @ Sat, 03 Jun 2017 12:28:55: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 12:28:55: #2 alternative fragment length(s) may be 3,48,569 bps INFO @ Sat, 03 Jun 2017 12:28:55: #2.2 Generate R script for model : SRX982106.05_model.r WARNING @ Sat, 03 Jun 2017 12:28:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:28:55: #2 You may need to consider one of the other alternative d(s): 3,48,569 WARNING @ Sat, 03 Jun 2017 12:28:55: #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 12:28:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:28:55: #2 number of paired peaks: 320 WARNING @ Sat, 03 Jun 2017 12:28:55: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sat, 03 Jun 2017 12:28:55: start model_add_line... INFO @ Sat, 03 Jun 2017 12:28:59: start X-correlation... INFO @ Sat, 03 Jun 2017 12:28:59: end of X-cor INFO @ Sat, 03 Jun 2017 12:28:59: #2 finished! INFO @ Sat, 03 Jun 2017 12:28:59: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 12:28:59: #2 alternative fragment length(s) may be 3,48,569 bps INFO @ Sat, 03 Jun 2017 12:28:59: #2.2 Generate R script for model : SRX982106.20_model.r WARNING @ Sat, 03 Jun 2017 12:28:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:28:59: #2 You may need to consider one of the other alternative d(s): 3,48,569 WARNING @ Sat, 03 Jun 2017 12:28:59: #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 12:28:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:29:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:29:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:29:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:30:17: #4 Write output xls file... SRX982106.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:30:17: #4 Write peak in narrowPeak format file... SRX982106.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:30:17: #4 Write summits bed file... SRX982106.10_summits.bed INFO @ Sat, 03 Jun 2017 12:30:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (397 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:30:25: #4 Write output xls file... SRX982106.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:30:25: #4 Write peak in narrowPeak format file... SRX982106.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:30:25: #4 Write summits bed file... SRX982106.05_summits.bed INFO @ Sat, 03 Jun 2017 12:30:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:30:28: #4 Write output xls file... SRX982106.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:30:28: #4 Write peak in narrowPeak format file... SRX982106.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:30:28: #4 Write summits bed file... SRX982106.20_summits.bed INFO @ Sat, 03 Jun 2017 12:30:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (159 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。