Job ID = 9028929 sra ファイルのダウンロード中... Completed: 749378K bytes transferred in 8 seconds (710009K 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 20110 0 20110 0 0 2597 0 --:--:-- 0:00:07 --:--:-- 15445 100 44110 0 44110 0 0 5145 0 --:--:-- 0:00:08 --:--:-- 20679 100 47382 0 47382 0 0 5422 0 --:--:-- 0:00:08 --:--:-- 20618 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 36906729 spots for /home/okishinya/chipatlas/results/ce10/SRX997748/SRR1977495.sra Written 36906729 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:25 36906729 reads; of these: 36906729 (100.00%) were unpaired; of these: 1564210 (4.24%) aligned 0 times 29039118 (78.68%) aligned exactly 1 time 6303401 (17.08%) aligned >1 times 95.76% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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 12 files... [bam_rmdupse_core] 29586554 / 35342519 = 0.8371 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 12:38:50: # Command line: callpeak -t SRX997748.bam -f BAM -g ce -n SRX997748.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997748.10 # format = BAM # ChIP-seq file = ['SRX997748.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 12:38:50: # Command line: callpeak -t SRX997748.bam -f BAM -g ce -n SRX997748.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997748.20 # format = BAM # ChIP-seq file = ['SRX997748.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 12:38:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:38:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:38:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:38:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:38:50: # Command line: callpeak -t SRX997748.bam -f BAM -g ce -n SRX997748.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997748.05 # format = BAM # ChIP-seq file = ['SRX997748.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 12:38:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:38:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:38:57: 1000000 INFO @ Sat, 03 Jun 2017 12:38:57: 1000000 INFO @ Sat, 03 Jun 2017 12:38:57: 1000000 INFO @ Sat, 03 Jun 2017 12:39:03: 2000000 INFO @ Sat, 03 Jun 2017 12:39:03: 2000000 INFO @ Sat, 03 Jun 2017 12:39:03: 2000000 INFO @ Sat, 03 Jun 2017 12:39:10: 3000000 INFO @ Sat, 03 Jun 2017 12:39:10: 3000000 INFO @ Sat, 03 Jun 2017 12:39:10: 3000000 INFO @ Sat, 03 Jun 2017 12:39:16: 4000000 INFO @ Sat, 03 Jun 2017 12:39:16: 4000000 INFO @ Sat, 03 Jun 2017 12:39:16: 4000000 INFO @ Sat, 03 Jun 2017 12:39:23: 5000000 INFO @ Sat, 03 Jun 2017 12:39:23: 5000000 INFO @ Sat, 03 Jun 2017 12:39:23: 5000000 INFO @ Sat, 03 Jun 2017 12:39:27: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:39:27: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:39:27: #1 total tags in treatment: 5755965 INFO @ Sat, 03 Jun 2017 12:39:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:39:27: #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 12:39:28: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:39:28: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:39:28: #1 total tags in treatment: 5755965 INFO @ Sat, 03 Jun 2017 12:39:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:39:28: #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 12:39:28: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:39:28: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:39:28: #1 total tags in treatment: 5755965 INFO @ Sat, 03 Jun 2017 12:39:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:39:28: #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 12:39:28: #1 tags after filtering in treatment: 5755405 INFO @ Sat, 03 Jun 2017 12:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:39:28: #1 finished! INFO @ Sat, 03 Jun 2017 12:39:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:39:29: #1 tags after filtering in treatment: 5755405 INFO @ Sat, 03 Jun 2017 12:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:39:29: #1 finished! INFO @ Sat, 03 Jun 2017 12:39:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:39:29: #1 tags after filtering in treatment: 5755405 INFO @ Sat, 03 Jun 2017 12:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:39:29: #1 finished! INFO @ Sat, 03 Jun 2017 12:39:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:39:30: #2 number of paired peaks: 965 WARNING @ Sat, 03 Jun 2017 12:39:30: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Sat, 03 Jun 2017 12:39:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:39:30: #2 number of paired peaks: 965 WARNING @ Sat, 03 Jun 2017 12:39:30: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Sat, 03 Jun 2017 12:39:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:39:30: #2 number of paired peaks: 965 WARNING @ Sat, 03 Jun 2017 12:39:30: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Sat, 03 Jun 2017 12:39:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:39:39: start X-correlation... INFO @ Sat, 03 Jun 2017 12:39:39: end of X-cor INFO @ Sat, 03 Jun 2017 12:39:39: #2 finished! INFO @ Sat, 03 Jun 2017 12:39:39: #2 predicted fragment length is 35 bps INFO @ Sat, 03 Jun 2017 12:39:39: #2 alternative fragment length(s) may be 2,35,568 bps INFO @ Sat, 03 Jun 2017 12:39:39: #2.2 Generate R script for model : SRX997748.10_model.r WARNING @ Sat, 03 Jun 2017 12:39:39: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:39:39: #2 You may need to consider one of the other alternative d(s): 2,35,568 WARNING @ Sat, 03 Jun 2017 12:39:39: #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 12:39:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:39:39: start X-correlation... INFO @ Sat, 03 Jun 2017 12:39:39: end of X-cor INFO @ Sat, 03 Jun 2017 12:39:39: #2 finished! INFO @ Sat, 03 Jun 2017 12:39:39: #2 predicted fragment length is 35 bps INFO @ Sat, 03 Jun 2017 12:39:39: #2 alternative fragment length(s) may be 2,35,568 bps INFO @ Sat, 03 Jun 2017 12:39:39: #2.2 Generate R script for model : SRX997748.20_model.r WARNING @ Sat, 03 Jun 2017 12:39:39: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:39:39: #2 You may need to consider one of the other alternative d(s): 2,35,568 WARNING @ Sat, 03 Jun 2017 12:39:39: #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 12:39:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:39:39: start X-correlation... INFO @ Sat, 03 Jun 2017 12:39:39: end of X-cor INFO @ Sat, 03 Jun 2017 12:39:39: #2 finished! INFO @ Sat, 03 Jun 2017 12:39:39: #2 predicted fragment length is 35 bps INFO @ Sat, 03 Jun 2017 12:39:39: #2 alternative fragment length(s) may be 2,35,568 bps INFO @ Sat, 03 Jun 2017 12:39:39: #2.2 Generate R script for model : SRX997748.05_model.r WARNING @ Sat, 03 Jun 2017 12:39:39: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:39:39: #2 You may need to consider one of the other alternative d(s): 2,35,568 WARNING @ Sat, 03 Jun 2017 12:39:39: #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 12:39:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:40:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:40:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:40:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:40:34: #4 Write output xls file... SRX997748.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:40:34: #4 Write peak in narrowPeak format file... SRX997748.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:40:34: #4 Write summits bed file... SRX997748.20_summits.bed INFO @ Sat, 03 Jun 2017 12:40:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (271 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:40:37: #4 Write output xls file... SRX997748.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:40:37: #4 Write peak in narrowPeak format file... SRX997748.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:40:37: #4 Write summits bed file... SRX997748.10_summits.bed INFO @ Sat, 03 Jun 2017 12:40:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (665 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:40:40: #4 Write output xls file... SRX997748.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:40:40: #4 Write peak in narrowPeak format file... SRX997748.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:40:40: #4 Write summits bed file... SRX997748.05_summits.bed INFO @ Sat, 03 Jun 2017 12:40:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2114 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。