Job ID = 2589825 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,904,727 reads read : 8,904,727 reads written : 8,904,727 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947454.sra.cache’: No such file or directory 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: 00:01:31 8904727 reads; of these: 8904727 (100.00%) were unpaired; of these: 1200524 (13.48%) aligned 0 times 6387850 (71.74%) aligned exactly 1 time 1316353 (14.78%) aligned >1 times 86.52% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 924987 / 7704203 = 0.1201 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 @ Mon, 12 Aug 2019 18:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.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 # Paired-End mode is off INFO @ Mon, 12 Aug 2019 18:35:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:35:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:35:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.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 # Paired-End mode is off INFO @ Mon, 12 Aug 2019 18:35:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:35:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:35:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.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 # Paired-End mode is off INFO @ Mon, 12 Aug 2019 18:35:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:35:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:35:58: 1000000 INFO @ Mon, 12 Aug 2019 18:35:59: 1000000 INFO @ Mon, 12 Aug 2019 18:35:59: 1000000 INFO @ Mon, 12 Aug 2019 18:36:05: 2000000 INFO @ Mon, 12 Aug 2019 18:36:06: 2000000 INFO @ Mon, 12 Aug 2019 18:36:07: 2000000 INFO @ Mon, 12 Aug 2019 18:36:11: 3000000 INFO @ Mon, 12 Aug 2019 18:36:13: 3000000 INFO @ Mon, 12 Aug 2019 18:36:15: 3000000 INFO @ Mon, 12 Aug 2019 18:36:18: 4000000 INFO @ Mon, 12 Aug 2019 18:36:20: 4000000 INFO @ Mon, 12 Aug 2019 18:36:23: 4000000 INFO @ Mon, 12 Aug 2019 18:36:24: 5000000 INFO @ Mon, 12 Aug 2019 18:36:27: 5000000 INFO @ Mon, 12 Aug 2019 18:36:30: 6000000 INFO @ Mon, 12 Aug 2019 18:36:31: 5000000 INFO @ Mon, 12 Aug 2019 18:36:34: 6000000 INFO @ Mon, 12 Aug 2019 18:36:35: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:36:35: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:36:35: #1 total tags in treatment: 6779216 INFO @ Mon, 12 Aug 2019 18:36:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:36:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:36:35: #1 tags after filtering in treatment: 6779216 INFO @ Mon, 12 Aug 2019 18:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:36:35: #1 finished! INFO @ Mon, 12 Aug 2019 18:36:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:36:36: #2 number of paired peaks: 490 WARNING @ Mon, 12 Aug 2019 18:36:36: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Mon, 12 Aug 2019 18:36:36: start model_add_line... INFO @ Mon, 12 Aug 2019 18:36:36: start X-correlation... INFO @ Mon, 12 Aug 2019 18:36:36: end of X-cor INFO @ Mon, 12 Aug 2019 18:36:36: #2 finished! INFO @ Mon, 12 Aug 2019 18:36:36: #2 predicted fragment length is 109 bps INFO @ Mon, 12 Aug 2019 18:36:36: #2 alternative fragment length(s) may be 4,109 bps INFO @ Mon, 12 Aug 2019 18:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.10_model.r INFO @ Mon, 12 Aug 2019 18:36:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:36:39: 6000000 INFO @ Mon, 12 Aug 2019 18:36:39: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:36:39: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:36:39: #1 total tags in treatment: 6779216 INFO @ Mon, 12 Aug 2019 18:36:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:36:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:36:40: #1 tags after filtering in treatment: 6779216 INFO @ Mon, 12 Aug 2019 18:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:36:40: #1 finished! INFO @ Mon, 12 Aug 2019 18:36:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:36:40: #2 number of paired peaks: 490 WARNING @ Mon, 12 Aug 2019 18:36:40: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Mon, 12 Aug 2019 18:36:40: start model_add_line... INFO @ Mon, 12 Aug 2019 18:36:40: start X-correlation... INFO @ Mon, 12 Aug 2019 18:36:40: end of X-cor INFO @ Mon, 12 Aug 2019 18:36:40: #2 finished! INFO @ Mon, 12 Aug 2019 18:36:40: #2 predicted fragment length is 109 bps INFO @ Mon, 12 Aug 2019 18:36:40: #2 alternative fragment length(s) may be 4,109 bps INFO @ Mon, 12 Aug 2019 18:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.20_model.r INFO @ Mon, 12 Aug 2019 18:36:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:36:45: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:36:45: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:36:45: #1 total tags in treatment: 6779216 INFO @ Mon, 12 Aug 2019 18:36:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:36:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:36:45: #1 tags after filtering in treatment: 6779216 INFO @ Mon, 12 Aug 2019 18:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:36:45: #1 finished! INFO @ Mon, 12 Aug 2019 18:36:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:36:46: #2 number of paired peaks: 490 WARNING @ Mon, 12 Aug 2019 18:36:46: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Mon, 12 Aug 2019 18:36:46: start model_add_line... INFO @ Mon, 12 Aug 2019 18:36:46: start X-correlation... INFO @ Mon, 12 Aug 2019 18:36:46: end of X-cor INFO @ Mon, 12 Aug 2019 18:36:46: #2 finished! INFO @ Mon, 12 Aug 2019 18:36:46: #2 predicted fragment length is 109 bps INFO @ Mon, 12 Aug 2019 18:36:46: #2 alternative fragment length(s) may be 4,109 bps INFO @ Mon, 12 Aug 2019 18:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.05_model.r INFO @ Mon, 12 Aug 2019 18:36:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:36:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:37:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.10_summits.bed INFO @ Mon, 12 Aug 2019 18:37:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1449 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:37:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:37:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:37:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:37:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.20_summits.bed INFO @ Mon, 12 Aug 2019 18:37:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (544 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331222/SRX331222.05_summits.bed INFO @ Mon, 12 Aug 2019 18:37:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2811 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。