Job ID = 2589828 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,565,750 reads read : 8,565,750 reads written : 8,565,750 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947457.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: 00:01:47 8565750 reads; of these: 8565750 (100.00%) were unpaired; of these: 78326 (0.91%) aligned 0 times 7090884 (82.78%) aligned exactly 1 time 1396540 (16.30%) aligned >1 times 99.09% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 661876 / 8487424 = 0.0780 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 18:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.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 18:36:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:36:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.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 18:36:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:36:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.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 18:36:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:36:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:36:37: 1000000 INFO @ Mon, 12 Aug 2019 18:36:40: 1000000 INFO @ Mon, 12 Aug 2019 18:36:40: 1000000 INFO @ Mon, 12 Aug 2019 18:36:44: 2000000 INFO @ Mon, 12 Aug 2019 18:36:47: 2000000 INFO @ Mon, 12 Aug 2019 18:36:49: 2000000 INFO @ Mon, 12 Aug 2019 18:36:50: 3000000 INFO @ Mon, 12 Aug 2019 18:36:55: 3000000 INFO @ Mon, 12 Aug 2019 18:36:56: 4000000 INFO @ Mon, 12 Aug 2019 18:36:57: 3000000 INFO @ Mon, 12 Aug 2019 18:37:02: 4000000 INFO @ Mon, 12 Aug 2019 18:37:03: 5000000 INFO @ Mon, 12 Aug 2019 18:37:05: 4000000 INFO @ Mon, 12 Aug 2019 18:37:09: 5000000 INFO @ Mon, 12 Aug 2019 18:37:09: 6000000 INFO @ Mon, 12 Aug 2019 18:37:13: 5000000 INFO @ Mon, 12 Aug 2019 18:37:16: 7000000 INFO @ Mon, 12 Aug 2019 18:37:16: 6000000 INFO @ Mon, 12 Aug 2019 18:37:21: 6000000 INFO @ Mon, 12 Aug 2019 18:37:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:37:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:37:21: #1 total tags in treatment: 7825548 INFO @ Mon, 12 Aug 2019 18:37:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:37:21: #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 18:37:21: #1 tags after filtering in treatment: 7825548 INFO @ Mon, 12 Aug 2019 18:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:37:21: #1 finished! INFO @ Mon, 12 Aug 2019 18:37:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:37:22: #2 number of paired peaks: 421 WARNING @ Mon, 12 Aug 2019 18:37:22: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Mon, 12 Aug 2019 18:37:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:37:22: start X-correlation... INFO @ Mon, 12 Aug 2019 18:37:22: end of X-cor INFO @ Mon, 12 Aug 2019 18:37:22: #2 finished! INFO @ Mon, 12 Aug 2019 18:37:22: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 18:37:22: #2 alternative fragment length(s) may be 2,35,573,576,579,586 bps INFO @ Mon, 12 Aug 2019 18:37:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.05_model.r WARNING @ Mon, 12 Aug 2019 18:37:22: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:37:22: #2 You may need to consider one of the other alternative d(s): 2,35,573,576,579,586 WARNING @ Mon, 12 Aug 2019 18:37:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:37:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:37:23: 7000000 INFO @ Mon, 12 Aug 2019 18:37:29: 7000000 INFO @ Mon, 12 Aug 2019 18:37:29: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:37:29: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:37:29: #1 total tags in treatment: 7825548 INFO @ Mon, 12 Aug 2019 18:37:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:37:29: #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 18:37:29: #1 tags after filtering in treatment: 7825548 INFO @ Mon, 12 Aug 2019 18:37:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:37:29: #1 finished! INFO @ Mon, 12 Aug 2019 18:37:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:37:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:37:30: #2 number of paired peaks: 421 WARNING @ Mon, 12 Aug 2019 18:37:30: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Mon, 12 Aug 2019 18:37:30: start model_add_line... INFO @ Mon, 12 Aug 2019 18:37:30: start X-correlation... INFO @ Mon, 12 Aug 2019 18:37:30: end of X-cor INFO @ Mon, 12 Aug 2019 18:37:30: #2 finished! INFO @ Mon, 12 Aug 2019 18:37:30: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 18:37:30: #2 alternative fragment length(s) may be 2,35,573,576,579,586 bps INFO @ Mon, 12 Aug 2019 18:37:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.20_model.r WARNING @ Mon, 12 Aug 2019 18:37:30: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:37:30: #2 You may need to consider one of the other alternative d(s): 2,35,573,576,579,586 WARNING @ Mon, 12 Aug 2019 18:37:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:37:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:37:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:37:35: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:37:35: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:37:35: #1 total tags in treatment: 7825548 INFO @ Mon, 12 Aug 2019 18:37:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:37:35: #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 18:37:35: #1 tags after filtering in treatment: 7825548 INFO @ Mon, 12 Aug 2019 18:37:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:37:35: #1 finished! INFO @ Mon, 12 Aug 2019 18:37:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:37:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:37:36: #2 number of paired peaks: 421 WARNING @ Mon, 12 Aug 2019 18:37:36: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Mon, 12 Aug 2019 18:37:36: start model_add_line... INFO @ Mon, 12 Aug 2019 18:37:36: start X-correlation... INFO @ Mon, 12 Aug 2019 18:37:36: end of X-cor INFO @ Mon, 12 Aug 2019 18:37:36: #2 finished! INFO @ Mon, 12 Aug 2019 18:37:36: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 18:37:36: #2 alternative fragment length(s) may be 2,35,573,576,579,586 bps INFO @ Mon, 12 Aug 2019 18:37:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.10_model.r WARNING @ Mon, 12 Aug 2019 18:37:36: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:37:36: #2 You may need to consider one of the other alternative d(s): 2,35,573,576,579,586 WARNING @ Mon, 12 Aug 2019 18:37:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:37:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:37:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:37:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:37:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:37:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:37:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.05_summits.bed INFO @ Mon, 12 Aug 2019 18:37:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (551 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:37:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:38:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:38:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:38:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.20_summits.bed INFO @ Mon, 12 Aug 2019 18:38:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:38:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:38:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:38:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331225/SRX331225.10_summits.bed INFO @ Mon, 12 Aug 2019 18:38:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (243 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。