Job ID = 2590052 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 45,330,527 reads read : 45,330,527 reads written : 45,330,527 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:04 45330527 reads; of these: 45330527 (100.00%) were unpaired; of these: 9826522 (21.68%) aligned 0 times 28092886 (61.97%) aligned exactly 1 time 7411119 (16.35%) aligned >1 times 78.32% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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 16 files... [bam_rmdupse_core] 31225448 / 35504005 = 0.8795 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 19:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.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 19:55:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:55:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:55:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.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 19:55:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:55:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.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 19:55:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:55:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:55:33: 1000000 INFO @ Mon, 12 Aug 2019 19:55:34: 1000000 INFO @ Mon, 12 Aug 2019 19:55:35: 1000000 INFO @ Mon, 12 Aug 2019 19:55:40: 2000000 INFO @ Mon, 12 Aug 2019 19:55:41: 2000000 INFO @ Mon, 12 Aug 2019 19:55:44: 2000000 INFO @ Mon, 12 Aug 2019 19:55:48: 3000000 INFO @ Mon, 12 Aug 2019 19:55:49: 3000000 INFO @ Mon, 12 Aug 2019 19:55:53: 3000000 INFO @ Mon, 12 Aug 2019 19:55:56: 4000000 INFO @ Mon, 12 Aug 2019 19:55:57: 4000000 INFO @ Mon, 12 Aug 2019 19:55:58: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:55:58: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:55:58: #1 total tags in treatment: 4278557 INFO @ Mon, 12 Aug 2019 19:55:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:55:58: #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 19:55:58: #1 tags after filtering in treatment: 4278557 INFO @ Mon, 12 Aug 2019 19:55:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:55:58: #1 finished! INFO @ Mon, 12 Aug 2019 19:55:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:55:59: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:55:59: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:55:59: #1 total tags in treatment: 4278557 INFO @ Mon, 12 Aug 2019 19:55:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:55:59: #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 19:55:59: #1 tags after filtering in treatment: 4278557 INFO @ Mon, 12 Aug 2019 19:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:55:59: #1 finished! INFO @ Mon, 12 Aug 2019 19:55:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:55:59: #2 number of paired peaks: 1589 INFO @ Mon, 12 Aug 2019 19:55:59: start model_add_line... INFO @ Mon, 12 Aug 2019 19:55:59: start X-correlation... INFO @ Mon, 12 Aug 2019 19:55:59: end of X-cor INFO @ Mon, 12 Aug 2019 19:55:59: #2 finished! INFO @ Mon, 12 Aug 2019 19:55:59: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 19:55:59: #2 alternative fragment length(s) may be 3,50,580 bps INFO @ Mon, 12 Aug 2019 19:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.05_model.r WARNING @ Mon, 12 Aug 2019 19:55:59: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:55:59: #2 You may need to consider one of the other alternative d(s): 3,50,580 WARNING @ Mon, 12 Aug 2019 19:55:59: #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 19:55:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:55:59: #2 number of paired peaks: 1589 INFO @ Mon, 12 Aug 2019 19:55:59: start model_add_line... INFO @ Mon, 12 Aug 2019 19:55:59: start X-correlation... INFO @ Mon, 12 Aug 2019 19:55:59: end of X-cor INFO @ Mon, 12 Aug 2019 19:55:59: #2 finished! INFO @ Mon, 12 Aug 2019 19:55:59: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 19:55:59: #2 alternative fragment length(s) may be 3,50,580 bps INFO @ Mon, 12 Aug 2019 19:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.10_model.r WARNING @ Mon, 12 Aug 2019 19:55:59: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:55:59: #2 You may need to consider one of the other alternative d(s): 3,50,580 WARNING @ Mon, 12 Aug 2019 19:55:59: #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 19:55:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:56:01: 4000000 INFO @ Mon, 12 Aug 2019 19:56:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:56:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:56:03: #1 total tags in treatment: 4278557 INFO @ Mon, 12 Aug 2019 19:56:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:56:03: #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 19:56:03: #1 tags after filtering in treatment: 4278557 INFO @ Mon, 12 Aug 2019 19:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:56:03: #1 finished! INFO @ Mon, 12 Aug 2019 19:56:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:56:04: #2 number of paired peaks: 1589 INFO @ Mon, 12 Aug 2019 19:56:04: start model_add_line... INFO @ Mon, 12 Aug 2019 19:56:04: start X-correlation... INFO @ Mon, 12 Aug 2019 19:56:04: end of X-cor INFO @ Mon, 12 Aug 2019 19:56:04: #2 finished! INFO @ Mon, 12 Aug 2019 19:56:04: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 19:56:04: #2 alternative fragment length(s) may be 3,50,580 bps INFO @ Mon, 12 Aug 2019 19:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.20_model.r WARNING @ Mon, 12 Aug 2019 19:56:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:56:04: #2 You may need to consider one of the other alternative d(s): 3,50,580 WARNING @ Mon, 12 Aug 2019 19:56:04: #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 19:56:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:56:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:56:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:56:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.05_summits.bed INFO @ Mon, 12 Aug 2019 19:56:18: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3892 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.10_summits.bed INFO @ Mon, 12 Aug 2019 19:56:19: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1614 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:56:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:56:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494896/SRX494896.20_summits.bed INFO @ Mon, 12 Aug 2019 19:56:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (449 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。