Job ID = 1293247 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,252,117 reads read : 8,252,117 reads written : 8,252,117 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:14 8252117 reads; of these: 8252117 (100.00%) were unpaired; of these: 267820 (3.25%) aligned 0 times 5880302 (71.26%) aligned exactly 1 time 2103995 (25.50%) aligned >1 times 96.75% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 1871524 / 7984297 = 0.2344 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 @ Sun, 02 Jun 2019 22:33:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.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 @ Sun, 02 Jun 2019 22:33:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:33:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.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 @ Sun, 02 Jun 2019 22:33:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:33:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.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 @ Sun, 02 Jun 2019 22:33:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:33:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:33:56: 1000000 INFO @ Sun, 02 Jun 2019 22:33:58: 1000000 INFO @ Sun, 02 Jun 2019 22:33:59: 1000000 INFO @ Sun, 02 Jun 2019 22:34:04: 2000000 INFO @ Sun, 02 Jun 2019 22:34:09: 2000000 INFO @ Sun, 02 Jun 2019 22:34:10: 2000000 INFO @ Sun, 02 Jun 2019 22:34:13: 3000000 INFO @ Sun, 02 Jun 2019 22:34:20: 3000000 INFO @ Sun, 02 Jun 2019 22:34:21: 4000000 INFO @ Sun, 02 Jun 2019 22:34:22: 3000000 INFO @ Sun, 02 Jun 2019 22:34:30: 5000000 INFO @ Sun, 02 Jun 2019 22:34:31: 4000000 INFO @ Sun, 02 Jun 2019 22:34:34: 4000000 INFO @ Sun, 02 Jun 2019 22:34:38: 6000000 INFO @ Sun, 02 Jun 2019 22:34:39: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:34:39: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:34:39: #1 total tags in treatment: 6112773 INFO @ Sun, 02 Jun 2019 22:34:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:34:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:34:39: #1 tags after filtering in treatment: 6112773 INFO @ Sun, 02 Jun 2019 22:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:34:39: #1 finished! INFO @ Sun, 02 Jun 2019 22:34:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:34:40: #2 number of paired peaks: 1521 INFO @ Sun, 02 Jun 2019 22:34:40: start model_add_line... INFO @ Sun, 02 Jun 2019 22:34:40: start X-correlation... INFO @ Sun, 02 Jun 2019 22:34:40: end of X-cor INFO @ Sun, 02 Jun 2019 22:34:40: #2 finished! INFO @ Sun, 02 Jun 2019 22:34:40: #2 predicted fragment length is 93 bps INFO @ Sun, 02 Jun 2019 22:34:40: #2 alternative fragment length(s) may be 2,69,93,592 bps INFO @ Sun, 02 Jun 2019 22:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.10_model.r WARNING @ Sun, 02 Jun 2019 22:34:40: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:34:40: #2 You may need to consider one of the other alternative d(s): 2,69,93,592 WARNING @ Sun, 02 Jun 2019 22:34:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:34:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:34:42: 5000000 INFO @ Sun, 02 Jun 2019 22:34:44: 5000000 INFO @ Sun, 02 Jun 2019 22:34:54: 6000000 INFO @ Sun, 02 Jun 2019 22:34:55: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:34:55: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:34:55: #1 total tags in treatment: 6112773 INFO @ Sun, 02 Jun 2019 22:34:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:34:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:34:55: #1 tags after filtering in treatment: 6112773 INFO @ Sun, 02 Jun 2019 22:34:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:34:55: #1 finished! INFO @ Sun, 02 Jun 2019 22:34:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:34:55: 6000000 INFO @ Sun, 02 Jun 2019 22:34:56: #2 number of paired peaks: 1521 INFO @ Sun, 02 Jun 2019 22:34:56: start model_add_line... INFO @ Sun, 02 Jun 2019 22:34:56: start X-correlation... INFO @ Sun, 02 Jun 2019 22:34:56: end of X-cor INFO @ Sun, 02 Jun 2019 22:34:56: #2 finished! INFO @ Sun, 02 Jun 2019 22:34:56: #2 predicted fragment length is 93 bps INFO @ Sun, 02 Jun 2019 22:34:56: #2 alternative fragment length(s) may be 2,69,93,592 bps INFO @ Sun, 02 Jun 2019 22:34:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.20_model.r WARNING @ Sun, 02 Jun 2019 22:34:56: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:34:56: #2 You may need to consider one of the other alternative d(s): 2,69,93,592 WARNING @ Sun, 02 Jun 2019 22:34:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:34:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:34:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:34:57: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:34:57: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:34:57: #1 total tags in treatment: 6112773 INFO @ Sun, 02 Jun 2019 22:34:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:34:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:34:57: #1 tags after filtering in treatment: 6112773 INFO @ Sun, 02 Jun 2019 22:34:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:34:57: #1 finished! INFO @ Sun, 02 Jun 2019 22:34:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:34:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:34:57: #2 number of paired peaks: 1521 INFO @ Sun, 02 Jun 2019 22:34:57: start model_add_line... INFO @ Sun, 02 Jun 2019 22:34:57: start X-correlation... INFO @ Sun, 02 Jun 2019 22:34:57: end of X-cor INFO @ Sun, 02 Jun 2019 22:34:57: #2 finished! INFO @ Sun, 02 Jun 2019 22:34:57: #2 predicted fragment length is 93 bps INFO @ Sun, 02 Jun 2019 22:34:57: #2 alternative fragment length(s) may be 2,69,93,592 bps INFO @ Sun, 02 Jun 2019 22:34:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.05_model.r WARNING @ Sun, 02 Jun 2019 22:34:57: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:34:57: #2 You may need to consider one of the other alternative d(s): 2,69,93,592 WARNING @ Sun, 02 Jun 2019 22:34:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:34:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:34:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:34:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.10_summits.bed INFO @ Sun, 02 Jun 2019 22:35:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:35:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:35:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:35:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:35:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:35:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.20_summits.bed INFO @ Sun, 02 Jun 2019 22:35:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554724/SRX554724.05_summits.bed INFO @ Sun, 02 Jun 2019 22:35:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1282 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。