Job ID = 1292382 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 64,808,971 reads read : 129,617,942 reads written : 64,808,971 reads 0-length : 64,808,971 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: 00:16:07 64808971 reads; of these: 64808971 (100.00%) were unpaired; of these: 2927376 (4.52%) aligned 0 times 52578513 (81.13%) aligned exactly 1 time 9303082 (14.35%) aligned >1 times 95.48% overall alignment rate Time searching: 00:16:07 Overall time: 00:16:07 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 28 files... [bam_rmdupse_core] 53356878 / 61881595 = 0.8622 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 18:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.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 18:53:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.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 18:53:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.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 18:53:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:58: 1000000 INFO @ Sun, 02 Jun 2019 18:53:59: 1000000 INFO @ Sun, 02 Jun 2019 18:54:01: 1000000 INFO @ Sun, 02 Jun 2019 18:54:07: 2000000 INFO @ Sun, 02 Jun 2019 18:54:07: 2000000 INFO @ Sun, 02 Jun 2019 18:54:12: 2000000 INFO @ Sun, 02 Jun 2019 18:54:15: 3000000 INFO @ Sun, 02 Jun 2019 18:54:16: 3000000 INFO @ Sun, 02 Jun 2019 18:54:23: 3000000 INFO @ Sun, 02 Jun 2019 18:54:23: 4000000 INFO @ Sun, 02 Jun 2019 18:54:24: 4000000 INFO @ Sun, 02 Jun 2019 18:54:31: 5000000 INFO @ Sun, 02 Jun 2019 18:54:32: 5000000 INFO @ Sun, 02 Jun 2019 18:54:33: 4000000 INFO @ Sun, 02 Jun 2019 18:54:39: 6000000 INFO @ Sun, 02 Jun 2019 18:54:41: 6000000 INFO @ Sun, 02 Jun 2019 18:54:44: 5000000 INFO @ Sun, 02 Jun 2019 18:54:48: 7000000 INFO @ Sun, 02 Jun 2019 18:54:49: 7000000 INFO @ Sun, 02 Jun 2019 18:54:54: 6000000 INFO @ Sun, 02 Jun 2019 18:54:56: 8000000 INFO @ Sun, 02 Jun 2019 18:54:57: 8000000 INFO @ Sun, 02 Jun 2019 18:55:00: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:55:00: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:55:00: #1 total tags in treatment: 8524717 INFO @ Sun, 02 Jun 2019 18:55:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:55:00: #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 18:55:00: #1 tags after filtering in treatment: 8524717 INFO @ Sun, 02 Jun 2019 18:55:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:55:00: #1 finished! INFO @ Sun, 02 Jun 2019 18:55:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:55:01: #2 number of paired peaks: 1737 INFO @ Sun, 02 Jun 2019 18:55:01: start model_add_line... INFO @ Sun, 02 Jun 2019 18:55:01: start X-correlation... INFO @ Sun, 02 Jun 2019 18:55:01: end of X-cor INFO @ Sun, 02 Jun 2019 18:55:01: #2 finished! INFO @ Sun, 02 Jun 2019 18:55:01: #2 predicted fragment length is 165 bps INFO @ Sun, 02 Jun 2019 18:55:01: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 02 Jun 2019 18:55:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.20_model.r INFO @ Sun, 02 Jun 2019 18:55:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:55:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:55:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:55:02: #1 total tags in treatment: 8524717 INFO @ Sun, 02 Jun 2019 18:55:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:55:02: #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 18:55:02: #1 tags after filtering in treatment: 8524717 INFO @ Sun, 02 Jun 2019 18:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:55:02: #1 finished! INFO @ Sun, 02 Jun 2019 18:55:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:55:03: #2 number of paired peaks: 1737 INFO @ Sun, 02 Jun 2019 18:55:03: start model_add_line... INFO @ Sun, 02 Jun 2019 18:55:03: start X-correlation... INFO @ Sun, 02 Jun 2019 18:55:03: end of X-cor INFO @ Sun, 02 Jun 2019 18:55:03: #2 finished! INFO @ Sun, 02 Jun 2019 18:55:03: #2 predicted fragment length is 165 bps INFO @ Sun, 02 Jun 2019 18:55:03: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 02 Jun 2019 18:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.10_model.r INFO @ Sun, 02 Jun 2019 18:55:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:55:04: 7000000 INFO @ Sun, 02 Jun 2019 18:55:14: 8000000 INFO @ Sun, 02 Jun 2019 18:55:19: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:55:19: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:55:19: #1 total tags in treatment: 8524717 INFO @ Sun, 02 Jun 2019 18:55:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:55:19: #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 18:55:19: #1 tags after filtering in treatment: 8524717 INFO @ Sun, 02 Jun 2019 18:55:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:55:19: #1 finished! INFO @ Sun, 02 Jun 2019 18:55:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:55:20: #2 number of paired peaks: 1737 INFO @ Sun, 02 Jun 2019 18:55:20: start model_add_line... INFO @ Sun, 02 Jun 2019 18:55:20: start X-correlation... INFO @ Sun, 02 Jun 2019 18:55:20: end of X-cor INFO @ Sun, 02 Jun 2019 18:55:20: #2 finished! INFO @ Sun, 02 Jun 2019 18:55:20: #2 predicted fragment length is 165 bps INFO @ Sun, 02 Jun 2019 18:55:20: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 02 Jun 2019 18:55:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.05_model.r INFO @ Sun, 02 Jun 2019 18:55:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:55:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:55:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.20_summits.bed INFO @ Sun, 02 Jun 2019 18:55:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3195 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:55:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:55:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:55:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.10_summits.bed INFO @ Sun, 02 Jun 2019 18:55:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5484 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:55:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923759/SRX3923759.05_summits.bed INFO @ Sun, 02 Jun 2019 18:56:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7863 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。