Job ID = 1293990 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 3,058,962 reads read : 3,058,962 reads written : 3,058,962 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: 00:04:04 23058962 reads; of these: 23058962 (100.00%) were unpaired; of these: 13274954 (57.57%) aligned 0 times 8571687 (37.17%) aligned exactly 1 time 1212321 (5.26%) aligned >1 times 42.43% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2264264 / 9784008 = 0.2314 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, 03 Jun 2019 04:05:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 04:05:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:05:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:05:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 04:05:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:05:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:05:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 04:05:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:05:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:05:11: 1000000 INFO @ Mon, 03 Jun 2019 04:05:12: 1000000 INFO @ Mon, 03 Jun 2019 04:05:12: 1000000 INFO @ Mon, 03 Jun 2019 04:05:19: 2000000 INFO @ Mon, 03 Jun 2019 04:05:21: 2000000 INFO @ Mon, 03 Jun 2019 04:05:21: 2000000 INFO @ Mon, 03 Jun 2019 04:05:26: 3000000 INFO @ Mon, 03 Jun 2019 04:05:29: 3000000 INFO @ Mon, 03 Jun 2019 04:05:30: 3000000 INFO @ Mon, 03 Jun 2019 04:05:35: 4000000 INFO @ Mon, 03 Jun 2019 04:05:37: 4000000 INFO @ Mon, 03 Jun 2019 04:05:38: 4000000 INFO @ Mon, 03 Jun 2019 04:05:42: 5000000 INFO @ Mon, 03 Jun 2019 04:05:45: 5000000 INFO @ Mon, 03 Jun 2019 04:05:47: 5000000 INFO @ Mon, 03 Jun 2019 04:05:50: 6000000 INFO @ Mon, 03 Jun 2019 04:05:54: 6000000 INFO @ Mon, 03 Jun 2019 04:05:55: 6000000 INFO @ Mon, 03 Jun 2019 04:05:58: 7000000 INFO @ Mon, 03 Jun 2019 04:06:02: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:06:02: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:06:02: #1 total tags in treatment: 7519744 INFO @ Mon, 03 Jun 2019 04:06:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:06:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:06:02: #1 tags after filtering in treatment: 7519744 INFO @ Mon, 03 Jun 2019 04:06:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:06:02: #1 finished! INFO @ Mon, 03 Jun 2019 04:06:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:06:02: 7000000 INFO @ Mon, 03 Jun 2019 04:06:03: #2 number of paired peaks: 2637 INFO @ Mon, 03 Jun 2019 04:06:03: start model_add_line... INFO @ Mon, 03 Jun 2019 04:06:03: start X-correlation... INFO @ Mon, 03 Jun 2019 04:06:03: end of X-cor INFO @ Mon, 03 Jun 2019 04:06:03: #2 finished! INFO @ Mon, 03 Jun 2019 04:06:03: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 04:06:03: #2 alternative fragment length(s) may be 2,229,250 bps INFO @ Mon, 03 Jun 2019 04:06:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.10_model.r INFO @ Mon, 03 Jun 2019 04:06:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:06:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:06:03: 7000000 INFO @ Mon, 03 Jun 2019 04:06:06: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:06:06: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:06:06: #1 total tags in treatment: 7519744 INFO @ Mon, 03 Jun 2019 04:06:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:06:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:06:06: #1 tags after filtering in treatment: 7519744 INFO @ Mon, 03 Jun 2019 04:06:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:06:06: #1 finished! INFO @ Mon, 03 Jun 2019 04:06:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:06:07: #2 number of paired peaks: 2637 INFO @ Mon, 03 Jun 2019 04:06:07: start model_add_line... INFO @ Mon, 03 Jun 2019 04:06:07: start X-correlation... INFO @ Mon, 03 Jun 2019 04:06:07: end of X-cor INFO @ Mon, 03 Jun 2019 04:06:07: #2 finished! INFO @ Mon, 03 Jun 2019 04:06:07: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 04:06:07: #2 alternative fragment length(s) may be 2,229,250 bps INFO @ Mon, 03 Jun 2019 04:06:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.20_model.r INFO @ Mon, 03 Jun 2019 04:06:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:06:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:06:08: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:06:08: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:06:08: #1 total tags in treatment: 7519744 INFO @ Mon, 03 Jun 2019 04:06:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:06:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:06:08: #1 tags after filtering in treatment: 7519744 INFO @ Mon, 03 Jun 2019 04:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:06:08: #1 finished! INFO @ Mon, 03 Jun 2019 04:06:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:06:09: #2 number of paired peaks: 2637 INFO @ Mon, 03 Jun 2019 04:06:09: start model_add_line... INFO @ Mon, 03 Jun 2019 04:06:09: start X-correlation... INFO @ Mon, 03 Jun 2019 04:06:09: end of X-cor INFO @ Mon, 03 Jun 2019 04:06:09: #2 finished! INFO @ Mon, 03 Jun 2019 04:06:09: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 04:06:09: #2 alternative fragment length(s) may be 2,229,250 bps INFO @ Mon, 03 Jun 2019 04:06:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.05_model.r INFO @ Mon, 03 Jun 2019 04:06:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:06:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:06:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:06:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:06:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:06:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:06:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:06:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.10_summits.bed INFO @ Mon, 03 Jun 2019 04:06:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.20_summits.bed INFO @ Mon, 03 Jun 2019 04:06:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:06:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:06:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:06:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550623/SRX1550623.05_summits.bed INFO @ Mon, 03 Jun 2019 04:06:43: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (433 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。