Job ID = 6454874 SRX = SRX2592466 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:25 prefetch.2.10.7: 1) Downloading 'SRR5289743'... 2020-06-21T09:48:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:39 prefetch.2.10.7: 1) 'SRR5289743' was downloaded successfully Read 17054008 spots for SRR5289743/SRR5289743.sra Written 17054008 spots for SRR5289743/SRR5289743.sra 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: 00:03:49 17054008 reads; of these: 17054008 (100.00%) were unpaired; of these: 2452319 (14.38%) aligned 0 times 12197626 (71.52%) aligned exactly 1 time 2404063 (14.10%) aligned >1 times 85.62% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4070813 / 14601689 = 0.2788 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.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 @ Sun, 21 Jun 2020 19:00:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:30: 1000000 INFO @ Sun, 21 Jun 2020 19:00:36: 2000000 INFO @ Sun, 21 Jun 2020 19:00:41: 3000000 INFO @ Sun, 21 Jun 2020 19:00:47: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:00:53: 5000000 INFO @ Sun, 21 Jun 2020 19:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.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 @ Sun, 21 Jun 2020 19:00:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:00: 6000000 INFO @ Sun, 21 Jun 2020 19:01:00: 1000000 INFO @ Sun, 21 Jun 2020 19:01:06: 7000000 INFO @ Sun, 21 Jun 2020 19:01:07: 2000000 INFO @ Sun, 21 Jun 2020 19:01:13: 8000000 INFO @ Sun, 21 Jun 2020 19:01:13: 3000000 INFO @ Sun, 21 Jun 2020 19:01:19: 9000000 INFO @ Sun, 21 Jun 2020 19:01:20: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.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 @ Sun, 21 Jun 2020 19:01:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:26: 10000000 INFO @ Sun, 21 Jun 2020 19:01:26: 5000000 INFO @ Sun, 21 Jun 2020 19:01:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:01:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:01:30: #1 total tags in treatment: 10530876 INFO @ Sun, 21 Jun 2020 19:01:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:01:30: #1 tags after filtering in treatment: 10530679 INFO @ Sun, 21 Jun 2020 19:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:30: 1000000 INFO @ Sun, 21 Jun 2020 19:01:31: #2 number of paired peaks: 7876 INFO @ Sun, 21 Jun 2020 19:01:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:31: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 19:01:31: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 19:01:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.05_model.r INFO @ Sun, 21 Jun 2020 19:01:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:33: 6000000 INFO @ Sun, 21 Jun 2020 19:01:37: 2000000 INFO @ Sun, 21 Jun 2020 19:01:39: 7000000 INFO @ Sun, 21 Jun 2020 19:01:43: 3000000 INFO @ Sun, 21 Jun 2020 19:01:46: 8000000 INFO @ Sun, 21 Jun 2020 19:01:49: 4000000 INFO @ Sun, 21 Jun 2020 19:01:52: 9000000 INFO @ Sun, 21 Jun 2020 19:01:56: 5000000 INFO @ Sun, 21 Jun 2020 19:01:59: 10000000 INFO @ Sun, 21 Jun 2020 19:02:02: 6000000 INFO @ Sun, 21 Jun 2020 19:02:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:02:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:02:03: #1 total tags in treatment: 10530876 INFO @ Sun, 21 Jun 2020 19:02:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:02:03: #1 tags after filtering in treatment: 10530679 INFO @ Sun, 21 Jun 2020 19:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:04: #2 number of paired peaks: 7876 INFO @ Sun, 21 Jun 2020 19:02:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:04: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 19:02:04: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 19:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.10_model.r INFO @ Sun, 21 Jun 2020 19:02:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:07: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:02:08: 7000000 INFO @ Sun, 21 Jun 2020 19:02:14: 8000000 INFO @ Sun, 21 Jun 2020 19:02:21: 9000000 INFO @ Sun, 21 Jun 2020 19:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.05_summits.bed INFO @ Sun, 21 Jun 2020 19:02:22: Done! pass1 - making usageList (163 chroms): 3 millis pass2 - checking and writing primary data (10001 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:02:27: 10000000 INFO @ Sun, 21 Jun 2020 19:02:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:02:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:02:30: #1 total tags in treatment: 10530876 INFO @ Sun, 21 Jun 2020 19:02:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:02:30: #1 tags after filtering in treatment: 10530679 INFO @ Sun, 21 Jun 2020 19:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:32: #2 number of paired peaks: 7876 INFO @ Sun, 21 Jun 2020 19:02:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:32: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 19:02:32: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 19:02:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.20_model.r INFO @ Sun, 21 Jun 2020 19:02:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.10_summits.bed INFO @ Sun, 21 Jun 2020 19:02:53: Done! pass1 - making usageList (131 chroms): 2 millis pass2 - checking and writing primary data (7537 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592466/SRX2592466.20_summits.bed INFO @ Sun, 21 Jun 2020 19:03:21: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (5295 records, 4 fields): 11 millis CompletedMACS2peakCalling