Job ID = 6458960 SRX = SRX5827829 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:59:04 prefetch.2.10.7: 1) Downloading 'SRR9051580'... 2020-06-21T12:59:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:01:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:01:36 prefetch.2.10.7: 'SRR9051580' is valid 2020-06-21T13:01:36 prefetch.2.10.7: 1) 'SRR9051580' was downloaded successfully 2020-06-21T13:01:36 prefetch.2.10.7: 'SRR9051580' has 0 unresolved dependencies Read 15035433 spots for SRR9051580/SRR9051580.sra Written 15035433 spots for SRR9051580/SRR9051580.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: 00:03:18 15035433 reads; of these: 15035433 (100.00%) were unpaired; of these: 3332792 (22.17%) aligned 0 times 9943996 (66.14%) aligned exactly 1 time 1758645 (11.70%) aligned >1 times 77.83% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 7463336 / 11702641 = 0.6377 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 22:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.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 22:08:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:46: 1000000 INFO @ Sun, 21 Jun 2020 22:08:51: 2000000 INFO @ Sun, 21 Jun 2020 22:08:56: 3000000 INFO @ Sun, 21 Jun 2020 22:09:02: 4000000 INFO @ Sun, 21 Jun 2020 22:09:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:09:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:09:03: #1 total tags in treatment: 4239305 INFO @ Sun, 21 Jun 2020 22:09:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:03: #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 22:09:04: #1 tags after filtering in treatment: 4239282 INFO @ Sun, 21 Jun 2020 22:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:04: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:04: #2 number of paired peaks: 1162 INFO @ Sun, 21 Jun 2020 22:09:04: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:04: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:04: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:04: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:04: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 22:09:04: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 22:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.05_model.r INFO @ Sun, 21 Jun 2020 22:09:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:04: #3 Pre-compute pvalue-qvalue table... 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 22:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.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 22:09:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:09:17: 1000000 INFO @ Sun, 21 Jun 2020 22:09:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.05_summits.bed INFO @ Sun, 21 Jun 2020 22:09:19: Done! pass1 - making usageList (436 chroms): 1 millis pass2 - checking and writing primary data (2579 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:09:22: 2000000 INFO @ Sun, 21 Jun 2020 22:09:27: 3000000 INFO @ Sun, 21 Jun 2020 22:09:32: 4000000 INFO @ Sun, 21 Jun 2020 22:09:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:09:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:09:34: #1 total tags in treatment: 4239305 INFO @ Sun, 21 Jun 2020 22:09:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:34: #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 22:09:34: #1 tags after filtering in treatment: 4239282 INFO @ Sun, 21 Jun 2020 22:09:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:34: #2 number of paired peaks: 1162 INFO @ Sun, 21 Jun 2020 22:09:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:34: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 22:09:34: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 22:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.10_model.r INFO @ Sun, 21 Jun 2020 22:09:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:34: #3 Pre-compute pvalue-qvalue table... 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 22:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.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 22:09:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:09:47: 1000000 INFO @ Sun, 21 Jun 2020 22:09:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.10_summits.bed INFO @ Sun, 21 Jun 2020 22:09:49: Done! pass1 - making usageList (327 chroms): 1 millis pass2 - checking and writing primary data (1334 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:09:52: 2000000 INFO @ Sun, 21 Jun 2020 22:09:57: 3000000 INFO @ Sun, 21 Jun 2020 22:10:02: 4000000 INFO @ Sun, 21 Jun 2020 22:10:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:10:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:10:03: #1 total tags in treatment: 4239305 INFO @ Sun, 21 Jun 2020 22:10:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:03: #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 22:10:04: #1 tags after filtering in treatment: 4239282 INFO @ Sun, 21 Jun 2020 22:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:04: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:04: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:10:04: #2 number of paired peaks: 1162 INFO @ Sun, 21 Jun 2020 22:10:04: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:04: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:04: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:04: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:04: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 22:10:04: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 22:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.20_model.r INFO @ Sun, 21 Jun 2020 22:10:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827829/SRX5827829.20_summits.bed INFO @ Sun, 21 Jun 2020 22:10:19: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 9 millis CompletedMACS2peakCalling