Job ID = 10165820 SRX = SRX5681711 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3638518 spots for SRR8895583/SRR8895583.sra Written 3638518 spots for SRR8895583/SRR8895583.sra Read 3860949 spots for SRR8895584/SRR8895584.sra Written 3860949 spots for SRR8895584/SRR8895584.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166178 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:27 7499467 reads; of these: 7499467 (100.00%) were paired; of these: 1936787 (25.83%) aligned concordantly 0 times 4981271 (66.42%) aligned concordantly exactly 1 time 581409 (7.75%) aligned concordantly >1 times ---- 1936787 pairs aligned concordantly 0 times; of these: 444351 (22.94%) aligned discordantly 1 time ---- 1492436 pairs aligned 0 times concordantly or discordantly; of these: 2984872 mates make up the pairs; of these: 2434294 (81.55%) aligned 0 times 395467 (13.25%) aligned exactly 1 time 155111 (5.20%) aligned >1 times 83.77% overall alignment rate Time searching: 00:10:27 Overall time: 00:10:27 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_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 296654 / 5986341 = 0.0496 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 @ Thu, 08 Oct 2020 20:12:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.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 @ Thu, 08 Oct 2020 20:12:14: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:12:14: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:12:19: 1000000 INFO @ Thu, 08 Oct 2020 20:12:24: 2000000 INFO @ Thu, 08 Oct 2020 20:12:29: 3000000 INFO @ Thu, 08 Oct 2020 20:12:35: 4000000 INFO @ Thu, 08 Oct 2020 20:12:40: 5000000 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 @ Thu, 08 Oct 2020 20:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.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 @ Thu, 08 Oct 2020 20:12:44: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:12:44: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:12:45: 6000000 INFO @ Thu, 08 Oct 2020 20:12:49: 1000000 INFO @ Thu, 08 Oct 2020 20:12:51: 7000000 INFO @ Thu, 08 Oct 2020 20:12:55: 2000000 INFO @ Thu, 08 Oct 2020 20:12:56: 8000000 INFO @ Thu, 08 Oct 2020 20:13:00: 3000000 INFO @ Thu, 08 Oct 2020 20:13:01: 9000000 INFO @ Thu, 08 Oct 2020 20:13:05: 4000000 INFO @ Thu, 08 Oct 2020 20:13:07: 10000000 INFO @ Thu, 08 Oct 2020 20:13:11: 5000000 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 @ Thu, 08 Oct 2020 20:13:12: 11000000 INFO @ Thu, 08 Oct 2020 20:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.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 @ Thu, 08 Oct 2020 20:13:14: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:13:14: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:13:16: 6000000 INFO @ Thu, 08 Oct 2020 20:13:17: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:13:17: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:13:17: #1 total tags in treatment: 5283944 INFO @ Thu, 08 Oct 2020 20:13:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:13:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:13:17: #1 tags after filtering in treatment: 4704323 INFO @ Thu, 08 Oct 2020 20:13:17: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 08 Oct 2020 20:13:17: #1 finished! INFO @ Thu, 08 Oct 2020 20:13:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:13:18: #2 number of paired peaks: 3552 INFO @ Thu, 08 Oct 2020 20:13:18: start model_add_line... INFO @ Thu, 08 Oct 2020 20:13:18: start X-correlation... INFO @ Thu, 08 Oct 2020 20:13:18: end of X-cor INFO @ Thu, 08 Oct 2020 20:13:18: #2 finished! INFO @ Thu, 08 Oct 2020 20:13:18: #2 predicted fragment length is 232 bps INFO @ Thu, 08 Oct 2020 20:13:18: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 08 Oct 2020 20:13:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05_model.r INFO @ Thu, 08 Oct 2020 20:13:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:13:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:13:19: 1000000 INFO @ Thu, 08 Oct 2020 20:13:21: 7000000 INFO @ Thu, 08 Oct 2020 20:13:24: 2000000 INFO @ Thu, 08 Oct 2020 20:13:27: 8000000 INFO @ Thu, 08 Oct 2020 20:13:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:13:30: 3000000 INFO @ Thu, 08 Oct 2020 20:13:32: 9000000 INFO @ Thu, 08 Oct 2020 20:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.05_summits.bed INFO @ Thu, 08 Oct 2020 20:13:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12338 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:13:35: 4000000 INFO @ Thu, 08 Oct 2020 20:13:37: 10000000 INFO @ Thu, 08 Oct 2020 20:13:41: 5000000 INFO @ Thu, 08 Oct 2020 20:13:43: 11000000 INFO @ Thu, 08 Oct 2020 20:13:46: 6000000 INFO @ Thu, 08 Oct 2020 20:13:48: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:13:48: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:13:48: #1 total tags in treatment: 5283944 INFO @ Thu, 08 Oct 2020 20:13:48: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:13:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:13:48: #1 tags after filtering in treatment: 4704323 INFO @ Thu, 08 Oct 2020 20:13:48: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 08 Oct 2020 20:13:48: #1 finished! INFO @ Thu, 08 Oct 2020 20:13:48: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:13:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:13:48: #2 number of paired peaks: 3552 INFO @ Thu, 08 Oct 2020 20:13:48: start model_add_line... INFO @ Thu, 08 Oct 2020 20:13:48: start X-correlation... INFO @ Thu, 08 Oct 2020 20:13:48: end of X-cor INFO @ Thu, 08 Oct 2020 20:13:48: #2 finished! INFO @ Thu, 08 Oct 2020 20:13:48: #2 predicted fragment length is 232 bps INFO @ Thu, 08 Oct 2020 20:13:48: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 08 Oct 2020 20:13:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10_model.r INFO @ Thu, 08 Oct 2020 20:13:48: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:13:51: 7000000 INFO @ Thu, 08 Oct 2020 20:13:57: 8000000 INFO @ Thu, 08 Oct 2020 20:13:59: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:14:02: 9000000 INFO @ Thu, 08 Oct 2020 20:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.10_summits.bed INFO @ Thu, 08 Oct 2020 20:14:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5151 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:14:08: 10000000 INFO @ Thu, 08 Oct 2020 20:14:13: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:14:18: #1 tag size is determined as 100 bps INFO @ Thu, 08 Oct 2020 20:14:18: #1 tag size = 100 INFO @ Thu, 08 Oct 2020 20:14:18: #1 total tags in treatment: 5283944 INFO @ Thu, 08 Oct 2020 20:14:18: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:14:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:14:18: #1 tags after filtering in treatment: 4704323 INFO @ Thu, 08 Oct 2020 20:14:18: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 08 Oct 2020 20:14:18: #1 finished! INFO @ Thu, 08 Oct 2020 20:14:18: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:14:19: #2 number of paired peaks: 3552 INFO @ Thu, 08 Oct 2020 20:14:19: start model_add_line... INFO @ Thu, 08 Oct 2020 20:14:19: start X-correlation... INFO @ Thu, 08 Oct 2020 20:14:19: end of X-cor INFO @ Thu, 08 Oct 2020 20:14:19: #2 finished! INFO @ Thu, 08 Oct 2020 20:14:19: #2 predicted fragment length is 232 bps INFO @ Thu, 08 Oct 2020 20:14:19: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 08 Oct 2020 20:14:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20_model.r INFO @ Thu, 08 Oct 2020 20:14:19: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:14:30: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:14:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:14:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:14:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5681711/SRX5681711.20_summits.bed INFO @ Thu, 08 Oct 2020 20:14:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。