Job ID = 14171112 SRX = SRX9555305 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5978210 spots for SRR13110791/SRR13110791.sra Written 5978210 spots for SRR13110791/SRR13110791.sra Read 5889539 spots for SRR13110792/SRR13110792.sra Written 5889539 spots for SRR13110792/SRR13110792.sra Read 6022812 spots for SRR13110793/SRR13110793.sra Written 6022812 spots for SRR13110793/SRR13110793.sra Read 5909655 spots for SRR13110794/SRR13110794.sra Written 5909655 spots for SRR13110794/SRR13110794.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171559 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:23 23800216 reads; of these: 23800216 (100.00%) were paired; of these: 23001278 (96.64%) aligned concordantly 0 times 643673 (2.70%) aligned concordantly exactly 1 time 155265 (0.65%) aligned concordantly >1 times ---- 23001278 pairs aligned concordantly 0 times; of these: 3376 (0.01%) aligned discordantly 1 time ---- 22997902 pairs aligned 0 times concordantly or discordantly; of these: 45995804 mates make up the pairs; of these: 45849384 (99.68%) aligned 0 times 55609 (0.12%) aligned exactly 1 time 90811 (0.20%) aligned >1 times 3.68% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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_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] 18361 / 802015 = 0.0229 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.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 @ Sat, 11 Dec 2021 09:42:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:17: 1000000 INFO @ Sat, 11 Dec 2021 09:42:20: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:42:20: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:42:20: #1 total tags in treatment: 780615 INFO @ Sat, 11 Dec 2021 09:42:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:42:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:42:20: #1 tags after filtering in treatment: 746428 INFO @ Sat, 11 Dec 2021 09:42:20: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 09:42:20: #1 finished! INFO @ Sat, 11 Dec 2021 09:42:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:42:21: #2 number of paired peaks: 7620 INFO @ Sat, 11 Dec 2021 09:42:21: start model_add_line... INFO @ Sat, 11 Dec 2021 09:42:21: start X-correlation... INFO @ Sat, 11 Dec 2021 09:42:21: end of X-cor INFO @ Sat, 11 Dec 2021 09:42:21: #2 finished! INFO @ Sat, 11 Dec 2021 09:42:21: #2 predicted fragment length is 230 bps INFO @ Sat, 11 Dec 2021 09:42:21: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 11 Dec 2021 09:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.05_model.r INFO @ Sat, 11 Dec 2021 09:42:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:42:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.05_summits.bed INFO @ Sat, 11 Dec 2021 09:42:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 2 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.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 @ Sat, 11 Dec 2021 09:42:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:47: 1000000 INFO @ Sat, 11 Dec 2021 09:42:50: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:42:50: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:42:50: #1 total tags in treatment: 780615 INFO @ Sat, 11 Dec 2021 09:42:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:42:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:42:50: #1 tags after filtering in treatment: 746428 INFO @ Sat, 11 Dec 2021 09:42:50: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 09:42:50: #1 finished! INFO @ Sat, 11 Dec 2021 09:42:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:42:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:42:51: #2 number of paired peaks: 7620 INFO @ Sat, 11 Dec 2021 09:42:51: start model_add_line... INFO @ Sat, 11 Dec 2021 09:42:51: start X-correlation... INFO @ Sat, 11 Dec 2021 09:42:51: end of X-cor INFO @ Sat, 11 Dec 2021 09:42:51: #2 finished! INFO @ Sat, 11 Dec 2021 09:42:51: #2 predicted fragment length is 230 bps INFO @ Sat, 11 Dec 2021 09:42:51: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 11 Dec 2021 09:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.10_model.r INFO @ Sat, 11 Dec 2021 09:42:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:42:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:42:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.10_summits.bed INFO @ Sat, 11 Dec 2021 09:42:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:43:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.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 @ Sat, 11 Dec 2021 09:43:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:18: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:43:21: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:43:21: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:43:21: #1 total tags in treatment: 780615 INFO @ Sat, 11 Dec 2021 09:43:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:43:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:43:21: #1 tags after filtering in treatment: 746428 INFO @ Sat, 11 Dec 2021 09:43:21: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 09:43:21: #1 finished! INFO @ Sat, 11 Dec 2021 09:43:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:43:21: #2 number of paired peaks: 7620 INFO @ Sat, 11 Dec 2021 09:43:21: start model_add_line... INFO @ Sat, 11 Dec 2021 09:43:21: start X-correlation... INFO @ Sat, 11 Dec 2021 09:43:21: end of X-cor INFO @ Sat, 11 Dec 2021 09:43:21: #2 finished! INFO @ Sat, 11 Dec 2021 09:43:21: #2 predicted fragment length is 230 bps INFO @ Sat, 11 Dec 2021 09:43:21: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 11 Dec 2021 09:43:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.20_model.r INFO @ Sat, 11 Dec 2021 09:43:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:43:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:43:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:43:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:43:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:43:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555305/SRX9555305.20_summits.bed INFO @ Sat, 11 Dec 2021 09:43:24: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 1 millis CompletedMACS2peakCalling