Job ID = 16439443 SRX = SRX5101712 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5941359 spots for SRR8287005/SRR8287005.sra Written 5941359 spots for SRR8287005/SRR8287005.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439528 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:32 5941359 reads; of these: 5941359 (100.00%) were paired; of these: 747962 (12.59%) aligned concordantly 0 times 1348844 (22.70%) aligned concordantly exactly 1 time 3844553 (64.71%) aligned concordantly >1 times ---- 747962 pairs aligned concordantly 0 times; of these: 147786 (19.76%) aligned discordantly 1 time ---- 600176 pairs aligned 0 times concordantly or discordantly; of these: 1200352 mates make up the pairs; of these: 176205 (14.68%) aligned 0 times 103583 (8.63%) aligned exactly 1 time 920564 (76.69%) aligned >1 times 98.52% overall alignment rate Time searching: 00:13:33 Overall time: 00:13:33 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] 4116287 / 5268324 = 0.7813 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.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 @ Tue, 02 Aug 2022 15:29:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:29:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:29:48: 1000000 INFO @ Tue, 02 Aug 2022 15:29:57: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:30:07: 3000000 INFO @ Tue, 02 Aug 2022 15:30:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.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 @ Tue, 02 Aug 2022 15:30:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:30:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:30:12: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 15:30:12: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 15:30:12: #1 total tags in treatment: 1146608 INFO @ Tue, 02 Aug 2022 15:30:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:30:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:30:12: #1 tags after filtering in treatment: 635480 INFO @ Tue, 02 Aug 2022 15:30:12: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 02 Aug 2022 15:30:12: #1 finished! INFO @ Tue, 02 Aug 2022 15:30:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:30:12: #2 number of paired peaks: 5884 INFO @ Tue, 02 Aug 2022 15:30:12: start model_add_line... INFO @ Tue, 02 Aug 2022 15:30:12: start X-correlation... INFO @ Tue, 02 Aug 2022 15:30:12: end of X-cor INFO @ Tue, 02 Aug 2022 15:30:12: #2 finished! INFO @ Tue, 02 Aug 2022 15:30:12: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 15:30:12: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 15:30:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.05_model.r INFO @ Tue, 02 Aug 2022 15:30:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:30:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:30:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:30:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:30:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:30:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.05_summits.bed INFO @ Tue, 02 Aug 2022 15:30:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2727 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:30:18: 1000000 INFO @ Tue, 02 Aug 2022 15:30:28: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:30:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.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 @ Tue, 02 Aug 2022 15:30:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:30:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:30:39: 3000000 INFO @ Tue, 02 Aug 2022 15:30:44: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 15:30:44: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 15:30:44: #1 total tags in treatment: 1146608 INFO @ Tue, 02 Aug 2022 15:30:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:30:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:30:44: #1 tags after filtering in treatment: 635480 INFO @ Tue, 02 Aug 2022 15:30:44: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 02 Aug 2022 15:30:44: #1 finished! INFO @ Tue, 02 Aug 2022 15:30:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:30:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:30:45: #2 number of paired peaks: 5884 INFO @ Tue, 02 Aug 2022 15:30:45: start model_add_line... INFO @ Tue, 02 Aug 2022 15:30:45: start X-correlation... INFO @ Tue, 02 Aug 2022 15:30:45: end of X-cor INFO @ Tue, 02 Aug 2022 15:30:45: #2 finished! INFO @ Tue, 02 Aug 2022 15:30:45: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 15:30:45: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 15:30:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.10_model.r INFO @ Tue, 02 Aug 2022 15:30:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:30:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:30:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.10_summits.bed INFO @ Tue, 02 Aug 2022 15:30:49: Done! INFO @ Tue, 02 Aug 2022 15:30:49: 1000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1037 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:31:00: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:31:11: 3000000 INFO @ Tue, 02 Aug 2022 15:31:16: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 15:31:16: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 15:31:16: #1 total tags in treatment: 1146608 INFO @ Tue, 02 Aug 2022 15:31:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:31:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:31:16: #1 tags after filtering in treatment: 635480 INFO @ Tue, 02 Aug 2022 15:31:16: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 02 Aug 2022 15:31:16: #1 finished! INFO @ Tue, 02 Aug 2022 15:31:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:31:17: #2 number of paired peaks: 5884 INFO @ Tue, 02 Aug 2022 15:31:17: start model_add_line... INFO @ Tue, 02 Aug 2022 15:31:17: start X-correlation... INFO @ Tue, 02 Aug 2022 15:31:17: end of X-cor INFO @ Tue, 02 Aug 2022 15:31:17: #2 finished! INFO @ Tue, 02 Aug 2022 15:31:17: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 15:31:17: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 15:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.20_model.r INFO @ Tue, 02 Aug 2022 15:31:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:31:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:31:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:31:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:31:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101712/SRX5101712.20_summits.bed INFO @ Tue, 02 Aug 2022 15:31:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 55 millis CompletedMACS2peakCalling