Job ID = 14171130 SRX = SRX9555312 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1506108 spots for SRR13110435/SRR13110435.sra Written 1506108 spots for SRR13110435/SRR13110435.sra Read 1486293 spots for SRR13110436/SRR13110436.sra Written 1486293 spots for SRR13110436/SRR13110436.sra Read 1524066 spots for SRR13110437/SRR13110437.sra Written 1524066 spots for SRR13110437/SRR13110437.sra Read 1504148 spots for SRR13110438/SRR13110438.sra Written 1504148 spots for SRR13110438/SRR13110438.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171568 ("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: 00:01:18 6020615 reads; of these: 6020615 (100.00%) were paired; of these: 5774476 (95.91%) aligned concordantly 0 times 176925 (2.94%) aligned concordantly exactly 1 time 69214 (1.15%) aligned concordantly >1 times ---- 5774476 pairs aligned concordantly 0 times; of these: 507 (0.01%) aligned discordantly 1 time ---- 5773969 pairs aligned 0 times concordantly or discordantly; of these: 11547938 mates make up the pairs; of these: 11512984 (99.70%) aligned 0 times 12437 (0.11%) aligned exactly 1 time 22517 (0.19%) aligned >1 times 4.39% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 5616 / 246482 = 0.0228 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 09:44:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.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 09:44:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:44:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:44:14: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:44:14: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:44:14: #1 total tags in treatment: 240527 INFO @ Sat, 11 Dec 2021 09:44:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:44:14: #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 09:44:14: #1 tags after filtering in treatment: 237763 INFO @ Sat, 11 Dec 2021 09:44:14: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 09:44:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:44:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:44:14: #2 number of paired peaks: 1009 INFO @ Sat, 11 Dec 2021 09:44:14: start model_add_line... INFO @ Sat, 11 Dec 2021 09:44:14: start X-correlation... INFO @ Sat, 11 Dec 2021 09:44:14: end of X-cor INFO @ Sat, 11 Dec 2021 09:44:14: #2 finished! INFO @ Sat, 11 Dec 2021 09:44:14: #2 predicted fragment length is 107 bps INFO @ Sat, 11 Dec 2021 09:44:14: #2 alternative fragment length(s) may be 107,188 bps INFO @ Sat, 11 Dec 2021 09:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.05_model.r INFO @ Sat, 11 Dec 2021 09:44:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:44:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:44:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:44:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.05_summits.bed INFO @ Sat, 11 Dec 2021 09:44:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 1 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 09:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.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 09:44:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:44:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:44:44: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:44:44: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:44:44: #1 total tags in treatment: 240527 INFO @ Sat, 11 Dec 2021 09:44:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:44:44: #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 09:44:44: #1 tags after filtering in treatment: 237763 INFO @ Sat, 11 Dec 2021 09:44:44: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 09:44:44: #1 finished! INFO @ Sat, 11 Dec 2021 09:44:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:44:44: #2 number of paired peaks: 1009 INFO @ Sat, 11 Dec 2021 09:44:44: start model_add_line... INFO @ Sat, 11 Dec 2021 09:44:44: start X-correlation... INFO @ Sat, 11 Dec 2021 09:44:44: end of X-cor INFO @ Sat, 11 Dec 2021 09:44:44: #2 finished! INFO @ Sat, 11 Dec 2021 09:44:44: #2 predicted fragment length is 107 bps INFO @ Sat, 11 Dec 2021 09:44:44: #2 alternative fragment length(s) may be 107,188 bps INFO @ Sat, 11 Dec 2021 09:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.10_model.r INFO @ Sat, 11 Dec 2021 09:44:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:44:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:44:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:44:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.10_summits.bed INFO @ Sat, 11 Dec 2021 09:44:45: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (40 records, 4 fields): 2 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 09:45:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.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 09:45:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:12: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:45:14: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:45:14: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:45:14: #1 total tags in treatment: 240527 INFO @ Sat, 11 Dec 2021 09:45:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:45:14: #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 09:45:14: #1 tags after filtering in treatment: 237763 INFO @ Sat, 11 Dec 2021 09:45:14: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 09:45:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:45:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:45:14: #2 number of paired peaks: 1009 INFO @ Sat, 11 Dec 2021 09:45:14: start model_add_line... INFO @ Sat, 11 Dec 2021 09:45:14: start X-correlation... INFO @ Sat, 11 Dec 2021 09:45:14: end of X-cor INFO @ Sat, 11 Dec 2021 09:45:14: #2 finished! INFO @ Sat, 11 Dec 2021 09:45:14: #2 predicted fragment length is 107 bps INFO @ Sat, 11 Dec 2021 09:45:14: #2 alternative fragment length(s) may be 107,188 bps INFO @ Sat, 11 Dec 2021 09:45:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.20_model.r BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:45:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:45:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:45:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:45:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555312/SRX9555312.20_summits.bed INFO @ Sat, 11 Dec 2021 09:45:15: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis CompletedMACS2peakCalling