Job ID = 14171435 SRX = SRX9555287 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2433325 spots for SRR13110719/SRR13110719.sra Written 2433325 spots for SRR13110719/SRR13110719.sra Read 2913088 spots for SRR13110720/SRR13110720.sra Written 2913088 spots for SRR13110720/SRR13110720.sra Read 2940380 spots for SRR13110721/SRR13110721.sra Written 2940380 spots for SRR13110721/SRR13110721.sra Read 2927121 spots for SRR13110722/SRR13110722.sra Written 2927121 spots for SRR13110722/SRR13110722.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171913 ("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: 00:02:05 11213914 reads; of these: 11213914 (100.00%) were paired; of these: 10996946 (98.07%) aligned concordantly 0 times 152714 (1.36%) aligned concordantly exactly 1 time 64254 (0.57%) aligned concordantly >1 times ---- 10996946 pairs aligned concordantly 0 times; of these: 933 (0.01%) aligned discordantly 1 time ---- 10996013 pairs aligned 0 times concordantly or discordantly; of these: 21992026 mates make up the pairs; of these: 21675743 (98.56%) aligned 0 times 76090 (0.35%) aligned exactly 1 time 240193 (1.09%) aligned >1 times 3.35% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 4339 / 217338 = 0.0200 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 11:42:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.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 11:42:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:42:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:42:51: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:42:51: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:42:51: #1 total tags in treatment: 212638 INFO @ Sat, 11 Dec 2021 11:42:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:42:51: #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 11:42:51: #1 tags after filtering in treatment: 210023 INFO @ Sat, 11 Dec 2021 11:42:51: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:42:51: #1 finished! INFO @ Sat, 11 Dec 2021 11:42:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:42:51: #2 number of paired peaks: 788 WARNING @ Sat, 11 Dec 2021 11:42:51: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sat, 11 Dec 2021 11:42:51: start model_add_line... INFO @ Sat, 11 Dec 2021 11:42:51: start X-correlation... INFO @ Sat, 11 Dec 2021 11:42:51: end of X-cor INFO @ Sat, 11 Dec 2021 11:42:51: #2 finished! INFO @ Sat, 11 Dec 2021 11:42:51: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Dec 2021 11:42:51: #2 alternative fragment length(s) may be 110,252 bps INFO @ Sat, 11 Dec 2021 11:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.05_model.r INFO @ Sat, 11 Dec 2021 11:42:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:42:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:42:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:42:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:42:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.05_summits.bed INFO @ Sat, 11 Dec 2021 11:42:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (62 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 11:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.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 11:43:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:43:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:43:21: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:43:21: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:43:21: #1 total tags in treatment: 212638 INFO @ Sat, 11 Dec 2021 11:43:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:21: #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 11:43:21: #1 tags after filtering in treatment: 210023 INFO @ Sat, 11 Dec 2021 11:43:21: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:43:21: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:21: #2 number of paired peaks: 788 WARNING @ Sat, 11 Dec 2021 11:43:21: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sat, 11 Dec 2021 11:43:21: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:21: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:21: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:21: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:21: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Dec 2021 11:43:21: #2 alternative fragment length(s) may be 110,252 bps INFO @ Sat, 11 Dec 2021 11:43:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.10_model.r INFO @ Sat, 11 Dec 2021 11:43:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.10_summits.bed INFO @ Sat, 11 Dec 2021 11:43:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (43 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 11:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.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 11:43:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:43:48: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:43:51: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:43:51: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:43:51: #1 total tags in treatment: 212638 INFO @ Sat, 11 Dec 2021 11:43:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:51: #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 11:43:51: #1 tags after filtering in treatment: 210023 INFO @ Sat, 11 Dec 2021 11:43:51: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:43:51: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:51: #2 number of paired peaks: 788 WARNING @ Sat, 11 Dec 2021 11:43:51: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sat, 11 Dec 2021 11:43:51: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:51: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:51: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:51: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:51: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Dec 2021 11:43:51: #2 alternative fragment length(s) may be 110,252 bps INFO @ Sat, 11 Dec 2021 11:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.20_model.r INFO @ Sat, 11 Dec 2021 11:43:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555287/SRX9555287.20_summits.bed INFO @ Sat, 11 Dec 2021 11:43:52: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling