Job ID = 14172319 SRX = SRX9281768 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2300759 spots for SRR12813281/SRR12813281.sra Written 2300759 spots for SRR12813281/SRR12813281.sra Read 2297498 spots for SRR12813282/SRR12813282.sra Written 2297498 spots for SRR12813282/SRR12813282.sra Read 2331348 spots for SRR12813283/SRR12813283.sra Written 2331348 spots for SRR12813283/SRR12813283.sra Read 2290904 spots for SRR12813284/SRR12813284.sra Written 2290904 spots for SRR12813284/SRR12813284.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172777 ("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: 00:01:44 9220509 reads; of these: 9220509 (100.00%) were paired; of these: 8856444 (96.05%) aligned concordantly 0 times 265223 (2.88%) aligned concordantly exactly 1 time 98842 (1.07%) aligned concordantly >1 times ---- 8856444 pairs aligned concordantly 0 times; of these: 804 (0.01%) aligned discordantly 1 time ---- 8855640 pairs aligned 0 times concordantly or discordantly; of these: 17711280 mates make up the pairs; of these: 17546794 (99.07%) aligned 0 times 46752 (0.26%) aligned exactly 1 time 117734 (0.66%) aligned >1 times 4.85% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 7318 / 364350 = 0.0201 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 15:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.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 15:09:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:09:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:09:59: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:09:59: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:09:59: #1 total tags in treatment: 356754 INFO @ Sat, 11 Dec 2021 15:09:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:09:59: #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 15:09:59: #1 tags after filtering in treatment: 352716 INFO @ Sat, 11 Dec 2021 15:09:59: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:09:59: #1 finished! INFO @ Sat, 11 Dec 2021 15:09:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:09:59: #2 number of paired peaks: 987 WARNING @ Sat, 11 Dec 2021 15:09:59: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sat, 11 Dec 2021 15:09:59: start model_add_line... INFO @ Sat, 11 Dec 2021 15:09:59: start X-correlation... INFO @ Sat, 11 Dec 2021 15:09:59: end of X-cor INFO @ Sat, 11 Dec 2021 15:09:59: #2 finished! INFO @ Sat, 11 Dec 2021 15:09:59: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 15:09:59: #2 alternative fragment length(s) may be 88,151 bps INFO @ Sat, 11 Dec 2021 15:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.05_model.r INFO @ Sat, 11 Dec 2021 15:09:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:09:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.05_summits.bed INFO @ Sat, 11 Dec 2021 15:10:00: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (73 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 15:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.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 15:10:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:10:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:10:29: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:10:29: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:10:29: #1 total tags in treatment: 356754 INFO @ Sat, 11 Dec 2021 15:10:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:10:29: #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 15:10:29: #1 tags after filtering in treatment: 352716 INFO @ Sat, 11 Dec 2021 15:10:29: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:10:29: #1 finished! INFO @ Sat, 11 Dec 2021 15:10:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:10:29: #2 number of paired peaks: 987 WARNING @ Sat, 11 Dec 2021 15:10:29: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sat, 11 Dec 2021 15:10:29: start model_add_line... INFO @ Sat, 11 Dec 2021 15:10:29: start X-correlation... INFO @ Sat, 11 Dec 2021 15:10:29: end of X-cor INFO @ Sat, 11 Dec 2021 15:10:29: #2 finished! INFO @ Sat, 11 Dec 2021 15:10:29: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 15:10:29: #2 alternative fragment length(s) may be 88,151 bps INFO @ Sat, 11 Dec 2021 15:10:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.10_model.r INFO @ Sat, 11 Dec 2021 15:10:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:10:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:10:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.10_summits.bed INFO @ Sat, 11 Dec 2021 15:10:30: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 87 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 15:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.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 15:10:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:10:54: #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 15:10:59: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:10:59: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:10:59: #1 total tags in treatment: 356754 INFO @ Sat, 11 Dec 2021 15:10:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:10:59: #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 15:10:59: #1 tags after filtering in treatment: 352716 INFO @ Sat, 11 Dec 2021 15:10:59: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:10:59: #1 finished! INFO @ Sat, 11 Dec 2021 15:10:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:10:59: #2 number of paired peaks: 987 WARNING @ Sat, 11 Dec 2021 15:10:59: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sat, 11 Dec 2021 15:10:59: start model_add_line... INFO @ Sat, 11 Dec 2021 15:10:59: start X-correlation... INFO @ Sat, 11 Dec 2021 15:10:59: end of X-cor INFO @ Sat, 11 Dec 2021 15:10:59: #2 finished! INFO @ Sat, 11 Dec 2021 15:10:59: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 15:10:59: #2 alternative fragment length(s) may be 88,151 bps INFO @ Sat, 11 Dec 2021 15:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.20_model.r INFO @ Sat, 11 Dec 2021 15:10:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:11:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:11:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:11:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:11:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281768/SRX9281768.20_summits.bed INFO @ Sat, 11 Dec 2021 15:11:00: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (33 records, 4 fields): 2 millis CompletedMACS2peakCalling