Job ID = 14172314 SRX = SRX9281764 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2296293 spots for SRR12813535/SRR12813535.sra Written 2296293 spots for SRR12813535/SRR12813535.sra Read 2287292 spots for SRR12813536/SRR12813536.sra Written 2287292 spots for SRR12813536/SRR12813536.sra Read 2325899 spots for SRR12813537/SRR12813537.sra Written 2325899 spots for SRR12813537/SRR12813537.sra Read 2284083 spots for SRR12813538/SRR12813538.sra Written 2284083 spots for SRR12813538/SRR12813538.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172776 ("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: 00:02:19 9193567 reads; of these: 9193567 (100.00%) were paired; of these: 8832214 (96.07%) aligned concordantly 0 times 264275 (2.87%) aligned concordantly exactly 1 time 97078 (1.06%) aligned concordantly >1 times ---- 8832214 pairs aligned concordantly 0 times; of these: 872 (0.01%) aligned discordantly 1 time ---- 8831342 pairs aligned 0 times concordantly or discordantly; of these: 17662684 mates make up the pairs; of these: 17492875 (99.04%) aligned 0 times 50589 (0.29%) aligned exactly 1 time 119220 (0.67%) aligned >1 times 4.86% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 7278 / 361650 = 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 15:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.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 15:09:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:09:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:09:54: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:09:54: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:09:54: #1 total tags in treatment: 354081 INFO @ Sat, 11 Dec 2021 15:09:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:09:54: #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 15:09:54: #1 tags after filtering in treatment: 350260 INFO @ Sat, 11 Dec 2021 15:09:54: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:09:54: #1 finished! INFO @ Sat, 11 Dec 2021 15:09:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:09:54: #2 number of paired peaks: 949 WARNING @ Sat, 11 Dec 2021 15:09:54: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Sat, 11 Dec 2021 15:09:54: start model_add_line... INFO @ Sat, 11 Dec 2021 15:09:54: start X-correlation... INFO @ Sat, 11 Dec 2021 15:09:54: end of X-cor INFO @ Sat, 11 Dec 2021 15:09:54: #2 finished! INFO @ Sat, 11 Dec 2021 15:09:54: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 15:09:54: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 15:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.05_model.r INFO @ Sat, 11 Dec 2021 15:09:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:09:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.05_summits.bed INFO @ Sat, 11 Dec 2021 15:09:55: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (84 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 15:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.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 15:10:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:10:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:10:24: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:10:24: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:10:24: #1 total tags in treatment: 354081 INFO @ Sat, 11 Dec 2021 15:10:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:10:24: #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 15:10:24: #1 tags after filtering in treatment: 350260 INFO @ Sat, 11 Dec 2021 15:10:24: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:10:24: #1 finished! INFO @ Sat, 11 Dec 2021 15:10:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:10:24: #2 number of paired peaks: 949 WARNING @ Sat, 11 Dec 2021 15:10:24: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Sat, 11 Dec 2021 15:10:24: start model_add_line... INFO @ Sat, 11 Dec 2021 15:10:24: start X-correlation... INFO @ Sat, 11 Dec 2021 15:10:24: end of X-cor INFO @ Sat, 11 Dec 2021 15:10:24: #2 finished! INFO @ Sat, 11 Dec 2021 15:10:24: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 15:10:24: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 15:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.10_model.r INFO @ Sat, 11 Dec 2021 15:10:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:10:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.10_summits.bed INFO @ Sat, 11 Dec 2021 15:10:25: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (43 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 15:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.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 15:10:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:10:49: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:10:54: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:10:54: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:10:54: #1 total tags in treatment: 354081 INFO @ Sat, 11 Dec 2021 15:10:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:10:54: #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 15:10:54: #1 tags after filtering in treatment: 350260 INFO @ Sat, 11 Dec 2021 15:10:54: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:10:54: #1 finished! INFO @ Sat, 11 Dec 2021 15:10:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:10:54: #2 number of paired peaks: 949 WARNING @ Sat, 11 Dec 2021 15:10:54: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Sat, 11 Dec 2021 15:10:54: start model_add_line... INFO @ Sat, 11 Dec 2021 15:10:54: start X-correlation... INFO @ Sat, 11 Dec 2021 15:10:54: end of X-cor INFO @ Sat, 11 Dec 2021 15:10:54: #2 finished! INFO @ Sat, 11 Dec 2021 15:10:54: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 15:10:54: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 15:10:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.20_model.r INFO @ Sat, 11 Dec 2021 15:10:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:10:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:10:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:10:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:10:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:10:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281764/SRX9281764.20_summits.bed INFO @ Sat, 11 Dec 2021 15:10:55: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 42 millis CompletedMACS2peakCalling