Job ID = 14171396 SRX = SRX9555267 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1826488 spots for SRR13110639/SRR13110639.sra Written 1826488 spots for SRR13110639/SRR13110639.sra Read 1831228 spots for SRR13110640/SRR13110640.sra Written 1831228 spots for SRR13110640/SRR13110640.sra Read 1866547 spots for SRR13110641/SRR13110641.sra Written 1866547 spots for SRR13110641/SRR13110641.sra Read 1854735 spots for SRR13110642/SRR13110642.sra Written 1854735 spots for SRR13110642/SRR13110642.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171857 ("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: 00:01:27 7378998 reads; of these: 7378998 (100.00%) were paired; of these: 6986693 (94.68%) aligned concordantly 0 times 278965 (3.78%) aligned concordantly exactly 1 time 113340 (1.54%) aligned concordantly >1 times ---- 6986693 pairs aligned concordantly 0 times; of these: 3108 (0.04%) aligned discordantly 1 time ---- 6983585 pairs aligned 0 times concordantly or discordantly; of these: 13967170 mates make up the pairs; of these: 13915269 (99.63%) aligned 0 times 20742 (0.15%) aligned exactly 1 time 31159 (0.22%) aligned >1 times 5.71% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 8860 / 395087 = 0.0224 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 11:34:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.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 11:34:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:34:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:34:52: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:34:52: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:34:52: #1 total tags in treatment: 383482 INFO @ Sat, 11 Dec 2021 11:34:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:34:52: #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 11:34:52: #1 tags after filtering in treatment: 377502 INFO @ Sat, 11 Dec 2021 11:34:52: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:34:52: #1 finished! INFO @ Sat, 11 Dec 2021 11:34:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:34:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:34:52: #2 number of paired peaks: 689 WARNING @ Sat, 11 Dec 2021 11:34:52: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Sat, 11 Dec 2021 11:34:52: start model_add_line... INFO @ Sat, 11 Dec 2021 11:34:52: start X-correlation... INFO @ Sat, 11 Dec 2021 11:34:52: end of X-cor INFO @ Sat, 11 Dec 2021 11:34:52: #2 finished! INFO @ Sat, 11 Dec 2021 11:34:52: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 11:34:52: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 11:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.05_model.r INFO @ Sat, 11 Dec 2021 11:34:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:34:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:34:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:34:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:34:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.05_summits.bed INFO @ Sat, 11 Dec 2021 11:34:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (71 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 11:35:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.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 11:35:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:35:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:35:22: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:35:22: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:35:22: #1 total tags in treatment: 383482 INFO @ Sat, 11 Dec 2021 11:35:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:35:22: #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 11:35:22: #1 tags after filtering in treatment: 377502 INFO @ Sat, 11 Dec 2021 11:35:22: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:35:22: #1 finished! INFO @ Sat, 11 Dec 2021 11:35:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:35:22: #2 number of paired peaks: 689 WARNING @ Sat, 11 Dec 2021 11:35:22: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Sat, 11 Dec 2021 11:35:22: start model_add_line... INFO @ Sat, 11 Dec 2021 11:35:22: start X-correlation... INFO @ Sat, 11 Dec 2021 11:35:22: end of X-cor INFO @ Sat, 11 Dec 2021 11:35:22: #2 finished! INFO @ Sat, 11 Dec 2021 11:35:22: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 11:35:22: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 11:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.10_model.r INFO @ Sat, 11 Dec 2021 11:35:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:35:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:35:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:35:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:35:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.10_summits.bed INFO @ Sat, 11 Dec 2021 11:35:24: Done! pass1 - making usageList (4 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 11:35:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.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 11:35:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:35:47: #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 11:35:52: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:35:52: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:35:52: #1 total tags in treatment: 383482 INFO @ Sat, 11 Dec 2021 11:35:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:35:52: #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 11:35:52: #1 tags after filtering in treatment: 377502 INFO @ Sat, 11 Dec 2021 11:35:52: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:35:52: #1 finished! INFO @ Sat, 11 Dec 2021 11:35:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:35:52: #2 number of paired peaks: 689 WARNING @ Sat, 11 Dec 2021 11:35:52: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Sat, 11 Dec 2021 11:35:52: start model_add_line... INFO @ Sat, 11 Dec 2021 11:35:52: start X-correlation... INFO @ Sat, 11 Dec 2021 11:35:52: end of X-cor INFO @ Sat, 11 Dec 2021 11:35:52: #2 finished! INFO @ Sat, 11 Dec 2021 11:35:52: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 11:35:52: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 11:35:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.20_model.r INFO @ Sat, 11 Dec 2021 11:35:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:35:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:35:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:35:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555267/SRX9555267.20_summits.bed INFO @ Sat, 11 Dec 2021 11:35:53: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (37 records, 4 fields): 25 millis CompletedMACS2peakCalling