Job ID = 14171232 SRX = SRX9555337 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2176757 spots for SRR13110853/SRR13110853.sra Written 2176757 spots for SRR13110853/SRR13110853.sra Read 2030808 spots for SRR13110854/SRR13110854.sra Written 2030808 spots for SRR13110854/SRR13110854.sra Read 2026063 spots for SRR13110855/SRR13110855.sra Written 2026063 spots for SRR13110855/SRR13110855.sra Read 1957207 spots for SRR13110856/SRR13110856.sra Written 1957207 spots for SRR13110856/SRR13110856.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171684 ("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: 00:01:36 8190835 reads; of these: 8190835 (100.00%) were paired; of these: 7978852 (97.41%) aligned concordantly 0 times 147809 (1.80%) aligned concordantly exactly 1 time 64174 (0.78%) aligned concordantly >1 times ---- 7978852 pairs aligned concordantly 0 times; of these: 1638 (0.02%) aligned discordantly 1 time ---- 7977214 pairs aligned 0 times concordantly or discordantly; of these: 15954428 mates make up the pairs; of these: 15927762 (99.83%) aligned 0 times 6946 (0.04%) aligned exactly 1 time 19720 (0.12%) aligned >1 times 2.77% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 1360 / 64390 = 0.0211 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 10:41:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.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 10:41:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:41:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:41:11: #1 tag size is determined as 69 bps INFO @ Sat, 11 Dec 2021 10:41:11: #1 tag size = 69 INFO @ Sat, 11 Dec 2021 10:41:11: #1 total tags in treatment: 210627 INFO @ Sat, 11 Dec 2021 10:41:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:41:11: #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 10:41:11: #1 tags after filtering in treatment: 204988 INFO @ Sat, 11 Dec 2021 10:41:11: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:41:11: #1 finished! INFO @ Sat, 11 Dec 2021 10:41:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:41:11: #2 number of paired peaks: 874 WARNING @ Sat, 11 Dec 2021 10:41:11: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 11 Dec 2021 10:41:11: start model_add_line... INFO @ Sat, 11 Dec 2021 10:41:11: start X-correlation... INFO @ Sat, 11 Dec 2021 10:41:11: end of X-cor INFO @ Sat, 11 Dec 2021 10:41:11: #2 finished! INFO @ Sat, 11 Dec 2021 10:41:11: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 10:41:11: #2 alternative fragment length(s) may be 45,239,475,542,581 bps INFO @ Sat, 11 Dec 2021 10:41:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.05_model.r WARNING @ Sat, 11 Dec 2021 10:41:11: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:41:11: #2 You may need to consider one of the other alternative d(s): 45,239,475,542,581 WARNING @ Sat, 11 Dec 2021 10:41:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 10:41:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:41:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:41:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:41:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.05_summits.bed INFO @ Sat, 11 Dec 2021 10:41:12: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (163 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 10:41:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.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 10:41:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:41:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:41:42: #1 tag size is determined as 69 bps INFO @ Sat, 11 Dec 2021 10:41:42: #1 tag size = 69 INFO @ Sat, 11 Dec 2021 10:41:42: #1 total tags in treatment: 210627 INFO @ Sat, 11 Dec 2021 10:41:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:41:42: #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 10:41:42: #1 tags after filtering in treatment: 204988 INFO @ Sat, 11 Dec 2021 10:41:42: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:41:42: #1 finished! INFO @ Sat, 11 Dec 2021 10:41:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:41:42: #2 number of paired peaks: 874 WARNING @ Sat, 11 Dec 2021 10:41:42: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 11 Dec 2021 10:41:42: start model_add_line... INFO @ Sat, 11 Dec 2021 10:41:42: start X-correlation... INFO @ Sat, 11 Dec 2021 10:41:42: end of X-cor INFO @ Sat, 11 Dec 2021 10:41:42: #2 finished! INFO @ Sat, 11 Dec 2021 10:41:42: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 10:41:42: #2 alternative fragment length(s) may be 45,239,475,542,581 bps INFO @ Sat, 11 Dec 2021 10:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.10_model.r WARNING @ Sat, 11 Dec 2021 10:41:42: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:41:42: #2 You may need to consider one of the other alternative d(s): 45,239,475,542,581 WARNING @ Sat, 11 Dec 2021 10:41:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 10:41:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:41:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:41:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:41:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:41:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.10_summits.bed INFO @ Sat, 11 Dec 2021 10:41:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 14 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 10:42:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.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 10:42:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:42:09: #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 10:42:12: #1 tag size is determined as 69 bps INFO @ Sat, 11 Dec 2021 10:42:12: #1 tag size = 69 INFO @ Sat, 11 Dec 2021 10:42:12: #1 total tags in treatment: 210627 INFO @ Sat, 11 Dec 2021 10:42:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:42:12: #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 10:42:12: #1 tags after filtering in treatment: 204988 INFO @ Sat, 11 Dec 2021 10:42:12: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:42:12: #1 finished! INFO @ Sat, 11 Dec 2021 10:42:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:42:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:42:12: #2 number of paired peaks: 874 WARNING @ Sat, 11 Dec 2021 10:42:12: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 11 Dec 2021 10:42:12: start model_add_line... INFO @ Sat, 11 Dec 2021 10:42:12: start X-correlation... INFO @ Sat, 11 Dec 2021 10:42:12: end of X-cor INFO @ Sat, 11 Dec 2021 10:42:12: #2 finished! INFO @ Sat, 11 Dec 2021 10:42:12: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 10:42:12: #2 alternative fragment length(s) may be 45,239,475,542,581 bps INFO @ Sat, 11 Dec 2021 10:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.20_model.r WARNING @ Sat, 11 Dec 2021 10:42:12: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:42:12: #2 You may need to consider one of the other alternative d(s): 45,239,475,542,581 WARNING @ Sat, 11 Dec 2021 10:42:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 10:42:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:42:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:42:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:42:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:42:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555337/SRX9555337.20_summits.bed INFO @ Sat, 11 Dec 2021 10:42:12: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 1 millis CompletedMACS2peakCalling