Job ID = 14171221 SRX = SRX9555334 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2204851 spots for SRR13110841/SRR13110841.sra Written 2204851 spots for SRR13110841/SRR13110841.sra Read 2047130 spots for SRR13110842/SRR13110842.sra Written 2047130 spots for SRR13110842/SRR13110842.sra Read 2086365 spots for SRR13110843/SRR13110843.sra Written 2086365 spots for SRR13110843/SRR13110843.sra Read 1962859 spots for SRR13110844/SRR13110844.sra Written 1962859 spots for SRR13110844/SRR13110844.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171679 ("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: 00:01:39 8301205 reads; of these: 8301205 (100.00%) were paired; of these: 8071863 (97.24%) aligned concordantly 0 times 160734 (1.94%) aligned concordantly exactly 1 time 68608 (0.83%) aligned concordantly >1 times ---- 8071863 pairs aligned concordantly 0 times; of these: 1657 (0.02%) aligned discordantly 1 time ---- 8070206 pairs aligned 0 times concordantly or discordantly; of these: 16140412 mates make up the pairs; of these: 16115917 (99.85%) aligned 0 times 7239 (0.04%) aligned exactly 1 time 17256 (0.11%) aligned >1 times 2.93% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 1504 / 67149 = 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 10:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.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 10:39:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:39:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:39:08: #1 tag size is determined as 44 bps INFO @ Sat, 11 Dec 2021 10:39:08: #1 tag size = 44 INFO @ Sat, 11 Dec 2021 10:39:08: #1 total tags in treatment: 227841 INFO @ Sat, 11 Dec 2021 10:39:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:39:08: #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 10:39:08: #1 tags after filtering in treatment: 222019 INFO @ Sat, 11 Dec 2021 10:39:08: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:39:08: #1 finished! INFO @ Sat, 11 Dec 2021 10:39:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:39:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:39:08: #2 number of paired peaks: 966 WARNING @ Sat, 11 Dec 2021 10:39:08: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 11 Dec 2021 10:39:08: start model_add_line... INFO @ Sat, 11 Dec 2021 10:39:08: start X-correlation... INFO @ Sat, 11 Dec 2021 10:39:08: end of X-cor INFO @ Sat, 11 Dec 2021 10:39:08: #2 finished! INFO @ Sat, 11 Dec 2021 10:39:08: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 10:39:08: #2 alternative fragment length(s) may be 46,162,192,288,528,592 bps INFO @ Sat, 11 Dec 2021 10:39:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.05_model.r WARNING @ Sat, 11 Dec 2021 10:39:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:39:08: #2 You may need to consider one of the other alternative d(s): 46,162,192,288,528,592 WARNING @ Sat, 11 Dec 2021 10:39:08: #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 10:39:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:39:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:39:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:39:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:39:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:39:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.05_summits.bed INFO @ Sat, 11 Dec 2021 10:39:09: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (148 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 10:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.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 10:39:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:39:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:39:38: #1 tag size is determined as 44 bps INFO @ Sat, 11 Dec 2021 10:39:38: #1 tag size = 44 INFO @ Sat, 11 Dec 2021 10:39:38: #1 total tags in treatment: 227841 INFO @ Sat, 11 Dec 2021 10:39:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:39:38: #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 10:39:38: #1 tags after filtering in treatment: 222019 INFO @ Sat, 11 Dec 2021 10:39:38: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:39:38: #1 finished! INFO @ Sat, 11 Dec 2021 10:39:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:39:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:39:38: #2 number of paired peaks: 966 WARNING @ Sat, 11 Dec 2021 10:39:38: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 11 Dec 2021 10:39:38: start model_add_line... INFO @ Sat, 11 Dec 2021 10:39:38: start X-correlation... INFO @ Sat, 11 Dec 2021 10:39:38: end of X-cor INFO @ Sat, 11 Dec 2021 10:39:38: #2 finished! INFO @ Sat, 11 Dec 2021 10:39:38: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 10:39:38: #2 alternative fragment length(s) may be 46,162,192,288,528,592 bps INFO @ Sat, 11 Dec 2021 10:39:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.10_model.r WARNING @ Sat, 11 Dec 2021 10:39:38: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:39:38: #2 You may need to consider one of the other alternative d(s): 46,162,192,288,528,592 WARNING @ Sat, 11 Dec 2021 10:39:38: #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 10:39:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:39:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:39:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:39:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:39:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:39:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.10_summits.bed INFO @ Sat, 11 Dec 2021 10:39:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (71 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 10:40:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.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 10:40:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:40:05: #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 10:40:08: #1 tag size is determined as 44 bps INFO @ Sat, 11 Dec 2021 10:40:08: #1 tag size = 44 INFO @ Sat, 11 Dec 2021 10:40:08: #1 total tags in treatment: 227841 INFO @ Sat, 11 Dec 2021 10:40:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:40:08: #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 10:40:08: #1 tags after filtering in treatment: 222019 INFO @ Sat, 11 Dec 2021 10:40:08: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:40:08: #1 finished! INFO @ Sat, 11 Dec 2021 10:40:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:40:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:40:08: #2 number of paired peaks: 966 WARNING @ Sat, 11 Dec 2021 10:40:08: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 11 Dec 2021 10:40:08: start model_add_line... INFO @ Sat, 11 Dec 2021 10:40:08: start X-correlation... INFO @ Sat, 11 Dec 2021 10:40:08: end of X-cor INFO @ Sat, 11 Dec 2021 10:40:08: #2 finished! INFO @ Sat, 11 Dec 2021 10:40:08: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 10:40:08: #2 alternative fragment length(s) may be 46,162,192,288,528,592 bps INFO @ Sat, 11 Dec 2021 10:40:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.20_model.r WARNING @ Sat, 11 Dec 2021 10:40:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:40:08: #2 You may need to consider one of the other alternative d(s): 46,162,192,288,528,592 WARNING @ Sat, 11 Dec 2021 10:40:08: #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 10:40:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:40:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:40:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:40:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:40:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:40:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555334/SRX9555334.20_summits.bed INFO @ Sat, 11 Dec 2021 10:40:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling