Job ID = 14171427 SRX = SRX9555281 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3764135 spots for SRR13110695/SRR13110695.sra Written 3764135 spots for SRR13110695/SRR13110695.sra Read 3637730 spots for SRR13110696/SRR13110696.sra Written 3637730 spots for SRR13110696/SRR13110696.sra Read 3837179 spots for SRR13110697/SRR13110697.sra Written 3837179 spots for SRR13110697/SRR13110697.sra Read 3705744 spots for SRR13110698/SRR13110698.sra Written 3705744 spots for SRR13110698/SRR13110698.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171926 ("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: 00:04:59 14944788 reads; of these: 14944788 (100.00%) were paired; of these: 14438015 (96.61%) aligned concordantly 0 times 369749 (2.47%) aligned concordantly exactly 1 time 137024 (0.92%) aligned concordantly >1 times ---- 14438015 pairs aligned concordantly 0 times; of these: 4529 (0.03%) aligned discordantly 1 time ---- 14433486 pairs aligned 0 times concordantly or discordantly; of these: 28866972 mates make up the pairs; of these: 28266486 (97.92%) aligned 0 times 273094 (0.95%) aligned exactly 1 time 327392 (1.13%) aligned >1 times 5.43% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 13646 / 507712 = 0.0269 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 11:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.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 11:45:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:45:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:02: 1000000 INFO @ Sat, 11 Dec 2021 11:46:06: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:46:06: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:46:06: #1 total tags in treatment: 493158 INFO @ Sat, 11 Dec 2021 11:46:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:06: #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 11:46:06: #1 tags after filtering in treatment: 486023 INFO @ Sat, 11 Dec 2021 11:46:06: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:46:06: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:06: #2 number of paired peaks: 694 WARNING @ Sat, 11 Dec 2021 11:46:06: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Sat, 11 Dec 2021 11:46:06: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:06: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:06: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:06: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:06: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 11:46:06: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 11:46:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.05_model.r INFO @ Sat, 11 Dec 2021 11:46:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:46:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.05_summits.bed INFO @ Sat, 11 Dec 2021 11:46:08: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (124 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 11:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.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 11:46:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:34: 1000000 INFO @ Sat, 11 Dec 2021 11:46:38: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:46:38: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:46:38: #1 total tags in treatment: 493158 INFO @ Sat, 11 Dec 2021 11:46:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:38: #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 11:46:38: #1 tags after filtering in treatment: 486023 INFO @ Sat, 11 Dec 2021 11:46:38: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:46:38: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:38: #2 number of paired peaks: 694 WARNING @ Sat, 11 Dec 2021 11:46:38: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Sat, 11 Dec 2021 11:46:38: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:38: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:38: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:38: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:38: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 11:46:38: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 11:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.10_model.r INFO @ Sat, 11 Dec 2021 11:46:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:46:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.10_summits.bed INFO @ Sat, 11 Dec 2021 11:46:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 3 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 11:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.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 11:46:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:54: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:47:02: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:47:06: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:47:06: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:47:06: #1 total tags in treatment: 493158 INFO @ Sat, 11 Dec 2021 11:47:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:47:06: #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 11:47:06: #1 tags after filtering in treatment: 486023 INFO @ Sat, 11 Dec 2021 11:47:06: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:47:06: #1 finished! INFO @ Sat, 11 Dec 2021 11:47:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:47:06: #2 number of paired peaks: 694 WARNING @ Sat, 11 Dec 2021 11:47:06: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Sat, 11 Dec 2021 11:47:06: start model_add_line... INFO @ Sat, 11 Dec 2021 11:47:06: start X-correlation... INFO @ Sat, 11 Dec 2021 11:47:06: end of X-cor INFO @ Sat, 11 Dec 2021 11:47:06: #2 finished! INFO @ Sat, 11 Dec 2021 11:47:06: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 11:47:06: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 11:47:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.20_model.r INFO @ Sat, 11 Dec 2021 11:47:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:47:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:47:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555281/SRX9555281.20_summits.bed INFO @ Sat, 11 Dec 2021 11:47:08: Done! pass1 - making usageList (3 chroms): 2 millis pass2 - checking and writing primary data (38 records, 4 fields): 3 millis CompletedMACS2peakCalling