Job ID = 14172387 SRX = SRX9281775 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2515074 spots for SRR12813309/SRR12813309.sra Written 2515074 spots for SRR12813309/SRR12813309.sra Read 2509573 spots for SRR12813310/SRR12813310.sra Written 2509573 spots for SRR12813310/SRR12813310.sra Read 2547878 spots for SRR12813311/SRR12813311.sra Written 2547878 spots for SRR12813311/SRR12813311.sra Read 2502693 spots for SRR12813312/SRR12813312.sra Written 2502693 spots for SRR12813312/SRR12813312.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172826 ("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: 00:02:14 10075218 reads; of these: 10075218 (100.00%) were paired; of these: 9771919 (96.99%) aligned concordantly 0 times 220043 (2.18%) aligned concordantly exactly 1 time 83256 (0.83%) aligned concordantly >1 times ---- 9771919 pairs aligned concordantly 0 times; of these: 570 (0.01%) aligned discordantly 1 time ---- 9771349 pairs aligned 0 times concordantly or discordantly; of these: 19542698 mates make up the pairs; of these: 19377498 (99.15%) aligned 0 times 39826 (0.20%) aligned exactly 1 time 125374 (0.64%) aligned >1 times 3.84% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 6485 / 303471 = 0.0214 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 15:18:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.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 15:18:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:18:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:18:39: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:18:39: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:18:39: #1 total tags in treatment: 296820 INFO @ Sat, 11 Dec 2021 15:18:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:18:39: #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 15:18:39: #1 tags after filtering in treatment: 293388 INFO @ Sat, 11 Dec 2021 15:18:39: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:18:39: #1 finished! INFO @ Sat, 11 Dec 2021 15:18:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:18:39: #2 number of paired peaks: 722 WARNING @ Sat, 11 Dec 2021 15:18:39: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sat, 11 Dec 2021 15:18:39: start model_add_line... INFO @ Sat, 11 Dec 2021 15:18:39: start X-correlation... INFO @ Sat, 11 Dec 2021 15:18:39: end of X-cor INFO @ Sat, 11 Dec 2021 15:18:39: #2 finished! INFO @ Sat, 11 Dec 2021 15:18:39: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 15:18:39: #2 alternative fragment length(s) may be 100,185,227,244,556 bps INFO @ Sat, 11 Dec 2021 15:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.05_model.r INFO @ Sat, 11 Dec 2021 15:18:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:18:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:18:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:18:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:18:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.05_summits.bed INFO @ Sat, 11 Dec 2021 15:18:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (68 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 15:19:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.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 15:19:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:19:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:19:09: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:19:09: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:19:09: #1 total tags in treatment: 296820 INFO @ Sat, 11 Dec 2021 15:19:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:19:09: #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 15:19:09: #1 tags after filtering in treatment: 293388 INFO @ Sat, 11 Dec 2021 15:19:09: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:19:09: #1 finished! INFO @ Sat, 11 Dec 2021 15:19:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:19:09: #2 number of paired peaks: 722 WARNING @ Sat, 11 Dec 2021 15:19:09: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sat, 11 Dec 2021 15:19:09: start model_add_line... INFO @ Sat, 11 Dec 2021 15:19:09: start X-correlation... INFO @ Sat, 11 Dec 2021 15:19:09: end of X-cor INFO @ Sat, 11 Dec 2021 15:19:09: #2 finished! INFO @ Sat, 11 Dec 2021 15:19:09: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 15:19:09: #2 alternative fragment length(s) may be 100,185,227,244,556 bps INFO @ Sat, 11 Dec 2021 15:19:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.10_model.r INFO @ Sat, 11 Dec 2021 15:19:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:19:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:19:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:19:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:19:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:19:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.10_summits.bed INFO @ Sat, 11 Dec 2021 15:19:10: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (45 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 15:19:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.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 15:19:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:19:34: #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 15:19:39: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:19:39: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:19:39: #1 total tags in treatment: 296820 INFO @ Sat, 11 Dec 2021 15:19:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:19:39: #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 15:19:39: #1 tags after filtering in treatment: 293388 INFO @ Sat, 11 Dec 2021 15:19:39: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:19:39: #1 finished! INFO @ Sat, 11 Dec 2021 15:19:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:19:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:19:39: #2 number of paired peaks: 722 WARNING @ Sat, 11 Dec 2021 15:19:39: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sat, 11 Dec 2021 15:19:39: start model_add_line... INFO @ Sat, 11 Dec 2021 15:19:39: start X-correlation... INFO @ Sat, 11 Dec 2021 15:19:39: end of X-cor INFO @ Sat, 11 Dec 2021 15:19:39: #2 finished! INFO @ Sat, 11 Dec 2021 15:19:39: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 15:19:39: #2 alternative fragment length(s) may be 100,185,227,244,556 bps INFO @ Sat, 11 Dec 2021 15:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.20_model.r INFO @ Sat, 11 Dec 2021 15:19:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:19:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:19:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:19:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:19:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281775/SRX9281775.20_summits.bed INFO @ Sat, 11 Dec 2021 15:19:40: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 millis CompletedMACS2peakCalling