Job ID = 14168288 SRX = SRX7175261 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5488550 spots for SRR10485701/SRR10485701.sra Written 5488550 spots for SRR10485701/SRR10485701.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169289 ("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: 00:16:15 5488550 reads; of these: 5488550 (100.00%) were paired; of these: 762473 (13.89%) aligned concordantly 0 times 2872492 (52.34%) aligned concordantly exactly 1 time 1853585 (33.77%) aligned concordantly >1 times ---- 762473 pairs aligned concordantly 0 times; of these: 38355 (5.03%) aligned discordantly 1 time ---- 724118 pairs aligned 0 times concordantly or discordantly; of these: 1448236 mates make up the pairs; of these: 1229751 (84.91%) aligned 0 times 96611 (6.67%) aligned exactly 1 time 121874 (8.42%) aligned >1 times 88.80% overall alignment rate Time searching: 00:16:15 Overall time: 00:16:15 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] 266984 / 4760587 = 0.0561 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 @ Fri, 10 Dec 2021 17:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.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 @ Fri, 10 Dec 2021 17:15:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:15:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:15:32: 1000000 INFO @ Fri, 10 Dec 2021 17:15:39: 2000000 INFO @ Fri, 10 Dec 2021 17:15:46: 3000000 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 @ Fri, 10 Dec 2021 17:15:53: 4000000 INFO @ Fri, 10 Dec 2021 17:15:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.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 @ Fri, 10 Dec 2021 17:15:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:15:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:16:01: 5000000 INFO @ Fri, 10 Dec 2021 17:16:02: 1000000 INFO @ Fri, 10 Dec 2021 17:16:08: 6000000 INFO @ Fri, 10 Dec 2021 17:16:08: 2000000 INFO @ Fri, 10 Dec 2021 17:16:15: 3000000 INFO @ Fri, 10 Dec 2021 17:16:16: 7000000 INFO @ Fri, 10 Dec 2021 17:16:22: 4000000 INFO @ Fri, 10 Dec 2021 17:16:23: 8000000 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 @ Fri, 10 Dec 2021 17:16:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.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 @ Fri, 10 Dec 2021 17:16:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:16:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:16:28: 5000000 INFO @ Fri, 10 Dec 2021 17:16:31: 9000000 INFO @ Fri, 10 Dec 2021 17:16:32: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:16:32: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:16:32: #1 total tags in treatment: 4459869 INFO @ Fri, 10 Dec 2021 17:16:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:16:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:16:32: #1 tags after filtering in treatment: 4267397 INFO @ Fri, 10 Dec 2021 17:16:32: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 17:16:32: #1 finished! INFO @ Fri, 10 Dec 2021 17:16:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:16:33: #2 number of paired peaks: 335 WARNING @ Fri, 10 Dec 2021 17:16:33: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 10 Dec 2021 17:16:33: start model_add_line... INFO @ Fri, 10 Dec 2021 17:16:33: start X-correlation... INFO @ Fri, 10 Dec 2021 17:16:33: end of X-cor INFO @ Fri, 10 Dec 2021 17:16:33: #2 finished! INFO @ Fri, 10 Dec 2021 17:16:33: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Dec 2021 17:16:33: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Dec 2021 17:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.05_model.r INFO @ Fri, 10 Dec 2021 17:16:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:16:33: 1000000 INFO @ Fri, 10 Dec 2021 17:16:35: 6000000 INFO @ Fri, 10 Dec 2021 17:16:40: 2000000 INFO @ Fri, 10 Dec 2021 17:16:42: 7000000 INFO @ Fri, 10 Dec 2021 17:16:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:16:48: 3000000 INFO @ Fri, 10 Dec 2021 17:16:49: 8000000 INFO @ Fri, 10 Dec 2021 17:16:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:16:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:16:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.05_summits.bed INFO @ Fri, 10 Dec 2021 17:16:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1775 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:16:55: 9000000 INFO @ Fri, 10 Dec 2021 17:16:56: 4000000 INFO @ Fri, 10 Dec 2021 17:16:57: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:16:57: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:16:57: #1 total tags in treatment: 4459869 INFO @ Fri, 10 Dec 2021 17:16:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:16:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:16:57: #1 tags after filtering in treatment: 4267397 INFO @ Fri, 10 Dec 2021 17:16:57: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 17:16:57: #1 finished! INFO @ Fri, 10 Dec 2021 17:16:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:16:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:16:57: #2 number of paired peaks: 335 WARNING @ Fri, 10 Dec 2021 17:16:57: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 10 Dec 2021 17:16:57: start model_add_line... INFO @ Fri, 10 Dec 2021 17:16:57: start X-correlation... INFO @ Fri, 10 Dec 2021 17:16:57: end of X-cor INFO @ Fri, 10 Dec 2021 17:16:57: #2 finished! INFO @ Fri, 10 Dec 2021 17:16:57: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Dec 2021 17:16:57: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Dec 2021 17:16:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.10_model.r INFO @ Fri, 10 Dec 2021 17:16:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:16:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:17:03: 5000000 INFO @ Fri, 10 Dec 2021 17:17:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:17:10: 6000000 INFO @ Fri, 10 Dec 2021 17:17:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:17:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:17:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.10_summits.bed INFO @ Fri, 10 Dec 2021 17:17:13: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (624 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:17:17: 7000000 INFO @ Fri, 10 Dec 2021 17:17:24: 8000000 INFO @ Fri, 10 Dec 2021 17:17:31: 9000000 INFO @ Fri, 10 Dec 2021 17:17:32: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:17:32: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:17:32: #1 total tags in treatment: 4459869 INFO @ Fri, 10 Dec 2021 17:17:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:17:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:17:33: #1 tags after filtering in treatment: 4267397 INFO @ Fri, 10 Dec 2021 17:17:33: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 17:17:33: #1 finished! INFO @ Fri, 10 Dec 2021 17:17:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:17:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:17:33: #2 number of paired peaks: 335 WARNING @ Fri, 10 Dec 2021 17:17:33: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 10 Dec 2021 17:17:33: start model_add_line... INFO @ Fri, 10 Dec 2021 17:17:33: start X-correlation... INFO @ Fri, 10 Dec 2021 17:17:33: end of X-cor INFO @ Fri, 10 Dec 2021 17:17:33: #2 finished! INFO @ Fri, 10 Dec 2021 17:17:33: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Dec 2021 17:17:33: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Dec 2021 17:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.20_model.r INFO @ Fri, 10 Dec 2021 17:17:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:17:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:17:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175261/SRX7175261.20_summits.bed INFO @ Fri, 10 Dec 2021 17:17:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (208 records, 4 fields): 16 millis CompletedMACS2peakCalling