Job ID = 14168225 SRX = SRX7175255 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5054883 spots for SRR10485695/SRR10485695.sra Written 5054883 spots for SRR10485695/SRR10485695.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169075 ("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: 00:15:18 5054883 reads; of these: 5054883 (100.00%) were paired; of these: 257496 (5.09%) aligned concordantly 0 times 2600513 (51.45%) aligned concordantly exactly 1 time 2196874 (43.46%) aligned concordantly >1 times ---- 257496 pairs aligned concordantly 0 times; of these: 10708 (4.16%) aligned discordantly 1 time ---- 246788 pairs aligned 0 times concordantly or discordantly; of these: 493576 mates make up the pairs; of these: 312507 (63.31%) aligned 0 times 77494 (15.70%) aligned exactly 1 time 103575 (20.98%) aligned >1 times 96.91% overall alignment rate Time searching: 00:15:18 Overall time: 00:15:18 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] 57869 / 4803483 = 0.0120 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 16:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.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 16:32:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:32:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:32:43: 1000000 INFO @ Fri, 10 Dec 2021 16:32:49: 2000000 INFO @ Fri, 10 Dec 2021 16:32:55: 3000000 INFO @ Fri, 10 Dec 2021 16:33:01: 4000000 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 16:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.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 16:33:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:33:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:33:08: 5000000 INFO @ Fri, 10 Dec 2021 16:33:15: 6000000 INFO @ Fri, 10 Dec 2021 16:33:16: 1000000 INFO @ Fri, 10 Dec 2021 16:33:22: 7000000 INFO @ Fri, 10 Dec 2021 16:33:25: 2000000 INFO @ Fri, 10 Dec 2021 16:33:29: 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 16:33:35: 3000000 INFO @ Fri, 10 Dec 2021 16:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.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 16:33:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:33:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:33:36: 9000000 INFO @ Fri, 10 Dec 2021 16:33:41: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:33:41: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:33:41: #1 total tags in treatment: 4739554 INFO @ Fri, 10 Dec 2021 16:33:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:33:41: #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 16:33:41: #1 tags after filtering in treatment: 4596452 INFO @ Fri, 10 Dec 2021 16:33:41: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 16:33:41: #1 finished! INFO @ Fri, 10 Dec 2021 16:33:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:33:42: #2 number of paired peaks: 868 WARNING @ Fri, 10 Dec 2021 16:33:42: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 10 Dec 2021 16:33:42: start model_add_line... INFO @ Fri, 10 Dec 2021 16:33:42: start X-correlation... INFO @ Fri, 10 Dec 2021 16:33:42: end of X-cor INFO @ Fri, 10 Dec 2021 16:33:42: #2 finished! INFO @ Fri, 10 Dec 2021 16:33:42: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 16:33:42: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 16:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.05_model.r INFO @ Fri, 10 Dec 2021 16:33:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:33:43: 1000000 INFO @ Fri, 10 Dec 2021 16:33:43: 4000000 INFO @ Fri, 10 Dec 2021 16:33:51: 2000000 INFO @ Fri, 10 Dec 2021 16:33:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:33:53: 5000000 INFO @ Fri, 10 Dec 2021 16:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.05_summits.bed INFO @ Fri, 10 Dec 2021 16:33:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3583 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:33:58: 3000000 INFO @ Fri, 10 Dec 2021 16:34:03: 6000000 INFO @ Fri, 10 Dec 2021 16:34:05: 4000000 INFO @ Fri, 10 Dec 2021 16:34:12: 7000000 INFO @ Fri, 10 Dec 2021 16:34:13: 5000000 INFO @ Fri, 10 Dec 2021 16:34:20: 6000000 INFO @ Fri, 10 Dec 2021 16:34:21: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:34:27: 7000000 INFO @ Fri, 10 Dec 2021 16:34:30: 9000000 INFO @ Fri, 10 Dec 2021 16:34:34: 8000000 INFO @ Fri, 10 Dec 2021 16:34:37: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:34:37: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:34:37: #1 total tags in treatment: 4739554 INFO @ Fri, 10 Dec 2021 16:34:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:34:37: #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 16:34:37: #1 tags after filtering in treatment: 4596452 INFO @ Fri, 10 Dec 2021 16:34:37: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 16:34:37: #1 finished! INFO @ Fri, 10 Dec 2021 16:34:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:34:37: #2 number of paired peaks: 868 WARNING @ Fri, 10 Dec 2021 16:34:37: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 10 Dec 2021 16:34:37: start model_add_line... INFO @ Fri, 10 Dec 2021 16:34:37: start X-correlation... INFO @ Fri, 10 Dec 2021 16:34:37: end of X-cor INFO @ Fri, 10 Dec 2021 16:34:37: #2 finished! INFO @ Fri, 10 Dec 2021 16:34:37: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 16:34:37: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 16:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.10_model.r INFO @ Fri, 10 Dec 2021 16:34:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:34:41: 9000000 INFO @ Fri, 10 Dec 2021 16:34:45: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:34:45: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:34:45: #1 total tags in treatment: 4739554 INFO @ Fri, 10 Dec 2021 16:34:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:34:45: #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 16:34:45: #1 tags after filtering in treatment: 4596452 INFO @ Fri, 10 Dec 2021 16:34:45: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 16:34:45: #1 finished! INFO @ Fri, 10 Dec 2021 16:34:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:34:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:34:45: #2 number of paired peaks: 868 WARNING @ Fri, 10 Dec 2021 16:34:45: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 10 Dec 2021 16:34:45: start model_add_line... INFO @ Fri, 10 Dec 2021 16:34:46: start X-correlation... INFO @ Fri, 10 Dec 2021 16:34:46: end of X-cor INFO @ Fri, 10 Dec 2021 16:34:46: #2 finished! INFO @ Fri, 10 Dec 2021 16:34:46: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 16:34:46: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 16:34:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.20_model.r INFO @ Fri, 10 Dec 2021 16:34:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:34:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:34:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:34:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.10_summits.bed INFO @ Fri, 10 Dec 2021 16:34:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1556 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:35:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:35:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:35:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175255/SRX7175255.20_summits.bed INFO @ Fri, 10 Dec 2021 16:35:01: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (518 records, 4 fields): 2 millis CompletedMACS2peakCalling