Job ID = 14168291 SRX = SRX7175263 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4603380 spots for SRR10485703/SRR10485703.sra Written 4603380 spots for SRR10485703/SRR10485703.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169296 ("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: 00:13:58 4603380 reads; of these: 4603380 (100.00%) were paired; of these: 420605 (9.14%) aligned concordantly 0 times 2659784 (57.78%) aligned concordantly exactly 1 time 1522991 (33.08%) aligned concordantly >1 times ---- 420605 pairs aligned concordantly 0 times; of these: 68990 (16.40%) aligned discordantly 1 time ---- 351615 pairs aligned 0 times concordantly or discordantly; of these: 703230 mates make up the pairs; of these: 471868 (67.10%) aligned 0 times 101522 (14.44%) aligned exactly 1 time 129840 (18.46%) aligned >1 times 94.87% overall alignment rate Time searching: 00:13:58 Overall time: 00:13:58 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] 132643 / 4244132 = 0.0313 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 17:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.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 17:16:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:16:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:17:03: 1000000 INFO @ Fri, 10 Dec 2021 17:17:08: 2000000 INFO @ Fri, 10 Dec 2021 17:17:14: 3000000 INFO @ Fri, 10 Dec 2021 17:17:19: 4000000 INFO @ Fri, 10 Dec 2021 17:17:25: 5000000 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 17:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.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 17:17:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:17:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:17:30: 6000000 INFO @ Fri, 10 Dec 2021 17:17:33: 1000000 INFO @ Fri, 10 Dec 2021 17:17:36: 7000000 INFO @ Fri, 10 Dec 2021 17:17:39: 2000000 INFO @ Fri, 10 Dec 2021 17:17:41: 8000000 INFO @ Fri, 10 Dec 2021 17:17:44: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:17:44: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:17:44: #1 total tags in treatment: 4050388 INFO @ Fri, 10 Dec 2021 17:17:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:17:44: #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 17:17:44: #1 tags after filtering in treatment: 3922563 INFO @ Fri, 10 Dec 2021 17:17:44: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 17:17:44: #1 finished! INFO @ Fri, 10 Dec 2021 17:17:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:17:44: 3000000 INFO @ Fri, 10 Dec 2021 17:17:45: #2 number of paired peaks: 671 WARNING @ Fri, 10 Dec 2021 17:17:45: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Fri, 10 Dec 2021 17:17:45: start model_add_line... INFO @ Fri, 10 Dec 2021 17:17:45: start X-correlation... INFO @ Fri, 10 Dec 2021 17:17:45: end of X-cor INFO @ Fri, 10 Dec 2021 17:17:45: #2 finished! INFO @ Fri, 10 Dec 2021 17:17:45: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Dec 2021 17:17:45: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Dec 2021 17:17:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.05_model.r INFO @ Fri, 10 Dec 2021 17:17:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:17:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:17:50: 4000000 INFO @ Fri, 10 Dec 2021 17:17:55: #3 Call peaks for each chromosome... 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 17:17:56: 5000000 INFO @ Fri, 10 Dec 2021 17:17:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.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 17:17:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:17:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.05_summits.bed INFO @ Fri, 10 Dec 2021 17:18:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2013 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:18:02: 6000000 INFO @ Fri, 10 Dec 2021 17:18:04: 1000000 INFO @ Fri, 10 Dec 2021 17:18:08: 7000000 INFO @ Fri, 10 Dec 2021 17:18:10: 2000000 INFO @ Fri, 10 Dec 2021 17:18:14: 8000000 INFO @ Fri, 10 Dec 2021 17:18:16: 3000000 INFO @ Fri, 10 Dec 2021 17:18:16: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:18:16: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:18:16: #1 total tags in treatment: 4050388 INFO @ Fri, 10 Dec 2021 17:18:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:18:16: #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 17:18:16: #1 tags after filtering in treatment: 3922563 INFO @ Fri, 10 Dec 2021 17:18:16: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 17:18:16: #1 finished! INFO @ Fri, 10 Dec 2021 17:18:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:18:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:18:17: #2 number of paired peaks: 671 WARNING @ Fri, 10 Dec 2021 17:18:17: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Fri, 10 Dec 2021 17:18:17: start model_add_line... INFO @ Fri, 10 Dec 2021 17:18:17: start X-correlation... INFO @ Fri, 10 Dec 2021 17:18:17: end of X-cor INFO @ Fri, 10 Dec 2021 17:18:17: #2 finished! INFO @ Fri, 10 Dec 2021 17:18:17: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Dec 2021 17:18:17: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Dec 2021 17:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.10_model.r INFO @ Fri, 10 Dec 2021 17:18:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:18:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:18:22: 4000000 INFO @ Fri, 10 Dec 2021 17:18:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:18:28: 5000000 INFO @ Fri, 10 Dec 2021 17:18:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:18:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:18:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.10_summits.bed INFO @ Fri, 10 Dec 2021 17:18:32: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (931 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:18:33: 6000000 INFO @ Fri, 10 Dec 2021 17:18:39: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:18:45: 8000000 INFO @ Fri, 10 Dec 2021 17:18:48: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:18:48: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:18:48: #1 total tags in treatment: 4050388 INFO @ Fri, 10 Dec 2021 17:18:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:18:48: #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 17:18:48: #1 tags after filtering in treatment: 3922563 INFO @ Fri, 10 Dec 2021 17:18:48: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 17:18:48: #1 finished! INFO @ Fri, 10 Dec 2021 17:18:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:18:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:18:49: #2 number of paired peaks: 671 WARNING @ Fri, 10 Dec 2021 17:18:49: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Fri, 10 Dec 2021 17:18:49: start model_add_line... INFO @ Fri, 10 Dec 2021 17:18:49: start X-correlation... INFO @ Fri, 10 Dec 2021 17:18:49: end of X-cor INFO @ Fri, 10 Dec 2021 17:18:49: #2 finished! INFO @ Fri, 10 Dec 2021 17:18:49: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Dec 2021 17:18:49: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Dec 2021 17:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.20_model.r INFO @ Fri, 10 Dec 2021 17:18:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:18:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:18:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:19:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:19:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175263/SRX7175263.20_summits.bed INFO @ Fri, 10 Dec 2021 17:19:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (371 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。