Job ID = 12265449 SRX = SRX7192189 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34395414 spots for SRR10503232/SRR10503232.sra Written 34395414 spots for SRR10503232/SRR10503232.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265630 ("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: 00:14:42 34395414 reads; of these: 34395414 (100.00%) were paired; of these: 27738444 (80.65%) aligned concordantly 0 times 5063010 (14.72%) aligned concordantly exactly 1 time 1593960 (4.63%) aligned concordantly >1 times ---- 27738444 pairs aligned concordantly 0 times; of these: 243645 (0.88%) aligned discordantly 1 time ---- 27494799 pairs aligned 0 times concordantly or discordantly; of these: 54989598 mates make up the pairs; of these: 54697326 (99.47%) aligned 0 times 168506 (0.31%) aligned exactly 1 time 123766 (0.23%) aligned >1 times 20.49% overall alignment rate Time searching: 00:14:42 Overall time: 00:14:42 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_sort_core] merging from 8 files... [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] 752606 / 6879136 = 0.1094 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.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, 03 Apr 2021 07:27:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:27:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:28:02: 1000000 INFO @ Sat, 03 Apr 2021 07:28:08: 2000000 INFO @ Sat, 03 Apr 2021 07:28:14: 3000000 INFO @ Sat, 03 Apr 2021 07:28:21: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:28:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.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, 03 Apr 2021 07:28:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:28:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:28:27: 5000000 INFO @ Sat, 03 Apr 2021 07:28:34: 1000000 INFO @ Sat, 03 Apr 2021 07:28:34: 6000000 INFO @ Sat, 03 Apr 2021 07:28:41: 7000000 INFO @ Sat, 03 Apr 2021 07:28:41: 2000000 INFO @ Sat, 03 Apr 2021 07:28:48: 8000000 INFO @ Sat, 03 Apr 2021 07:28:48: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:28:55: 9000000 INFO @ Sat, 03 Apr 2021 07:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.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, 03 Apr 2021 07:28:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:28:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:28:56: 4000000 INFO @ Sat, 03 Apr 2021 07:29:02: 10000000 INFO @ Sat, 03 Apr 2021 07:29:04: 1000000 INFO @ Sat, 03 Apr 2021 07:29:04: 5000000 INFO @ Sat, 03 Apr 2021 07:29:10: 11000000 INFO @ Sat, 03 Apr 2021 07:29:12: 2000000 INFO @ Sat, 03 Apr 2021 07:29:12: 6000000 INFO @ Sat, 03 Apr 2021 07:29:18: 12000000 INFO @ Sat, 03 Apr 2021 07:29:20: 3000000 INFO @ Sat, 03 Apr 2021 07:29:21: 7000000 INFO @ Sat, 03 Apr 2021 07:29:23: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:29:23: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:29:23: #1 total tags in treatment: 5913100 INFO @ Sat, 03 Apr 2021 07:29:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:29:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:29:23: #1 tags after filtering in treatment: 5260160 INFO @ Sat, 03 Apr 2021 07:29:23: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 03 Apr 2021 07:29:23: #1 finished! INFO @ Sat, 03 Apr 2021 07:29:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:29:23: #2 number of paired peaks: 285 WARNING @ Sat, 03 Apr 2021 07:29:23: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sat, 03 Apr 2021 07:29:23: start model_add_line... INFO @ Sat, 03 Apr 2021 07:29:24: start X-correlation... INFO @ Sat, 03 Apr 2021 07:29:24: end of X-cor INFO @ Sat, 03 Apr 2021 07:29:24: #2 finished! INFO @ Sat, 03 Apr 2021 07:29:24: #2 predicted fragment length is 106 bps INFO @ Sat, 03 Apr 2021 07:29:24: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 03 Apr 2021 07:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.05_model.r INFO @ Sat, 03 Apr 2021 07:29:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:29:28: 4000000 INFO @ Sat, 03 Apr 2021 07:29:29: 8000000 INFO @ Sat, 03 Apr 2021 07:29:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:29:37: 5000000 INFO @ Sat, 03 Apr 2021 07:29:37: 9000000 INFO @ Sat, 03 Apr 2021 07:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.05_summits.bed INFO @ Sat, 03 Apr 2021 07:29:43: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1959 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:29:45: 10000000 INFO @ Sat, 03 Apr 2021 07:29:46: 6000000 INFO @ Sat, 03 Apr 2021 07:29:53: 11000000 INFO @ Sat, 03 Apr 2021 07:29:54: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:30:02: 12000000 INFO @ Sat, 03 Apr 2021 07:30:03: 8000000 INFO @ Sat, 03 Apr 2021 07:30:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:30:06: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:30:06: #1 total tags in treatment: 5913100 INFO @ Sat, 03 Apr 2021 07:30:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:30:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:30:07: #1 tags after filtering in treatment: 5260160 INFO @ Sat, 03 Apr 2021 07:30:07: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 03 Apr 2021 07:30:07: #1 finished! INFO @ Sat, 03 Apr 2021 07:30:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:30:07: #2 number of paired peaks: 285 WARNING @ Sat, 03 Apr 2021 07:30:07: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sat, 03 Apr 2021 07:30:07: start model_add_line... INFO @ Sat, 03 Apr 2021 07:30:07: start X-correlation... INFO @ Sat, 03 Apr 2021 07:30:07: end of X-cor INFO @ Sat, 03 Apr 2021 07:30:07: #2 finished! INFO @ Sat, 03 Apr 2021 07:30:07: #2 predicted fragment length is 106 bps INFO @ Sat, 03 Apr 2021 07:30:07: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 03 Apr 2021 07:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.10_model.r INFO @ Sat, 03 Apr 2021 07:30:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:30:10: 9000000 INFO @ Sat, 03 Apr 2021 07:30:18: 10000000 INFO @ Sat, 03 Apr 2021 07:30:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:30:26: 11000000 INFO @ Sat, 03 Apr 2021 07:30:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:30:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:30:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.10_summits.bed INFO @ Sat, 03 Apr 2021 07:30:27: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (680 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:30:33: 12000000 INFO @ Sat, 03 Apr 2021 07:30:38: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:30:38: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:30:38: #1 total tags in treatment: 5913100 INFO @ Sat, 03 Apr 2021 07:30:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:30:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:30:38: #1 tags after filtering in treatment: 5260160 INFO @ Sat, 03 Apr 2021 07:30:38: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 03 Apr 2021 07:30:38: #1 finished! INFO @ Sat, 03 Apr 2021 07:30:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:30:38: #2 number of paired peaks: 285 WARNING @ Sat, 03 Apr 2021 07:30:38: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sat, 03 Apr 2021 07:30:38: start model_add_line... INFO @ Sat, 03 Apr 2021 07:30:38: start X-correlation... INFO @ Sat, 03 Apr 2021 07:30:38: end of X-cor INFO @ Sat, 03 Apr 2021 07:30:38: #2 finished! INFO @ Sat, 03 Apr 2021 07:30:38: #2 predicted fragment length is 106 bps INFO @ Sat, 03 Apr 2021 07:30:38: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 03 Apr 2021 07:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.20_model.r INFO @ Sat, 03 Apr 2021 07:30:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:30:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192189/SRX7192189.20_summits.bed INFO @ Sat, 03 Apr 2021 07:30:58: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling