Job ID = 14170558 SRX = SRX9372359 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17617059 spots for SRR12907636/SRR12907636.sra Written 17617059 spots for SRR12907636/SRR12907636.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171034 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:57 17617059 reads; of these: 17617059 (100.00%) were paired; of these: 7781258 (44.17%) aligned concordantly 0 times 7425279 (42.15%) aligned concordantly exactly 1 time 2410522 (13.68%) aligned concordantly >1 times ---- 7781258 pairs aligned concordantly 0 times; of these: 427336 (5.49%) aligned discordantly 1 time ---- 7353922 pairs aligned 0 times concordantly or discordantly; of these: 14707844 mates make up the pairs; of these: 13394431 (91.07%) aligned 0 times 786219 (5.35%) aligned exactly 1 time 527194 (3.58%) aligned >1 times 61.98% overall alignment rate Time searching: 00:25:58 Overall time: 00:25:58 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_sort_core] merging from 12 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] 884531 / 10131572 = 0.0873 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 07:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.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 07:46:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:46:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:46:30: 1000000 INFO @ Sat, 11 Dec 2021 07:46:36: 2000000 INFO @ Sat, 11 Dec 2021 07:46:42: 3000000 INFO @ Sat, 11 Dec 2021 07:46:48: 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 @ Sat, 11 Dec 2021 07:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.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 07:46:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:46:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:46:54: 5000000 INFO @ Sat, 11 Dec 2021 07:47:01: 6000000 INFO @ Sat, 11 Dec 2021 07:47:01: 1000000 INFO @ Sat, 11 Dec 2021 07:47:07: 7000000 INFO @ Sat, 11 Dec 2021 07:47:08: 2000000 INFO @ Sat, 11 Dec 2021 07:47:14: 8000000 INFO @ Sat, 11 Dec 2021 07:47:15: 3000000 INFO @ Sat, 11 Dec 2021 07:47:20: 9000000 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 07:47:22: 4000000 INFO @ Sat, 11 Dec 2021 07:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.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 07:47:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:47:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:47:26: 10000000 INFO @ Sat, 11 Dec 2021 07:47:29: 5000000 INFO @ Sat, 11 Dec 2021 07:47:31: 1000000 INFO @ Sat, 11 Dec 2021 07:47:33: 11000000 INFO @ Sat, 11 Dec 2021 07:47:37: 6000000 INFO @ Sat, 11 Dec 2021 07:47:39: 2000000 INFO @ Sat, 11 Dec 2021 07:47:40: 12000000 INFO @ Sat, 11 Dec 2021 07:47:45: 7000000 INFO @ Sat, 11 Dec 2021 07:47:46: 3000000 INFO @ Sat, 11 Dec 2021 07:47:47: 13000000 INFO @ Sat, 11 Dec 2021 07:47:52: 8000000 INFO @ Sat, 11 Dec 2021 07:47:53: 14000000 INFO @ Sat, 11 Dec 2021 07:47:54: 4000000 INFO @ Sat, 11 Dec 2021 07:48:00: 9000000 INFO @ Sat, 11 Dec 2021 07:48:00: 15000000 INFO @ Sat, 11 Dec 2021 07:48:02: 5000000 INFO @ Sat, 11 Dec 2021 07:48:07: 16000000 INFO @ Sat, 11 Dec 2021 07:48:07: 10000000 INFO @ Sat, 11 Dec 2021 07:48:09: 6000000 INFO @ Sat, 11 Dec 2021 07:48:14: 17000000 INFO @ Sat, 11 Dec 2021 07:48:15: 11000000 INFO @ Sat, 11 Dec 2021 07:48:17: 7000000 INFO @ Sat, 11 Dec 2021 07:48:21: 18000000 INFO @ Sat, 11 Dec 2021 07:48:22: 12000000 INFO @ Sat, 11 Dec 2021 07:48:24: 8000000 INFO @ Sat, 11 Dec 2021 07:48:28: 19000000 INFO @ Sat, 11 Dec 2021 07:48:30: 13000000 INFO @ Sat, 11 Dec 2021 07:48:32: 9000000 INFO @ Sat, 11 Dec 2021 07:48:34: 20000000 INFO @ Sat, 11 Dec 2021 07:48:35: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:48:35: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:48:35: #1 total tags in treatment: 8968647 INFO @ Sat, 11 Dec 2021 07:48:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:48:35: #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 07:48:35: #1 tags after filtering in treatment: 8582731 INFO @ Sat, 11 Dec 2021 07:48:35: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 07:48:35: #1 finished! INFO @ Sat, 11 Dec 2021 07:48:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:48:35: #2 number of paired peaks: 273 WARNING @ Sat, 11 Dec 2021 07:48:35: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sat, 11 Dec 2021 07:48:35: start model_add_line... INFO @ Sat, 11 Dec 2021 07:48:35: start X-correlation... INFO @ Sat, 11 Dec 2021 07:48:35: end of X-cor INFO @ Sat, 11 Dec 2021 07:48:35: #2 finished! INFO @ Sat, 11 Dec 2021 07:48:35: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Dec 2021 07:48:35: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Dec 2021 07:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.05_model.r INFO @ Sat, 11 Dec 2021 07:48:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:48:38: 14000000 INFO @ Sat, 11 Dec 2021 07:48:40: 10000000 INFO @ Sat, 11 Dec 2021 07:48:45: 15000000 INFO @ Sat, 11 Dec 2021 07:48:47: 11000000 INFO @ Sat, 11 Dec 2021 07:48:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:48:53: 16000000 INFO @ Sat, 11 Dec 2021 07:48:55: 12000000 INFO @ Sat, 11 Dec 2021 07:49:00: 17000000 INFO @ Sat, 11 Dec 2021 07:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.05_summits.bed INFO @ Sat, 11 Dec 2021 07:49:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1113 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:49:02: 13000000 INFO @ Sat, 11 Dec 2021 07:49:07: 18000000 INFO @ Sat, 11 Dec 2021 07:49:10: 14000000 INFO @ Sat, 11 Dec 2021 07:49:15: 19000000 INFO @ Sat, 11 Dec 2021 07:49:17: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:49:22: 20000000 INFO @ Sat, 11 Dec 2021 07:49:22: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:49:22: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:49:22: #1 total tags in treatment: 8968647 INFO @ Sat, 11 Dec 2021 07:49:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:49:22: #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 07:49:23: #1 tags after filtering in treatment: 8582731 INFO @ Sat, 11 Dec 2021 07:49:23: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 07:49:23: #1 finished! INFO @ Sat, 11 Dec 2021 07:49:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:49:23: #2 number of paired peaks: 273 WARNING @ Sat, 11 Dec 2021 07:49:23: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sat, 11 Dec 2021 07:49:23: start model_add_line... INFO @ Sat, 11 Dec 2021 07:49:23: start X-correlation... INFO @ Sat, 11 Dec 2021 07:49:23: end of X-cor INFO @ Sat, 11 Dec 2021 07:49:23: #2 finished! INFO @ Sat, 11 Dec 2021 07:49:23: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Dec 2021 07:49:23: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Dec 2021 07:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.10_model.r INFO @ Sat, 11 Dec 2021 07:49:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:49:25: 16000000 INFO @ Sat, 11 Dec 2021 07:49:32: 17000000 INFO @ Sat, 11 Dec 2021 07:49:39: 18000000 INFO @ Sat, 11 Dec 2021 07:49:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:49:45: 19000000 INFO @ Sat, 11 Dec 2021 07:49:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:49:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.10_summits.bed INFO @ Sat, 11 Dec 2021 07:49:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (799 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:49:52: 20000000 INFO @ Sat, 11 Dec 2021 07:49:52: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:49:52: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:49:52: #1 total tags in treatment: 8968647 INFO @ Sat, 11 Dec 2021 07:49:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:49:52: #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 07:49:52: #1 tags after filtering in treatment: 8582731 INFO @ Sat, 11 Dec 2021 07:49:52: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 07:49:52: #1 finished! INFO @ Sat, 11 Dec 2021 07:49:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:49:53: #2 number of paired peaks: 273 WARNING @ Sat, 11 Dec 2021 07:49:53: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sat, 11 Dec 2021 07:49:53: start model_add_line... INFO @ Sat, 11 Dec 2021 07:49:53: start X-correlation... INFO @ Sat, 11 Dec 2021 07:49:53: end of X-cor INFO @ Sat, 11 Dec 2021 07:49:53: #2 finished! INFO @ Sat, 11 Dec 2021 07:49:53: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Dec 2021 07:49:53: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Dec 2021 07:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.20_model.r INFO @ Sat, 11 Dec 2021 07:49:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:50:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:50:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:50:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:50:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372359/SRX9372359.20_summits.bed INFO @ Sat, 11 Dec 2021 07:50:18: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (538 records, 4 fields): 2 millis CompletedMACS2peakCalling