Job ID = 14167285 SRX = SRX8076976 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14610047 spots for SRR11504848/SRR11504848.sra Written 14610047 spots for SRR11504848/SRR11504848.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167956 ("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: 00:17:30 14610047 reads; of these: 14610047 (100.00%) were paired; of these: 6256281 (42.82%) aligned concordantly 0 times 6347408 (43.45%) aligned concordantly exactly 1 time 2006358 (13.73%) aligned concordantly >1 times ---- 6256281 pairs aligned concordantly 0 times; of these: 327478 (5.23%) aligned discordantly 1 time ---- 5928803 pairs aligned 0 times concordantly or discordantly; of these: 11857606 mates make up the pairs; of these: 11138826 (93.94%) aligned 0 times 433647 (3.66%) aligned exactly 1 time 285133 (2.40%) aligned >1 times 61.88% overall alignment rate Time searching: 00:17:30 Overall time: 00:17:30 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] 674930 / 8672185 = 0.0778 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 11:59:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.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 11:59:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:59:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:59:53: 1000000 INFO @ Fri, 10 Dec 2021 11:59:59: 2000000 INFO @ Fri, 10 Dec 2021 12:00:04: 3000000 INFO @ Fri, 10 Dec 2021 12:00:10: 4000000 INFO @ Fri, 10 Dec 2021 12:00:15: 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 12:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.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 12:00:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:00:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:00:20: 6000000 INFO @ Fri, 10 Dec 2021 12:00:23: 1000000 INFO @ Fri, 10 Dec 2021 12:00:26: 7000000 INFO @ Fri, 10 Dec 2021 12:00:29: 2000000 INFO @ Fri, 10 Dec 2021 12:00:31: 8000000 INFO @ Fri, 10 Dec 2021 12:00:35: 3000000 INFO @ Fri, 10 Dec 2021 12:00:37: 9000000 INFO @ Fri, 10 Dec 2021 12:00:40: 4000000 INFO @ Fri, 10 Dec 2021 12:00:43: 10000000 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 12:00:46: 5000000 INFO @ Fri, 10 Dec 2021 12:00:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.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 12:00:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:00:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:00:48: 11000000 INFO @ Fri, 10 Dec 2021 12:00:52: 6000000 INFO @ Fri, 10 Dec 2021 12:00:54: 1000000 INFO @ Fri, 10 Dec 2021 12:00:54: 12000000 INFO @ Fri, 10 Dec 2021 12:00:58: 7000000 INFO @ Fri, 10 Dec 2021 12:00:59: 2000000 INFO @ Fri, 10 Dec 2021 12:01:00: 13000000 INFO @ Fri, 10 Dec 2021 12:01:04: 8000000 INFO @ Fri, 10 Dec 2021 12:01:05: 3000000 INFO @ Fri, 10 Dec 2021 12:01:06: 14000000 INFO @ Fri, 10 Dec 2021 12:01:10: 9000000 INFO @ Fri, 10 Dec 2021 12:01:11: 4000000 INFO @ Fri, 10 Dec 2021 12:01:12: 15000000 INFO @ Fri, 10 Dec 2021 12:01:16: 10000000 INFO @ Fri, 10 Dec 2021 12:01:16: 5000000 INFO @ Fri, 10 Dec 2021 12:01:17: 16000000 INFO @ Fri, 10 Dec 2021 12:01:21: 11000000 INFO @ Fri, 10 Dec 2021 12:01:22: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 12:01:22: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 12:01:22: #1 total tags in treatment: 7699422 INFO @ Fri, 10 Dec 2021 12:01:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:01:22: #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 12:01:22: #1 tags after filtering in treatment: 7469356 INFO @ Fri, 10 Dec 2021 12:01:22: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 12:01:22: #1 finished! INFO @ Fri, 10 Dec 2021 12:01:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:01:22: 6000000 INFO @ Fri, 10 Dec 2021 12:01:22: #2 number of paired peaks: 150 WARNING @ Fri, 10 Dec 2021 12:01:22: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 10 Dec 2021 12:01:22: start model_add_line... INFO @ Fri, 10 Dec 2021 12:01:22: start X-correlation... INFO @ Fri, 10 Dec 2021 12:01:22: end of X-cor INFO @ Fri, 10 Dec 2021 12:01:22: #2 finished! INFO @ Fri, 10 Dec 2021 12:01:22: #2 predicted fragment length is 152 bps INFO @ Fri, 10 Dec 2021 12:01:22: #2 alternative fragment length(s) may be 152 bps INFO @ Fri, 10 Dec 2021 12:01:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.05_model.r INFO @ Fri, 10 Dec 2021 12:01:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:01:27: 12000000 INFO @ Fri, 10 Dec 2021 12:01:27: 7000000 INFO @ Fri, 10 Dec 2021 12:01:33: 13000000 INFO @ Fri, 10 Dec 2021 12:01:33: 8000000 INFO @ Fri, 10 Dec 2021 12:01:38: 9000000 INFO @ Fri, 10 Dec 2021 12:01:38: 14000000 INFO @ Fri, 10 Dec 2021 12:01:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:01:44: 10000000 INFO @ Fri, 10 Dec 2021 12:01:44: 15000000 INFO @ Fri, 10 Dec 2021 12:01:49: 11000000 INFO @ Fri, 10 Dec 2021 12:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.05_summits.bed INFO @ Fri, 10 Dec 2021 12:01:49: Done! pass1 - making usageList (14 chroms): 0 millis INFO @ Fri, 10 Dec 2021 12:01:50: 16000000 pass2 - checking and writing primary data (717 records, 4 fields): 130 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:01:54: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 12:01:54: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 12:01:54: #1 total tags in treatment: 7699422 INFO @ Fri, 10 Dec 2021 12:01:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:01:54: #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 12:01:54: #1 tags after filtering in treatment: 7469356 INFO @ Fri, 10 Dec 2021 12:01:54: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 12:01:54: #1 finished! INFO @ Fri, 10 Dec 2021 12:01:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:01:55: 12000000 INFO @ Fri, 10 Dec 2021 12:01:55: #2 number of paired peaks: 150 WARNING @ Fri, 10 Dec 2021 12:01:55: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 10 Dec 2021 12:01:55: start model_add_line... INFO @ Fri, 10 Dec 2021 12:01:55: start X-correlation... INFO @ Fri, 10 Dec 2021 12:01:55: end of X-cor INFO @ Fri, 10 Dec 2021 12:01:55: #2 finished! INFO @ Fri, 10 Dec 2021 12:01:55: #2 predicted fragment length is 152 bps INFO @ Fri, 10 Dec 2021 12:01:55: #2 alternative fragment length(s) may be 152 bps INFO @ Fri, 10 Dec 2021 12:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.10_model.r INFO @ Fri, 10 Dec 2021 12:01:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:02:00: 13000000 INFO @ Fri, 10 Dec 2021 12:02:06: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:02:11: 15000000 INFO @ Fri, 10 Dec 2021 12:02:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:02:17: 16000000 INFO @ Fri, 10 Dec 2021 12:02:21: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 12:02:21: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 12:02:21: #1 total tags in treatment: 7699422 INFO @ Fri, 10 Dec 2021 12:02:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:02:21: #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 12:02:21: #1 tags after filtering in treatment: 7469356 INFO @ Fri, 10 Dec 2021 12:02:21: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 12:02:21: #1 finished! INFO @ Fri, 10 Dec 2021 12:02:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:02:21: #2 number of paired peaks: 150 WARNING @ Fri, 10 Dec 2021 12:02:21: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 10 Dec 2021 12:02:21: start model_add_line... INFO @ Fri, 10 Dec 2021 12:02:21: start X-correlation... INFO @ Fri, 10 Dec 2021 12:02:21: end of X-cor INFO @ Fri, 10 Dec 2021 12:02:21: #2 finished! INFO @ Fri, 10 Dec 2021 12:02:21: #2 predicted fragment length is 152 bps INFO @ Fri, 10 Dec 2021 12:02:21: #2 alternative fragment length(s) may be 152 bps INFO @ Fri, 10 Dec 2021 12:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.20_model.r INFO @ Fri, 10 Dec 2021 12:02:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.10_summits.bed INFO @ Fri, 10 Dec 2021 12:02:22: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (519 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:02:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076976/SRX8076976.20_summits.bed INFO @ Fri, 10 Dec 2021 12:02:48: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (327 records, 4 fields): 2 millis CompletedMACS2peakCalling