Job ID = 14168283 SRX = SRX11078117 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T07:49:07 prefetch.2.10.7: 1) Downloading 'SRR14743545'... 2021-12-10T07:49:07 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T07:50:05 prefetch.2.10.7: HTTPS download succeed 2021-12-10T07:50:05 prefetch.2.10.7: 1) 'SRR14743545' was downloaded successfully 2021-12-10T07:50:05 prefetch.2.10.7: 'SRR14743545' has 0 unresolved dependencies Read 29801899 spots for SRR14743545/SRR14743545.sra Written 29801899 spots for SRR14743545/SRR14743545.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169282 ("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: 00:14:26 29801899 reads; of these: 29801899 (100.00%) were paired; of these: 24531593 (82.32%) aligned concordantly 0 times 4050485 (13.59%) aligned concordantly exactly 1 time 1219821 (4.09%) aligned concordantly >1 times ---- 24531593 pairs aligned concordantly 0 times; of these: 8093 (0.03%) aligned discordantly 1 time ---- 24523500 pairs aligned 0 times concordantly or discordantly; of these: 49047000 mates make up the pairs; of these: 48667617 (99.23%) aligned 0 times 192119 (0.39%) aligned exactly 1 time 187264 (0.38%) aligned >1 times 18.35% overall alignment rate Time searching: 00:14:26 Overall time: 00:14:26 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] 371927 / 5274659 = 0.0705 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 17:11:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.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 17:11:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:11:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:11:44: 1000000 INFO @ Fri, 10 Dec 2021 17:11:53: 2000000 INFO @ Fri, 10 Dec 2021 17:12:01: 3000000 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 17:12:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.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 17:12:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:12:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:12:10: 4000000 INFO @ Fri, 10 Dec 2021 17:12:14: 1000000 INFO @ Fri, 10 Dec 2021 17:12:18: 5000000 INFO @ Fri, 10 Dec 2021 17:12:21: 2000000 INFO @ Fri, 10 Dec 2021 17:12:27: 6000000 INFO @ Fri, 10 Dec 2021 17:12:28: 3000000 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 17:12:35: 4000000 INFO @ Fri, 10 Dec 2021 17:12:35: 7000000 INFO @ Fri, 10 Dec 2021 17:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.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 17:12:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:12:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:12:41: 5000000 INFO @ Fri, 10 Dec 2021 17:12:44: 1000000 INFO @ Fri, 10 Dec 2021 17:12:44: 8000000 INFO @ Fri, 10 Dec 2021 17:12:48: 6000000 INFO @ Fri, 10 Dec 2021 17:12:51: 2000000 INFO @ Fri, 10 Dec 2021 17:12:53: 9000000 INFO @ Fri, 10 Dec 2021 17:12:54: 7000000 INFO @ Fri, 10 Dec 2021 17:12:57: 3000000 INFO @ Fri, 10 Dec 2021 17:13:00: 8000000 INFO @ Fri, 10 Dec 2021 17:13:01: 10000000 INFO @ Fri, 10 Dec 2021 17:13:03: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 17:13:03: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 17:13:03: #1 total tags in treatment: 4898526 INFO @ Fri, 10 Dec 2021 17:13:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:13:03: #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 17:13:03: #1 tags after filtering in treatment: 4550500 INFO @ Fri, 10 Dec 2021 17:13:03: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:13:03: #1 finished! INFO @ Fri, 10 Dec 2021 17:13:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:13:04: #2 number of paired peaks: 577 WARNING @ Fri, 10 Dec 2021 17:13:04: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Fri, 10 Dec 2021 17:13:04: start model_add_line... INFO @ Fri, 10 Dec 2021 17:13:04: start X-correlation... INFO @ Fri, 10 Dec 2021 17:13:04: end of X-cor INFO @ Fri, 10 Dec 2021 17:13:04: #2 finished! INFO @ Fri, 10 Dec 2021 17:13:04: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Dec 2021 17:13:04: #2 alternative fragment length(s) may be 4,100,140 bps INFO @ Fri, 10 Dec 2021 17:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.05_model.r INFO @ Fri, 10 Dec 2021 17:13:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:13:04: 4000000 INFO @ Fri, 10 Dec 2021 17:13:07: 9000000 INFO @ Fri, 10 Dec 2021 17:13:11: 5000000 INFO @ Fri, 10 Dec 2021 17:13:13: 10000000 INFO @ Fri, 10 Dec 2021 17:13:14: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 17:13:14: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 17:13:14: #1 total tags in treatment: 4898526 INFO @ Fri, 10 Dec 2021 17:13:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:13:14: #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 17:13:14: #1 tags after filtering in treatment: 4550500 INFO @ Fri, 10 Dec 2021 17:13:14: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:13:14: #1 finished! INFO @ Fri, 10 Dec 2021 17:13:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:13:15: #2 number of paired peaks: 577 WARNING @ Fri, 10 Dec 2021 17:13:15: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Fri, 10 Dec 2021 17:13:15: start model_add_line... INFO @ Fri, 10 Dec 2021 17:13:15: start X-correlation... INFO @ Fri, 10 Dec 2021 17:13:15: end of X-cor INFO @ Fri, 10 Dec 2021 17:13:15: #2 finished! INFO @ Fri, 10 Dec 2021 17:13:15: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Dec 2021 17:13:15: #2 alternative fragment length(s) may be 4,100,140 bps INFO @ Fri, 10 Dec 2021 17:13:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.10_model.r INFO @ Fri, 10 Dec 2021 17:13:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:13:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:13:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:13:18: 6000000 INFO @ Fri, 10 Dec 2021 17:13:24: 7000000 INFO @ Fri, 10 Dec 2021 17:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:13:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.05_summits.bed INFO @ Fri, 10 Dec 2021 17:13:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:13:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:13:31: 8000000 INFO @ Fri, 10 Dec 2021 17:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.10_summits.bed INFO @ Fri, 10 Dec 2021 17:13:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:13:37: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:13:44: 10000000 INFO @ Fri, 10 Dec 2021 17:13:45: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 17:13:45: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 17:13:45: #1 total tags in treatment: 4898526 INFO @ Fri, 10 Dec 2021 17:13:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:13:45: #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 17:13:45: #1 tags after filtering in treatment: 4550500 INFO @ Fri, 10 Dec 2021 17:13:45: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:13:45: #1 finished! INFO @ Fri, 10 Dec 2021 17:13:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:13:45: #2 number of paired peaks: 577 WARNING @ Fri, 10 Dec 2021 17:13:45: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Fri, 10 Dec 2021 17:13:45: start model_add_line... INFO @ Fri, 10 Dec 2021 17:13:45: start X-correlation... INFO @ Fri, 10 Dec 2021 17:13:45: end of X-cor INFO @ Fri, 10 Dec 2021 17:13:45: #2 finished! INFO @ Fri, 10 Dec 2021 17:13:45: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Dec 2021 17:13:45: #2 alternative fragment length(s) may be 4,100,140 bps INFO @ Fri, 10 Dec 2021 17:13:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.20_model.r INFO @ Fri, 10 Dec 2021 17:13:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:13:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078117/SRX11078117.20_summits.bed INFO @ Fri, 10 Dec 2021 17:14:06: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (99 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。