Job ID = 6626471 SRX = SRX5736456 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10653424 spots for SRR8956867/SRR8956867.sra Written 10653424 spots for SRR8956867/SRR8956867.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626674 ("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: 00:25:55 10653424 reads; of these: 10653424 (100.00%) were paired; of these: 1618664 (15.19%) aligned concordantly 0 times 6962857 (65.36%) aligned concordantly exactly 1 time 2071903 (19.45%) aligned concordantly >1 times ---- 1618664 pairs aligned concordantly 0 times; of these: 198190 (12.24%) aligned discordantly 1 time ---- 1420474 pairs aligned 0 times concordantly or discordantly; of these: 2840948 mates make up the pairs; of these: 1989740 (70.04%) aligned 0 times 361342 (12.72%) aligned exactly 1 time 489866 (17.24%) aligned >1 times 90.66% overall alignment rate Time searching: 00:25:56 Overall time: 00:25:56 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] 854322 / 9174026 = 0.0931 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:38:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.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 @ Tue, 14 Jul 2020 07:38:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:38:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:38:49: 1000000 INFO @ Tue, 14 Jul 2020 07:38:55: 2000000 INFO @ Tue, 14 Jul 2020 07:39:01: 3000000 INFO @ Tue, 14 Jul 2020 07:39:07: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:39:13: 5000000 INFO @ Tue, 14 Jul 2020 07:39:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.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 @ Tue, 14 Jul 2020 07:39:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:39:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:39:20: 6000000 INFO @ Tue, 14 Jul 2020 07:39:21: 1000000 INFO @ Tue, 14 Jul 2020 07:39:26: 7000000 INFO @ Tue, 14 Jul 2020 07:39:30: 2000000 INFO @ Tue, 14 Jul 2020 07:39:33: 8000000 INFO @ Tue, 14 Jul 2020 07:39:38: 3000000 INFO @ Tue, 14 Jul 2020 07:39:40: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.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 @ Tue, 14 Jul 2020 07:39:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:39:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:39:46: 10000000 INFO @ Tue, 14 Jul 2020 07:39:47: 4000000 INFO @ Tue, 14 Jul 2020 07:39:50: 1000000 INFO @ Tue, 14 Jul 2020 07:39:54: 11000000 INFO @ Tue, 14 Jul 2020 07:39:56: 5000000 INFO @ Tue, 14 Jul 2020 07:39:58: 2000000 INFO @ Tue, 14 Jul 2020 07:40:01: 12000000 INFO @ Tue, 14 Jul 2020 07:40:05: 6000000 INFO @ Tue, 14 Jul 2020 07:40:05: 3000000 INFO @ Tue, 14 Jul 2020 07:40:08: 13000000 INFO @ Tue, 14 Jul 2020 07:40:13: 4000000 INFO @ Tue, 14 Jul 2020 07:40:14: 7000000 INFO @ Tue, 14 Jul 2020 07:40:16: 14000000 INFO @ Tue, 14 Jul 2020 07:40:20: 5000000 INFO @ Tue, 14 Jul 2020 07:40:23: 8000000 INFO @ Tue, 14 Jul 2020 07:40:23: 15000000 INFO @ Tue, 14 Jul 2020 07:40:28: 6000000 INFO @ Tue, 14 Jul 2020 07:40:30: 16000000 INFO @ Tue, 14 Jul 2020 07:40:32: 9000000 INFO @ Tue, 14 Jul 2020 07:40:36: 7000000 INFO @ Tue, 14 Jul 2020 07:40:38: 17000000 INFO @ Tue, 14 Jul 2020 07:40:41: 10000000 INFO @ Tue, 14 Jul 2020 07:40:42: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:40:42: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:40:42: #1 total tags in treatment: 8186207 INFO @ Tue, 14 Jul 2020 07:40:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:40:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:40:42: #1 tags after filtering in treatment: 7393275 INFO @ Tue, 14 Jul 2020 07:40:42: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:40:42: #1 finished! INFO @ Tue, 14 Jul 2020 07:40:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:40:43: #2 number of paired peaks: 187 WARNING @ Tue, 14 Jul 2020 07:40:43: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 14 Jul 2020 07:40:43: start model_add_line... INFO @ Tue, 14 Jul 2020 07:40:43: start X-correlation... INFO @ Tue, 14 Jul 2020 07:40:43: end of X-cor INFO @ Tue, 14 Jul 2020 07:40:43: #2 finished! INFO @ Tue, 14 Jul 2020 07:40:43: #2 predicted fragment length is 213 bps INFO @ Tue, 14 Jul 2020 07:40:43: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 14 Jul 2020 07:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.05_model.r INFO @ Tue, 14 Jul 2020 07:40:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:40:43: 8000000 INFO @ Tue, 14 Jul 2020 07:40:50: 11000000 INFO @ Tue, 14 Jul 2020 07:40:51: 9000000 INFO @ Tue, 14 Jul 2020 07:40:58: 10000000 INFO @ Tue, 14 Jul 2020 07:41:00: 12000000 INFO @ Tue, 14 Jul 2020 07:41:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:41:06: 11000000 INFO @ Tue, 14 Jul 2020 07:41:09: 13000000 INFO @ Tue, 14 Jul 2020 07:41:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:41:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:41:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.05_summits.bed INFO @ Tue, 14 Jul 2020 07:41:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4734 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:41:13: 12000000 INFO @ Tue, 14 Jul 2020 07:41:18: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:41:21: 13000000 INFO @ Tue, 14 Jul 2020 07:41:27: 15000000 INFO @ Tue, 14 Jul 2020 07:41:29: 14000000 INFO @ Tue, 14 Jul 2020 07:41:36: 16000000 INFO @ Tue, 14 Jul 2020 07:41:36: 15000000 INFO @ Tue, 14 Jul 2020 07:41:44: 16000000 INFO @ Tue, 14 Jul 2020 07:41:45: 17000000 INFO @ Tue, 14 Jul 2020 07:41:50: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:41:50: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:41:50: #1 total tags in treatment: 8186207 INFO @ Tue, 14 Jul 2020 07:41:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:41:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:41:50: #1 tags after filtering in treatment: 7393275 INFO @ Tue, 14 Jul 2020 07:41:50: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:41:50: #1 finished! INFO @ Tue, 14 Jul 2020 07:41:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:41:51: #2 number of paired peaks: 187 WARNING @ Tue, 14 Jul 2020 07:41:51: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 14 Jul 2020 07:41:51: start model_add_line... INFO @ Tue, 14 Jul 2020 07:41:51: start X-correlation... INFO @ Tue, 14 Jul 2020 07:41:51: end of X-cor INFO @ Tue, 14 Jul 2020 07:41:51: #2 finished! INFO @ Tue, 14 Jul 2020 07:41:51: #2 predicted fragment length is 213 bps INFO @ Tue, 14 Jul 2020 07:41:51: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 14 Jul 2020 07:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.10_model.r INFO @ Tue, 14 Jul 2020 07:41:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:41:52: 17000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:41:56: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:41:56: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:41:56: #1 total tags in treatment: 8186207 INFO @ Tue, 14 Jul 2020 07:41:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:41:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:41:56: #1 tags after filtering in treatment: 7393275 INFO @ Tue, 14 Jul 2020 07:41:56: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:41:56: #1 finished! INFO @ Tue, 14 Jul 2020 07:41:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:41:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:41:57: #2 number of paired peaks: 187 WARNING @ Tue, 14 Jul 2020 07:41:57: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 14 Jul 2020 07:41:57: start model_add_line... INFO @ Tue, 14 Jul 2020 07:41:57: start X-correlation... INFO @ Tue, 14 Jul 2020 07:41:57: end of X-cor INFO @ Tue, 14 Jul 2020 07:41:57: #2 finished! INFO @ Tue, 14 Jul 2020 07:41:57: #2 predicted fragment length is 213 bps INFO @ Tue, 14 Jul 2020 07:41:57: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 14 Jul 2020 07:41:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.20_model.r INFO @ Tue, 14 Jul 2020 07:41:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:41:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:42:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:42:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:42:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:42:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:42:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.10_summits.bed INFO @ Tue, 14 Jul 2020 07:42:20: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2457 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736456/SRX5736456.20_summits.bed INFO @ Tue, 14 Jul 2020 07:42:22: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (575 records, 4 fields): 14 millis CompletedMACS2peakCalling