Job ID = 6626525 SRX = SRX5736499 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13794590 spots for SRR8956910/SRR8956910.sra Written 13794590 spots for SRR8956910/SRR8956910.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626724 ("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: 00:28:51 13794590 reads; of these: 13794590 (100.00%) were paired; of these: 5280892 (38.28%) aligned concordantly 0 times 5829437 (42.26%) aligned concordantly exactly 1 time 2684261 (19.46%) aligned concordantly >1 times ---- 5280892 pairs aligned concordantly 0 times; of these: 489996 (9.28%) aligned discordantly 1 time ---- 4790896 pairs aligned 0 times concordantly or discordantly; of these: 9581792 mates make up the pairs; of these: 8398352 (87.65%) aligned 0 times 418336 (4.37%) aligned exactly 1 time 765104 (7.98%) aligned >1 times 69.56% overall alignment rate Time searching: 00:28:51 Overall time: 00:28:51 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] 4075851 / 8989424 = 0.4534 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 07:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.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 07:54:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:54:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:54:40: 1000000 INFO @ Tue, 14 Jul 2020 07:54:45: 2000000 INFO @ Tue, 14 Jul 2020 07:54:51: 3000000 INFO @ Tue, 14 Jul 2020 07:54:56: 4000000 INFO @ Tue, 14 Jul 2020 07:55:02: 5000000 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 07:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.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 07:55:04: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:55:04: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:55:08: 6000000 INFO @ Tue, 14 Jul 2020 07:55:11: 1000000 INFO @ Tue, 14 Jul 2020 07:55:14: 7000000 INFO @ Tue, 14 Jul 2020 07:55:17: 2000000 INFO @ Tue, 14 Jul 2020 07:55:21: 8000000 INFO @ Tue, 14 Jul 2020 07:55:23: 3000000 INFO @ Tue, 14 Jul 2020 07:55:27: 9000000 INFO @ Tue, 14 Jul 2020 07:55:30: 4000000 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 07:55:33: 10000000 INFO @ Tue, 14 Jul 2020 07:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.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 07:55:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:55:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:55:36: 5000000 INFO @ Tue, 14 Jul 2020 07:55:40: 11000000 INFO @ Tue, 14 Jul 2020 07:55:40: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:55:40: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:55:40: #1 total tags in treatment: 4645899 INFO @ Tue, 14 Jul 2020 07:55:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:55:40: #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 07:55:40: #1 tags after filtering in treatment: 4268596 INFO @ Tue, 14 Jul 2020 07:55:40: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:55:40: #1 finished! INFO @ Tue, 14 Jul 2020 07:55:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:55:40: #2 number of paired peaks: 1211 INFO @ Tue, 14 Jul 2020 07:55:40: start model_add_line... INFO @ Tue, 14 Jul 2020 07:55:40: start X-correlation... INFO @ Tue, 14 Jul 2020 07:55:40: end of X-cor INFO @ Tue, 14 Jul 2020 07:55:40: #2 finished! INFO @ Tue, 14 Jul 2020 07:55:40: #2 predicted fragment length is 243 bps INFO @ Tue, 14 Jul 2020 07:55:40: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 14 Jul 2020 07:55:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.05_model.r INFO @ Tue, 14 Jul 2020 07:55:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:55:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:55:41: 1000000 INFO @ Tue, 14 Jul 2020 07:55:43: 6000000 INFO @ Tue, 14 Jul 2020 07:55:48: 2000000 INFO @ Tue, 14 Jul 2020 07:55:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:55:50: 7000000 INFO @ Tue, 14 Jul 2020 07:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.05_summits.bed INFO @ Tue, 14 Jul 2020 07:55:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5292 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:55:55: 3000000 INFO @ Tue, 14 Jul 2020 07:55:57: 8000000 INFO @ Tue, 14 Jul 2020 07:56:02: 4000000 INFO @ Tue, 14 Jul 2020 07:56:03: 9000000 INFO @ Tue, 14 Jul 2020 07:56:08: 5000000 INFO @ Tue, 14 Jul 2020 07:56:10: 10000000 INFO @ Tue, 14 Jul 2020 07:56:15: 6000000 INFO @ Tue, 14 Jul 2020 07:56:16: 11000000 INFO @ Tue, 14 Jul 2020 07:56:16: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:56:16: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:56:16: #1 total tags in treatment: 4645899 INFO @ Tue, 14 Jul 2020 07:56:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:56:16: #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 07:56:16: #1 tags after filtering in treatment: 4268596 INFO @ Tue, 14 Jul 2020 07:56:16: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:56:16: #1 finished! INFO @ Tue, 14 Jul 2020 07:56:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:56:17: #2 number of paired peaks: 1211 INFO @ Tue, 14 Jul 2020 07:56:17: start model_add_line... INFO @ Tue, 14 Jul 2020 07:56:17: start X-correlation... INFO @ Tue, 14 Jul 2020 07:56:17: end of X-cor INFO @ Tue, 14 Jul 2020 07:56:17: #2 finished! INFO @ Tue, 14 Jul 2020 07:56:17: #2 predicted fragment length is 243 bps INFO @ Tue, 14 Jul 2020 07:56:17: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 14 Jul 2020 07:56:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.10_model.r INFO @ Tue, 14 Jul 2020 07:56:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:56:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:56:21: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:56:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:56:28: 8000000 INFO @ Tue, 14 Jul 2020 07:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:56:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:56:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.10_summits.bed INFO @ Tue, 14 Jul 2020 07:56:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2448 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:56:34: 9000000 INFO @ Tue, 14 Jul 2020 07:56:40: 10000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:56:46: 11000000 INFO @ Tue, 14 Jul 2020 07:56:46: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:56:46: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:56:46: #1 total tags in treatment: 4645899 INFO @ Tue, 14 Jul 2020 07:56:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:56:46: #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 07:56:46: #1 tags after filtering in treatment: 4268596 INFO @ Tue, 14 Jul 2020 07:56:46: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:56:46: #1 finished! INFO @ Tue, 14 Jul 2020 07:56:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:56:47: #2 number of paired peaks: 1211 INFO @ Tue, 14 Jul 2020 07:56:47: start model_add_line... INFO @ Tue, 14 Jul 2020 07:56:47: start X-correlation... INFO @ Tue, 14 Jul 2020 07:56:47: end of X-cor INFO @ Tue, 14 Jul 2020 07:56:47: #2 finished! INFO @ Tue, 14 Jul 2020 07:56:47: #2 predicted fragment length is 243 bps INFO @ Tue, 14 Jul 2020 07:56:47: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 14 Jul 2020 07:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.20_model.r INFO @ Tue, 14 Jul 2020 07:56:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:56:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:56:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:57:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:57:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736499/SRX5736499.20_summits.bed INFO @ Tue, 14 Jul 2020 07:57:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (772 records, 4 fields): 8 millis CompletedMACS2peakCalling