Job ID = 16438523 SRX = SRX12622684 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3227286 spots for SRR16345100/SRR16345100.sra Written 3227286 spots for SRR16345100/SRR16345100.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438592 ("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: 00:00:46 3227286 reads; of these: 3227286 (100.00%) were paired; of these: 3138280 (97.24%) aligned concordantly 0 times 61851 (1.92%) aligned concordantly exactly 1 time 27155 (0.84%) aligned concordantly >1 times ---- 3138280 pairs aligned concordantly 0 times; of these: 156 (0.00%) aligned discordantly 1 time ---- 3138124 pairs aligned 0 times concordantly or discordantly; of these: 6276248 mates make up the pairs; of these: 6260233 (99.74%) aligned 0 times 5024 (0.08%) aligned exactly 1 time 10991 (0.18%) aligned >1 times 3.01% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 1352 / 89110 = 0.0152 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.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, 02 Aug 2022 13:57:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:57:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:57:50: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 13:57:50: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 13:57:50: #1 total tags in treatment: 87655 INFO @ Tue, 02 Aug 2022 13:57:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:57:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:57:50: #1 tags after filtering in treatment: 86439 INFO @ Tue, 02 Aug 2022 13:57:50: #1 Redundant rate of treatment: 0.01 INFO @ Tue, 02 Aug 2022 13:57:50: #1 finished! INFO @ Tue, 02 Aug 2022 13:57:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:57:50: #2 number of paired peaks: 3967 INFO @ Tue, 02 Aug 2022 13:57:50: start model_add_line... INFO @ Tue, 02 Aug 2022 13:57:50: start X-correlation... INFO @ Tue, 02 Aug 2022 13:57:50: end of X-cor INFO @ Tue, 02 Aug 2022 13:57:50: #2 finished! INFO @ Tue, 02 Aug 2022 13:57:50: #2 predicted fragment length is 299 bps INFO @ Tue, 02 Aug 2022 13:57:50: #2 alternative fragment length(s) may be 299 bps INFO @ Tue, 02 Aug 2022 13:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.05_model.r INFO @ Tue, 02 Aug 2022 13:57:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:57:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:57:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:57:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:57:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.05_summits.bed INFO @ Tue, 02 Aug 2022 13:57:51: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 29 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.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, 02 Aug 2022 13:58:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:58:18: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 13:58:18: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 13:58:18: #1 total tags in treatment: 87655 INFO @ Tue, 02 Aug 2022 13:58:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:58:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:58:18: #1 tags after filtering in treatment: 86439 INFO @ Tue, 02 Aug 2022 13:58:18: #1 Redundant rate of treatment: 0.01 INFO @ Tue, 02 Aug 2022 13:58:18: #1 finished! INFO @ Tue, 02 Aug 2022 13:58:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:58:18: #2 number of paired peaks: 3967 INFO @ Tue, 02 Aug 2022 13:58:18: start model_add_line... INFO @ Tue, 02 Aug 2022 13:58:18: start X-correlation... INFO @ Tue, 02 Aug 2022 13:58:18: end of X-cor INFO @ Tue, 02 Aug 2022 13:58:18: #2 finished! INFO @ Tue, 02 Aug 2022 13:58:18: #2 predicted fragment length is 299 bps INFO @ Tue, 02 Aug 2022 13:58:18: #2 alternative fragment length(s) may be 299 bps INFO @ Tue, 02 Aug 2022 13:58:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.10_model.r INFO @ Tue, 02 Aug 2022 13:58:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:58:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:58:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:58:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:58:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:58:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.10_summits.bed INFO @ Tue, 02 Aug 2022 13:58:19: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:58:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.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, 02 Aug 2022 13:58:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:58:48: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 13:58:48: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 13:58:48: #1 total tags in treatment: 87655 INFO @ Tue, 02 Aug 2022 13:58:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:58:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:58:48: #1 tags after filtering in treatment: 86439 INFO @ Tue, 02 Aug 2022 13:58:48: #1 Redundant rate of treatment: 0.01 INFO @ Tue, 02 Aug 2022 13:58:48: #1 finished! INFO @ Tue, 02 Aug 2022 13:58:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:58:48: #2 number of paired peaks: 3967 INFO @ Tue, 02 Aug 2022 13:58:48: start model_add_line... INFO @ Tue, 02 Aug 2022 13:58:48: start X-correlation... INFO @ Tue, 02 Aug 2022 13:58:48: end of X-cor INFO @ Tue, 02 Aug 2022 13:58:48: #2 finished! INFO @ Tue, 02 Aug 2022 13:58:48: #2 predicted fragment length is 299 bps INFO @ Tue, 02 Aug 2022 13:58:48: #2 alternative fragment length(s) may be 299 bps INFO @ Tue, 02 Aug 2022 13:58:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.20_model.r INFO @ Tue, 02 Aug 2022 13:58:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:58:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:58:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:58:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:58:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622684/SRX12622684.20_summits.bed INFO @ Tue, 02 Aug 2022 13:58:49: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 44 millis CompletedMACS2peakCalling