Job ID = 16438409 SRX = SRX12622678 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 47078879 spots for SRR16345094/SRR16345094.sra Written 47078879 spots for SRR16345094/SRR16345094.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438685 ("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: 00:07:02 47078879 reads; of these: 47078879 (100.00%) were paired; of these: 45826232 (97.34%) aligned concordantly 0 times 902250 (1.92%) aligned concordantly exactly 1 time 350397 (0.74%) aligned concordantly >1 times ---- 45826232 pairs aligned concordantly 0 times; of these: 4904 (0.01%) aligned discordantly 1 time ---- 45821328 pairs aligned 0 times concordantly or discordantly; of these: 91642656 mates make up the pairs; of these: 91382139 (99.72%) aligned 0 times 80506 (0.09%) aligned exactly 1 time 180011 (0.20%) aligned >1 times 2.95% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 35652 / 1256713 = 0.0284 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 14:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.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 14:02:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:02:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:02:13: 1000000 INFO @ Tue, 02 Aug 2022 14:02:19: 2000000 INFO @ Tue, 02 Aug 2022 14:02:23: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 14:02:23: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 14:02:23: #1 total tags in treatment: 1217064 INFO @ Tue, 02 Aug 2022 14:02:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:02:23: #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 14:02:23: #1 tags after filtering in treatment: 1172019 INFO @ Tue, 02 Aug 2022 14:02:23: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:02:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:02:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:02:23: #2 number of paired peaks: 1533 INFO @ Tue, 02 Aug 2022 14:02:23: start model_add_line... INFO @ Tue, 02 Aug 2022 14:02:23: start X-correlation... INFO @ Tue, 02 Aug 2022 14:02:24: end of X-cor INFO @ Tue, 02 Aug 2022 14:02:24: #2 finished! INFO @ Tue, 02 Aug 2022 14:02:24: #2 predicted fragment length is 93 bps INFO @ Tue, 02 Aug 2022 14:02:24: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 02 Aug 2022 14:02:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.05_model.r INFO @ Tue, 02 Aug 2022 14:02:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:02:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:02:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.05_summits.bed INFO @ Tue, 02 Aug 2022 14:02:28: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 81 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 14:02:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.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 14:02:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:02:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:02:43: 1000000 INFO @ Tue, 02 Aug 2022 14:02:49: 2000000 INFO @ Tue, 02 Aug 2022 14:02:54: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 14:02:54: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 14:02:54: #1 total tags in treatment: 1217064 INFO @ Tue, 02 Aug 2022 14:02:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:02:54: #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 14:02:54: #1 tags after filtering in treatment: 1172019 INFO @ Tue, 02 Aug 2022 14:02:54: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:02:54: #1 finished! INFO @ Tue, 02 Aug 2022 14:02:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:02:54: #2 number of paired peaks: 1533 INFO @ Tue, 02 Aug 2022 14:02:54: start model_add_line... INFO @ Tue, 02 Aug 2022 14:02:54: start X-correlation... INFO @ Tue, 02 Aug 2022 14:02:54: end of X-cor INFO @ Tue, 02 Aug 2022 14:02:54: #2 finished! INFO @ Tue, 02 Aug 2022 14:02:54: #2 predicted fragment length is 93 bps INFO @ Tue, 02 Aug 2022 14:02:54: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 02 Aug 2022 14:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.10_model.r INFO @ Tue, 02 Aug 2022 14:02:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:02:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.10_summits.bed INFO @ Tue, 02 Aug 2022 14:02:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 31 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 INFO @ Tue, 02 Aug 2022 14:03:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.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 14:03:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:03:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:03:13: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:03:20: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:03:24: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 14:03:24: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 14:03:24: #1 total tags in treatment: 1217064 INFO @ Tue, 02 Aug 2022 14:03:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:03:24: #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 14:03:24: #1 tags after filtering in treatment: 1172019 INFO @ Tue, 02 Aug 2022 14:03:24: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:03:24: #1 finished! INFO @ Tue, 02 Aug 2022 14:03:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:03:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:03:24: #2 number of paired peaks: 1533 INFO @ Tue, 02 Aug 2022 14:03:24: start model_add_line... INFO @ Tue, 02 Aug 2022 14:03:24: start X-correlation... INFO @ Tue, 02 Aug 2022 14:03:24: end of X-cor INFO @ Tue, 02 Aug 2022 14:03:24: #2 finished! INFO @ Tue, 02 Aug 2022 14:03:24: #2 predicted fragment length is 93 bps INFO @ Tue, 02 Aug 2022 14:03:24: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 02 Aug 2022 14:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.20_model.r INFO @ Tue, 02 Aug 2022 14:03:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:03:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622678/SRX12622678.20_summits.bed INFO @ Tue, 02 Aug 2022 14:03:28: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 20 millis CompletedMACS2peakCalling