Job ID = 16438205 SRX = SRX12622675 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 44074417 spots for SRR16345091/SRR16345091.sra Written 44074417 spots for SRR16345091/SRR16345091.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438682 ("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: 00:07:40 44074417 reads; of these: 44074417 (100.00%) were paired; of these: 43190786 (98.00%) aligned concordantly 0 times 634710 (1.44%) aligned concordantly exactly 1 time 248921 (0.56%) aligned concordantly >1 times ---- 43190786 pairs aligned concordantly 0 times; of these: 2336 (0.01%) aligned discordantly 1 time ---- 43188450 pairs aligned 0 times concordantly or discordantly; of these: 86376900 mates make up the pairs; of these: 86146428 (99.73%) aligned 0 times 67313 (0.08%) aligned exactly 1 time 163159 (0.19%) aligned >1 times 2.27% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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] 21268 / 885297 = 0.0240 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 14:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.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 14:01:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:01:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:01:32: 1000000 INFO @ Tue, 02 Aug 2022 14:01:38: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 14:01:38: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 14:01:38: #1 total tags in treatment: 862407 INFO @ Tue, 02 Aug 2022 14:01:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:01:38: #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 14:01:38: #1 tags after filtering in treatment: 836821 INFO @ Tue, 02 Aug 2022 14:01:38: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 14:01:38: #1 finished! INFO @ Tue, 02 Aug 2022 14:01:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:01:39: #2 number of paired peaks: 1834 INFO @ Tue, 02 Aug 2022 14:01:39: start model_add_line... INFO @ Tue, 02 Aug 2022 14:01:39: start X-correlation... INFO @ Tue, 02 Aug 2022 14:01:39: end of X-cor INFO @ Tue, 02 Aug 2022 14:01:39: #2 finished! INFO @ Tue, 02 Aug 2022 14:01:39: #2 predicted fragment length is 106 bps INFO @ Tue, 02 Aug 2022 14:01:39: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 02 Aug 2022 14:01:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.05_model.r INFO @ Tue, 02 Aug 2022 14:01:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:01:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:01:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:01:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:01:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.05_summits.bed INFO @ Tue, 02 Aug 2022 14:01:42: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 24 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 14:01:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.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 14:01:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:01:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:02:01: 1000000 INFO @ Tue, 02 Aug 2022 14:02:07: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 14:02:07: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 14:02:07: #1 total tags in treatment: 862407 INFO @ Tue, 02 Aug 2022 14:02:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:02:07: #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 14:02:07: #1 tags after filtering in treatment: 836821 INFO @ Tue, 02 Aug 2022 14:02:07: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 14:02:07: #1 finished! INFO @ Tue, 02 Aug 2022 14:02:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:02:08: #2 number of paired peaks: 1834 INFO @ Tue, 02 Aug 2022 14:02:08: start model_add_line... INFO @ Tue, 02 Aug 2022 14:02:08: start X-correlation... INFO @ Tue, 02 Aug 2022 14:02:08: end of X-cor INFO @ Tue, 02 Aug 2022 14:02:08: #2 finished! INFO @ Tue, 02 Aug 2022 14:02:08: #2 predicted fragment length is 106 bps INFO @ Tue, 02 Aug 2022 14:02:08: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 02 Aug 2022 14:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.10_model.r INFO @ Tue, 02 Aug 2022 14:02:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:02:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:02:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:02:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:02:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.10_summits.bed INFO @ Tue, 02 Aug 2022 14:02:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (116 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 INFO @ Tue, 02 Aug 2022 14:02:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.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 14:02:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:02:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:02:31: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:02:36: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 14:02:36: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 14:02:36: #1 total tags in treatment: 862407 INFO @ Tue, 02 Aug 2022 14:02:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:02:36: #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 14:02:36: #1 tags after filtering in treatment: 836821 INFO @ Tue, 02 Aug 2022 14:02:36: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 14:02:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:02:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:02:36: #2 number of paired peaks: 1834 INFO @ Tue, 02 Aug 2022 14:02:36: start model_add_line... INFO @ Tue, 02 Aug 2022 14:02:36: start X-correlation... INFO @ Tue, 02 Aug 2022 14:02:36: end of X-cor INFO @ Tue, 02 Aug 2022 14:02:36: #2 finished! INFO @ Tue, 02 Aug 2022 14:02:36: #2 predicted fragment length is 106 bps INFO @ Tue, 02 Aug 2022 14:02:36: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 02 Aug 2022 14:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.20_model.r INFO @ Tue, 02 Aug 2022 14:02:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:02:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:02:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:02:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622675/SRX12622675.20_summits.bed INFO @ Tue, 02 Aug 2022 14:02:39: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (50 records, 4 fields): 113 millis CompletedMACS2peakCalling