Job ID = 16439447 SRX = SRX5101715 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6445742 spots for SRR8287008/SRR8287008.sra Written 6445742 spots for SRR8287008/SRR8287008.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439513 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:11 6445742 reads; of these: 6445742 (100.00%) were paired; of these: 677400 (10.51%) aligned concordantly 0 times 1823037 (28.28%) aligned concordantly exactly 1 time 3945305 (61.21%) aligned concordantly >1 times ---- 677400 pairs aligned concordantly 0 times; of these: 127613 (18.84%) aligned discordantly 1 time ---- 549787 pairs aligned 0 times concordantly or discordantly; of these: 1099574 mates make up the pairs; of these: 398656 (36.26%) aligned 0 times 113706 (10.34%) aligned exactly 1 time 587212 (53.40%) aligned >1 times 96.91% overall alignment rate Time searching: 00:09:12 Overall time: 00:09:12 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] 4193236 / 5808210 = 0.7219 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 15:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.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 15:24:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:24:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:25:05: 1000000 INFO @ Tue, 02 Aug 2022 15:25:12: 2000000 INFO @ Tue, 02 Aug 2022 15:25:18: 3000000 INFO @ Tue, 02 Aug 2022 15:25:25: 4000000 INFO @ Tue, 02 Aug 2022 15:25:26: #1 tag size is determined as 71 bps INFO @ Tue, 02 Aug 2022 15:25:26: #1 tag size = 71 INFO @ Tue, 02 Aug 2022 15:25:26: #1 total tags in treatment: 1617283 INFO @ Tue, 02 Aug 2022 15:25:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:25:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 15:25:26: #1 tags after filtering in treatment: 941149 INFO @ Tue, 02 Aug 2022 15:25:26: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 02 Aug 2022 15:25:26: #1 finished! INFO @ Tue, 02 Aug 2022 15:25:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:25:26: #2 number of paired peaks: 5351 INFO @ Tue, 02 Aug 2022 15:25:26: start model_add_line... INFO @ Tue, 02 Aug 2022 15:25:26: start X-correlation... INFO @ Tue, 02 Aug 2022 15:25:26: end of X-cor INFO @ Tue, 02 Aug 2022 15:25:26: #2 finished! INFO @ Tue, 02 Aug 2022 15:25:26: #2 predicted fragment length is 201 bps INFO @ Tue, 02 Aug 2022 15:25:26: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 02 Aug 2022 15:25:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.05_model.r INFO @ Tue, 02 Aug 2022 15:25:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:25:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.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 15:25:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:25:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:25:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:25:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:25:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.05_summits.bed INFO @ Tue, 02 Aug 2022 15:25:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3359 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:25:34: 1000000 INFO @ Tue, 02 Aug 2022 15:25:41: 2000000 INFO @ Tue, 02 Aug 2022 15:25:47: 3000000 INFO @ Tue, 02 Aug 2022 15:25:54: 4000000 INFO @ Tue, 02 Aug 2022 15:25:54: #1 tag size is determined as 71 bps INFO @ Tue, 02 Aug 2022 15:25:54: #1 tag size = 71 INFO @ Tue, 02 Aug 2022 15:25:54: #1 total tags in treatment: 1617283 INFO @ Tue, 02 Aug 2022 15:25:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:25:54: #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 15:25:54: #1 tags after filtering in treatment: 941149 INFO @ Tue, 02 Aug 2022 15:25:54: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 02 Aug 2022 15:25:54: #1 finished! INFO @ Tue, 02 Aug 2022 15:25:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:25:55: #2 number of paired peaks: 5351 INFO @ Tue, 02 Aug 2022 15:25:55: start model_add_line... INFO @ Tue, 02 Aug 2022 15:25:55: start X-correlation... INFO @ Tue, 02 Aug 2022 15:25:55: end of X-cor INFO @ Tue, 02 Aug 2022 15:25:55: #2 finished! INFO @ Tue, 02 Aug 2022 15:25:55: #2 predicted fragment length is 201 bps INFO @ Tue, 02 Aug 2022 15:25:55: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 02 Aug 2022 15:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.10_model.r INFO @ Tue, 02 Aug 2022 15:25:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:25:55: #3 Pre-compute pvalue-qvalue table... 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 15:25:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.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 15:25:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:25:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.10_summits.bed INFO @ Tue, 02 Aug 2022 15:25:59: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1395 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:26:04: 1000000 INFO @ Tue, 02 Aug 2022 15:26:11: 2000000 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 15:26:18: 3000000 INFO @ Tue, 02 Aug 2022 15:26:25: 4000000 INFO @ Tue, 02 Aug 2022 15:26:25: #1 tag size is determined as 71 bps INFO @ Tue, 02 Aug 2022 15:26:25: #1 tag size = 71 INFO @ Tue, 02 Aug 2022 15:26:25: #1 total tags in treatment: 1617283 INFO @ Tue, 02 Aug 2022 15:26:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:26:25: #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 15:26:25: #1 tags after filtering in treatment: 941149 INFO @ Tue, 02 Aug 2022 15:26:25: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 02 Aug 2022 15:26:25: #1 finished! INFO @ Tue, 02 Aug 2022 15:26:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:26:25: #2 number of paired peaks: 5351 INFO @ Tue, 02 Aug 2022 15:26:25: start model_add_line... INFO @ Tue, 02 Aug 2022 15:26:25: start X-correlation... INFO @ Tue, 02 Aug 2022 15:26:25: end of X-cor INFO @ Tue, 02 Aug 2022 15:26:25: #2 finished! INFO @ Tue, 02 Aug 2022 15:26:25: #2 predicted fragment length is 201 bps INFO @ Tue, 02 Aug 2022 15:26:25: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 02 Aug 2022 15:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.20_model.r INFO @ Tue, 02 Aug 2022 15:26:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:26:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5101715/SRX5101715.20_summits.bed INFO @ Tue, 02 Aug 2022 15:26:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (482 records, 4 fields): 52 millis CompletedMACS2peakCalling