Job ID = 14171113 SRX = SRX9555306 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7337074 spots for SRR13110795/SRR13110795.sra Written 7337074 spots for SRR13110795/SRR13110795.sra Read 7282480 spots for SRR13110796/SRR13110796.sra Written 7282480 spots for SRR13110796/SRR13110796.sra Read 7476708 spots for SRR13110797/SRR13110797.sra Written 7476708 spots for SRR13110797/SRR13110797.sra Read 7364407 spots for SRR13110798/SRR13110798.sra Written 7364407 spots for SRR13110798/SRR13110798.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171569 ("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: 00:04:57 29460669 reads; of these: 29460669 (100.00%) were paired; of these: 27625049 (93.77%) aligned concordantly 0 times 1492210 (5.07%) aligned concordantly exactly 1 time 343410 (1.17%) aligned concordantly >1 times ---- 27625049 pairs aligned concordantly 0 times; of these: 12720 (0.05%) aligned discordantly 1 time ---- 27612329 pairs aligned 0 times concordantly or discordantly; of these: 55224658 mates make up the pairs; of these: 54965183 (99.53%) aligned 0 times 114310 (0.21%) aligned exactly 1 time 145165 (0.26%) aligned >1 times 6.71% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 57990 / 1847322 = 0.0314 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.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 @ Sat, 11 Dec 2021 09:45:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:45:14: 1000000 INFO @ Sat, 11 Dec 2021 09:45:20: 2000000 INFO @ Sat, 11 Dec 2021 09:45:26: 3000000 INFO @ Sat, 11 Dec 2021 09:45:31: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:45:31: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:45:31: #1 total tags in treatment: 1777824 INFO @ Sat, 11 Dec 2021 09:45:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:45:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:45:31: #1 tags after filtering in treatment: 1646234 INFO @ Sat, 11 Dec 2021 09:45:31: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 09:45:31: #1 finished! INFO @ Sat, 11 Dec 2021 09:45:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:45:31: #2 number of paired peaks: 5277 INFO @ Sat, 11 Dec 2021 09:45:31: start model_add_line... INFO @ Sat, 11 Dec 2021 09:45:31: start X-correlation... INFO @ Sat, 11 Dec 2021 09:45:31: end of X-cor INFO @ Sat, 11 Dec 2021 09:45:31: #2 finished! INFO @ Sat, 11 Dec 2021 09:45:31: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 09:45:31: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 09:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.05_model.r INFO @ Sat, 11 Dec 2021 09:45:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:45:35: #3 Call peaks for each chromosome... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:45:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.05_summits.bed INFO @ Sat, 11 Dec 2021 09:45:37: Done! INFO @ Sat, 11 Dec 2021 09:45:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.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 @ Sat, 11 Dec 2021 09:45:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:39: #1 read treatment tags... pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1294 records, 4 fields): 2489 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:45:44: 1000000 INFO @ Sat, 11 Dec 2021 09:45:50: 2000000 INFO @ Sat, 11 Dec 2021 09:45:56: 3000000 INFO @ Sat, 11 Dec 2021 09:46:01: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:46:01: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:46:01: #1 total tags in treatment: 1777824 INFO @ Sat, 11 Dec 2021 09:46:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:46:01: #1 tags after filtering in treatment: 1646234 INFO @ Sat, 11 Dec 2021 09:46:01: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 09:46:01: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:46:01: #2 number of paired peaks: 5277 INFO @ Sat, 11 Dec 2021 09:46:01: start model_add_line... INFO @ Sat, 11 Dec 2021 09:46:01: start X-correlation... INFO @ Sat, 11 Dec 2021 09:46:01: end of X-cor INFO @ Sat, 11 Dec 2021 09:46:01: #2 finished! INFO @ Sat, 11 Dec 2021 09:46:01: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 09:46:01: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 09:46:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.10_model.r INFO @ Sat, 11 Dec 2021 09:46:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:46:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:46:05: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:46:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:46:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:46:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.10_summits.bed INFO @ Sat, 11 Dec 2021 09:46:07: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (426 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.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 @ Sat, 11 Dec 2021 09:46:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:46:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:46:13: 1000000 INFO @ Sat, 11 Dec 2021 09:46:18: 2000000 INFO @ Sat, 11 Dec 2021 09:46:22: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:46:26: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:46:26: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:46:26: #1 total tags in treatment: 1777824 INFO @ Sat, 11 Dec 2021 09:46:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:46:26: #1 tags after filtering in treatment: 1646234 INFO @ Sat, 11 Dec 2021 09:46:26: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 09:46:26: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:46:27: #2 number of paired peaks: 5277 INFO @ Sat, 11 Dec 2021 09:46:27: start model_add_line... INFO @ Sat, 11 Dec 2021 09:46:27: start X-correlation... INFO @ Sat, 11 Dec 2021 09:46:27: end of X-cor INFO @ Sat, 11 Dec 2021 09:46:27: #2 finished! INFO @ Sat, 11 Dec 2021 09:46:27: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 09:46:27: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 09:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.20_model.r INFO @ Sat, 11 Dec 2021 09:46:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:46:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555306/SRX9555306.20_summits.bed INFO @ Sat, 11 Dec 2021 09:46:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling