Job ID = 14171107 SRX = SRX9555302 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3679672 spots for SRR13110779/SRR13110779.sra Written 3679672 spots for SRR13110779/SRR13110779.sra Read 3633492 spots for SRR13110780/SRR13110780.sra Written 3633492 spots for SRR13110780/SRR13110780.sra Read 3640066 spots for SRR13110781/SRR13110781.sra Written 3640066 spots for SRR13110781/SRR13110781.sra Read 3603627 spots for SRR13110782/SRR13110782.sra Written 3603627 spots for SRR13110782/SRR13110782.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171551 ("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: 00:03:19 14556857 reads; of these: 14556857 (100.00%) were paired; of these: 12676706 (87.08%) aligned concordantly 0 times 1651939 (11.35%) aligned concordantly exactly 1 time 228212 (1.57%) aligned concordantly >1 times ---- 12676706 pairs aligned concordantly 0 times; of these: 4731 (0.04%) aligned discordantly 1 time ---- 12671975 pairs aligned 0 times concordantly or discordantly; of these: 25343950 mates make up the pairs; of these: 25248850 (99.62%) aligned 0 times 50127 (0.20%) aligned exactly 1 time 44973 (0.18%) aligned >1 times 13.28% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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] 179139 / 1884186 = 0.0951 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 09:41:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.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 09:41:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:41:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:41:08: 1000000 INFO @ Sat, 11 Dec 2021 09:41:13: 2000000 INFO @ Sat, 11 Dec 2021 09:41:19: 3000000 INFO @ Sat, 11 Dec 2021 09:41:21: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:41:21: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:41:21: #1 total tags in treatment: 1701080 INFO @ Sat, 11 Dec 2021 09:41:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:41:21: #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 09:41:21: #1 tags after filtering in treatment: 1218138 INFO @ Sat, 11 Dec 2021 09:41:21: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 11 Dec 2021 09:41:21: #1 finished! INFO @ Sat, 11 Dec 2021 09:41:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:41:22: #2 number of paired peaks: 11488 INFO @ Sat, 11 Dec 2021 09:41:22: start model_add_line... INFO @ Sat, 11 Dec 2021 09:41:22: start X-correlation... INFO @ Sat, 11 Dec 2021 09:41:22: end of X-cor INFO @ Sat, 11 Dec 2021 09:41:22: #2 finished! INFO @ Sat, 11 Dec 2021 09:41:22: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 09:41:22: #2 alternative fragment length(s) may be 155,224,309 bps INFO @ Sat, 11 Dec 2021 09:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.05_model.r INFO @ Sat, 11 Dec 2021 09:41:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:41:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.05_summits.bed INFO @ Sat, 11 Dec 2021 09:41:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7300 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 09:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.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 09:41:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:41:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:41:37: 1000000 INFO @ Sat, 11 Dec 2021 09:41:43: 2000000 INFO @ Sat, 11 Dec 2021 09:41:48: 3000000 INFO @ Sat, 11 Dec 2021 09:41:50: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:41:50: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:41:50: #1 total tags in treatment: 1701080 INFO @ Sat, 11 Dec 2021 09:41:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:41:50: #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 09:41:50: #1 tags after filtering in treatment: 1218138 INFO @ Sat, 11 Dec 2021 09:41:50: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 11 Dec 2021 09:41:50: #1 finished! INFO @ Sat, 11 Dec 2021 09:41:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:41:51: #2 number of paired peaks: 11488 INFO @ Sat, 11 Dec 2021 09:41:51: start model_add_line... INFO @ Sat, 11 Dec 2021 09:41:51: start X-correlation... INFO @ Sat, 11 Dec 2021 09:41:51: end of X-cor INFO @ Sat, 11 Dec 2021 09:41:51: #2 finished! INFO @ Sat, 11 Dec 2021 09:41:51: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 09:41:51: #2 alternative fragment length(s) may be 155,224,309 bps INFO @ Sat, 11 Dec 2021 09:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.10_model.r INFO @ Sat, 11 Dec 2021 09:41:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:41:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:41:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:41:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:41:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.10_summits.bed INFO @ Sat, 11 Dec 2021 09:41:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4312 records, 4 fields): 6 millis CompletedMACS2peakCalling 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 09:42:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.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 09:42:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:07: 1000000 INFO @ Sat, 11 Dec 2021 09:42:12: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:42:17: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:42:20: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:42:20: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:42:20: #1 total tags in treatment: 1701080 INFO @ Sat, 11 Dec 2021 09:42:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:42:20: #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 09:42:20: #1 tags after filtering in treatment: 1218138 INFO @ Sat, 11 Dec 2021 09:42:20: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 11 Dec 2021 09:42:20: #1 finished! INFO @ Sat, 11 Dec 2021 09:42:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:42:20: #2 number of paired peaks: 11488 INFO @ Sat, 11 Dec 2021 09:42:20: start model_add_line... INFO @ Sat, 11 Dec 2021 09:42:20: start X-correlation... INFO @ Sat, 11 Dec 2021 09:42:20: end of X-cor INFO @ Sat, 11 Dec 2021 09:42:20: #2 finished! INFO @ Sat, 11 Dec 2021 09:42:20: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 09:42:20: #2 alternative fragment length(s) may be 155,224,309 bps INFO @ Sat, 11 Dec 2021 09:42:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.20_model.r INFO @ Sat, 11 Dec 2021 09:42:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:42:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:42:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:42:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:42:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:42:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555302/SRX9555302.20_summits.bed INFO @ Sat, 11 Dec 2021 09:42:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1177 records, 4 fields): 3 millis CompletedMACS2peakCalling