Job ID = 14171103 SRX = SRX9555300 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4119604 spots for SRR13110771/SRR13110771.sra Written 4119604 spots for SRR13110771/SRR13110771.sra Read 4086004 spots for SRR13110772/SRR13110772.sra Written 4086004 spots for SRR13110772/SRR13110772.sra Read 4156425 spots for SRR13110773/SRR13110773.sra Written 4156425 spots for SRR13110773/SRR13110773.sra Read 4099345 spots for SRR13110774/SRR13110774.sra Written 4099345 spots for SRR13110774/SRR13110774.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171558 ("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: 00:04:49 16461378 reads; of these: 16461378 (100.00%) were paired; of these: 14198775 (86.26%) aligned concordantly 0 times 2039263 (12.39%) aligned concordantly exactly 1 time 223340 (1.36%) aligned concordantly >1 times ---- 14198775 pairs aligned concordantly 0 times; of these: 5372 (0.04%) aligned discordantly 1 time ---- 14193403 pairs aligned 0 times concordantly or discordantly; of these: 28386806 mates make up the pairs; of these: 28277449 (99.61%) aligned 0 times 61730 (0.22%) aligned exactly 1 time 47627 (0.17%) aligned >1 times 14.11% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 286801 / 2266721 = 0.1265 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 09:42:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.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 09:42:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:52: 1000000 INFO @ Sat, 11 Dec 2021 09:42:59: 2000000 INFO @ Sat, 11 Dec 2021 09:43:06: 3000000 INFO @ Sat, 11 Dec 2021 09:43:13: 4000000 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 09:43:13: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:43:13: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:43:13: #1 total tags in treatment: 1975882 INFO @ Sat, 11 Dec 2021 09:43:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:43:13: #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 09:43:13: #1 tags after filtering in treatment: 1319218 INFO @ Sat, 11 Dec 2021 09:43:13: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 09:43:13: #1 finished! INFO @ Sat, 11 Dec 2021 09:43:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:43:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:43:14: #2 number of paired peaks: 11291 INFO @ Sat, 11 Dec 2021 09:43:14: start model_add_line... INFO @ Sat, 11 Dec 2021 09:43:14: start X-correlation... INFO @ Sat, 11 Dec 2021 09:43:14: end of X-cor INFO @ Sat, 11 Dec 2021 09:43:14: #2 finished! INFO @ Sat, 11 Dec 2021 09:43:14: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 09:43:14: #2 alternative fragment length(s) may be 1,155,301 bps INFO @ Sat, 11 Dec 2021 09:43:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.05_model.r INFO @ Sat, 11 Dec 2021 09:43:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:43:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:43:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.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 09:43:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.05_summits.bed INFO @ Sat, 11 Dec 2021 09:43:21: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7539 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:43:22: 1000000 INFO @ Sat, 11 Dec 2021 09:43:29: 2000000 INFO @ Sat, 11 Dec 2021 09:43:36: 3000000 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 09:43:43: 4000000 INFO @ Sat, 11 Dec 2021 09:43:43: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:43:43: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:43:43: #1 total tags in treatment: 1975882 INFO @ Sat, 11 Dec 2021 09:43:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:43:43: #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 09:43:43: #1 tags after filtering in treatment: 1319218 INFO @ Sat, 11 Dec 2021 09:43:43: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 09:43:43: #1 finished! INFO @ Sat, 11 Dec 2021 09:43:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:43:44: #2 number of paired peaks: 11291 INFO @ Sat, 11 Dec 2021 09:43:44: start model_add_line... INFO @ Sat, 11 Dec 2021 09:43:44: start X-correlation... INFO @ Sat, 11 Dec 2021 09:43:44: end of X-cor INFO @ Sat, 11 Dec 2021 09:43:44: #2 finished! INFO @ Sat, 11 Dec 2021 09:43:44: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 09:43:44: #2 alternative fragment length(s) may be 1,155,301 bps INFO @ Sat, 11 Dec 2021 09:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.10_model.r INFO @ Sat, 11 Dec 2021 09:43:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:43:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.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 09:43:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.10_summits.bed INFO @ Sat, 11 Dec 2021 09:43:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5272 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:43:53: 1000000 INFO @ Sat, 11 Dec 2021 09:44:01: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:44:08: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:44:16: 4000000 INFO @ Sat, 11 Dec 2021 09:44:17: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:44:17: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:44:17: #1 total tags in treatment: 1975882 INFO @ Sat, 11 Dec 2021 09:44:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:44:17: #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 09:44:17: #1 tags after filtering in treatment: 1319218 INFO @ Sat, 11 Dec 2021 09:44:17: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 09:44:17: #1 finished! INFO @ Sat, 11 Dec 2021 09:44:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:44:17: #2 number of paired peaks: 11291 INFO @ Sat, 11 Dec 2021 09:44:17: start model_add_line... INFO @ Sat, 11 Dec 2021 09:44:17: start X-correlation... INFO @ Sat, 11 Dec 2021 09:44:17: end of X-cor INFO @ Sat, 11 Dec 2021 09:44:17: #2 finished! INFO @ Sat, 11 Dec 2021 09:44:17: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 09:44:17: #2 alternative fragment length(s) may be 1,155,301 bps INFO @ Sat, 11 Dec 2021 09:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.20_model.r INFO @ Sat, 11 Dec 2021 09:44:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:44:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555300/SRX9555300.20_summits.bed INFO @ Sat, 11 Dec 2021 09:44:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1872 records, 4 fields): 5 millis CompletedMACS2peakCalling