Job ID = 14171437 SRX = SRX9555289 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12310674 spots for SRR13110727/SRR13110727.sra Written 12310674 spots for SRR13110727/SRR13110727.sra Read 12199252 spots for SRR13110728/SRR13110728.sra Written 12199252 spots for SRR13110728/SRR13110728.sra Read 12272948 spots for SRR13110729/SRR13110729.sra Written 12272948 spots for SRR13110729/SRR13110729.sra Read 12185294 spots for SRR13110730/SRR13110730.sra Written 12185294 spots for SRR13110730/SRR13110730.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171965 ("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: 00:07:44 48968168 reads; of these: 48968168 (100.00%) were paired; of these: 46921427 (95.82%) aligned concordantly 0 times 1545440 (3.16%) aligned concordantly exactly 1 time 501301 (1.02%) aligned concordantly >1 times ---- 46921427 pairs aligned concordantly 0 times; of these: 5310 (0.01%) aligned discordantly 1 time ---- 46916117 pairs aligned 0 times concordantly or discordantly; of these: 93832234 mates make up the pairs; of these: 93517270 (99.66%) aligned 0 times 121441 (0.13%) aligned exactly 1 time 193523 (0.21%) aligned >1 times 4.51% overall alignment rate Time searching: 00:07:45 Overall time: 00:07:45 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] 121830 / 2050980 = 0.0594 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 11:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.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 11:53:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:53:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:53:26: 1000000 INFO @ Sat, 11 Dec 2021 11:53:30: 2000000 INFO @ Sat, 11 Dec 2021 11:53:35: 3000000 INFO @ Sat, 11 Dec 2021 11:53:39: 4000000 INFO @ Sat, 11 Dec 2021 11:53:40: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:53:40: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:53:40: #1 total tags in treatment: 1925004 INFO @ Sat, 11 Dec 2021 11:53:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:53:40: #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 11:53:40: #1 tags after filtering in treatment: 1609922 INFO @ Sat, 11 Dec 2021 11:53:40: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 11:53:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:53:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:53:41: #2 number of paired peaks: 8417 INFO @ Sat, 11 Dec 2021 11:53:41: start model_add_line... INFO @ Sat, 11 Dec 2021 11:53:41: start X-correlation... INFO @ Sat, 11 Dec 2021 11:53:41: end of X-cor INFO @ Sat, 11 Dec 2021 11:53:41: #2 finished! INFO @ Sat, 11 Dec 2021 11:53:41: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 11:53:41: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 11 Dec 2021 11:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.05_model.r INFO @ Sat, 11 Dec 2021 11:53:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.05_summits.bed INFO @ Sat, 11 Dec 2021 11:53:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5188 records, 4 fields): 6 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 11:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.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 11:53:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:53:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:53:56: 1000000 INFO @ Sat, 11 Dec 2021 11:54:00: 2000000 INFO @ Sat, 11 Dec 2021 11:54:05: 3000000 INFO @ Sat, 11 Dec 2021 11:54:09: 4000000 INFO @ Sat, 11 Dec 2021 11:54:10: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:54:10: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:54:10: #1 total tags in treatment: 1925004 INFO @ Sat, 11 Dec 2021 11:54:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:54:10: #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 11:54:10: #1 tags after filtering in treatment: 1609922 INFO @ Sat, 11 Dec 2021 11:54:10: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 11:54:10: #1 finished! INFO @ Sat, 11 Dec 2021 11:54:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:54:11: #2 number of paired peaks: 8417 INFO @ Sat, 11 Dec 2021 11:54:11: start model_add_line... INFO @ Sat, 11 Dec 2021 11:54:11: start X-correlation... INFO @ Sat, 11 Dec 2021 11:54:11: end of X-cor INFO @ Sat, 11 Dec 2021 11:54:11: #2 finished! INFO @ Sat, 11 Dec 2021 11:54:11: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 11:54:11: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 11 Dec 2021 11:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.10_model.r INFO @ Sat, 11 Dec 2021 11:54:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:54:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:54:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:54:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.10_summits.bed INFO @ Sat, 11 Dec 2021 11:54:16: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2207 records, 4 fields): 4 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 11:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.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 11:54:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:54:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:54:26: 1000000 INFO @ Sat, 11 Dec 2021 11:54:30: 2000000 INFO @ Sat, 11 Dec 2021 11:54:35: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:54:40: 4000000 INFO @ Sat, 11 Dec 2021 11:54:40: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:54:40: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:54:40: #1 total tags in treatment: 1925004 INFO @ Sat, 11 Dec 2021 11:54:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:54:40: #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 11:54:40: #1 tags after filtering in treatment: 1609922 INFO @ Sat, 11 Dec 2021 11:54:40: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 11:54:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:54:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:54:41: #2 number of paired peaks: 8417 INFO @ Sat, 11 Dec 2021 11:54:41: start model_add_line... INFO @ Sat, 11 Dec 2021 11:54:41: start X-correlation... INFO @ Sat, 11 Dec 2021 11:54:41: end of X-cor INFO @ Sat, 11 Dec 2021 11:54:41: #2 finished! INFO @ Sat, 11 Dec 2021 11:54:41: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 11:54:41: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 11 Dec 2021 11:54:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.20_model.r INFO @ Sat, 11 Dec 2021 11:54:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:54:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:54:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555289/SRX9555289.20_summits.bed INFO @ Sat, 11 Dec 2021 11:54:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling