Job ID = 14171422 SRX = SRX9555279 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9745314 spots for SRR13110687/SRR13110687.sra Written 9745314 spots for SRR13110687/SRR13110687.sra Read 11701232 spots for SRR13110688/SRR13110688.sra Written 11701232 spots for SRR13110688/SRR13110688.sra Read 11765418 spots for SRR13110689/SRR13110689.sra Written 11765418 spots for SRR13110689/SRR13110689.sra Read 11743912 spots for SRR13110690/SRR13110690.sra Written 11743912 spots for SRR13110690/SRR13110690.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171943 ("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: 00:07:36 44955876 reads; of these: 44955876 (100.00%) were paired; of these: 44007419 (97.89%) aligned concordantly 0 times 748966 (1.67%) aligned concordantly exactly 1 time 199491 (0.44%) aligned concordantly >1 times ---- 44007419 pairs aligned concordantly 0 times; of these: 6295 (0.01%) aligned discordantly 1 time ---- 44001124 pairs aligned 0 times concordantly or discordantly; of these: 88002248 mates make up the pairs; of these: 87048065 (98.92%) aligned 0 times 130833 (0.15%) aligned exactly 1 time 823350 (0.94%) aligned >1 times 3.18% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 44471 / 953425 = 0.0466 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 11:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.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 11:49:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:17: 1000000 INFO @ Sat, 11 Dec 2021 11:49:23: 2000000 INFO @ Sat, 11 Dec 2021 11:49:27: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:49:27: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:49:27: #1 total tags in treatment: 904180 INFO @ Sat, 11 Dec 2021 11:49:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:27: #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 11:49:27: #1 tags after filtering in treatment: 881136 INFO @ Sat, 11 Dec 2021 11:49:27: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:49:27: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:27: #2 number of paired peaks: 3633 INFO @ Sat, 11 Dec 2021 11:49:27: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:27: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:27: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:27: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:27: #2 predicted fragment length is 286 bps INFO @ Sat, 11 Dec 2021 11:49:27: #2 alternative fragment length(s) may be 4,286 bps INFO @ Sat, 11 Dec 2021 11:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.05_model.r INFO @ Sat, 11 Dec 2021 11:49:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:49:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:49:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:49:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:49:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.05_summits.bed INFO @ Sat, 11 Dec 2021 11:49:30: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 1 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 11:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.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 11:49:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:47: 1000000 INFO @ Sat, 11 Dec 2021 11:49:53: 2000000 INFO @ Sat, 11 Dec 2021 11:49:58: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:49:58: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:49:58: #1 total tags in treatment: 904180 INFO @ Sat, 11 Dec 2021 11:49:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:49:58: #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 11:49:58: #1 tags after filtering in treatment: 881136 INFO @ Sat, 11 Dec 2021 11:49:58: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:49:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:49:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:49:58: #2 number of paired peaks: 3633 INFO @ Sat, 11 Dec 2021 11:49:58: start model_add_line... INFO @ Sat, 11 Dec 2021 11:49:58: start X-correlation... INFO @ Sat, 11 Dec 2021 11:49:58: end of X-cor INFO @ Sat, 11 Dec 2021 11:49:58: #2 finished! INFO @ Sat, 11 Dec 2021 11:49:58: #2 predicted fragment length is 286 bps INFO @ Sat, 11 Dec 2021 11:49:58: #2 alternative fragment length(s) may be 4,286 bps INFO @ Sat, 11 Dec 2021 11:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.10_model.r INFO @ Sat, 11 Dec 2021 11:49:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:50:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.10_summits.bed INFO @ Sat, 11 Dec 2021 11:50:01: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (106 records, 4 fields): 2 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 11:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.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 11:50:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:50:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:17: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:50:23: 2000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:50:27: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:50:27: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:50:27: #1 total tags in treatment: 904180 INFO @ Sat, 11 Dec 2021 11:50:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:50:27: #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 11:50:27: #1 tags after filtering in treatment: 881136 INFO @ Sat, 11 Dec 2021 11:50:27: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:50:27: #1 finished! INFO @ Sat, 11 Dec 2021 11:50:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:50:28: #2 number of paired peaks: 3633 INFO @ Sat, 11 Dec 2021 11:50:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:50:28: start X-correlation... INFO @ Sat, 11 Dec 2021 11:50:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:50:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:50:28: #2 predicted fragment length is 286 bps INFO @ Sat, 11 Dec 2021 11:50:28: #2 alternative fragment length(s) may be 4,286 bps INFO @ Sat, 11 Dec 2021 11:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.20_model.r INFO @ Sat, 11 Dec 2021 11:50:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:50:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555279/SRX9555279.20_summits.bed INFO @ Sat, 11 Dec 2021 11:50:31: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 millis CompletedMACS2peakCalling