Job ID = 14171114 SRX = SRX9555307 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8658891 spots for SRR13110416/SRR13110416.sra Written 8658891 spots for SRR13110416/SRR13110416.sra Read 8883396 spots for SRR13110417/SRR13110417.sra Written 8883396 spots for SRR13110417/SRR13110417.sra Read 8770297 spots for SRR13110418/SRR13110418.sra Written 8770297 spots for SRR13110418/SRR13110418.sra Read 8709494 spots for SRR13110799/SRR13110799.sra Written 8709494 spots for SRR13110799/SRR13110799.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171572 ("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: 00:04:40 35022078 reads; of these: 35022078 (100.00%) were paired; of these: 33968400 (96.99%) aligned concordantly 0 times 865457 (2.47%) aligned concordantly exactly 1 time 188221 (0.54%) aligned concordantly >1 times ---- 33968400 pairs aligned concordantly 0 times; of these: 5263 (0.02%) aligned discordantly 1 time ---- 33963137 pairs aligned 0 times concordantly or discordantly; of these: 67926274 mates make up the pairs; of these: 67678826 (99.64%) aligned 0 times 86580 (0.13%) aligned exactly 1 time 160868 (0.24%) aligned >1 times 3.38% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 31743 / 1058448 = 0.0300 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 09:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.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 09:45:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:45:19: 1000000 INFO @ Sat, 11 Dec 2021 09:45:23: 2000000 INFO @ Sat, 11 Dec 2021 09:45:25: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:45:25: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:45:25: #1 total tags in treatment: 1022009 INFO @ Sat, 11 Dec 2021 09:45:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:45:25: #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 09:45:25: #1 tags after filtering in treatment: 963224 INFO @ Sat, 11 Dec 2021 09:45:25: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:45:25: #1 finished! INFO @ Sat, 11 Dec 2021 09:45:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:45:25: #2 number of paired peaks: 7997 INFO @ Sat, 11 Dec 2021 09:45:25: start model_add_line... INFO @ Sat, 11 Dec 2021 09:45:25: start X-correlation... INFO @ Sat, 11 Dec 2021 09:45:25: end of X-cor INFO @ Sat, 11 Dec 2021 09:45:25: #2 finished! INFO @ Sat, 11 Dec 2021 09:45:25: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 09:45:25: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 09:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.05_model.r INFO @ Sat, 11 Dec 2021 09:45:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:45:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:45:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.05_summits.bed INFO @ Sat, 11 Dec 2021 09:45:28: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (915 records, 4 fields): 3 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 09:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.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 09:45:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:45:49: 1000000 INFO @ Sat, 11 Dec 2021 09:45:53: 2000000 INFO @ Sat, 11 Dec 2021 09:45:55: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:45:55: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:45:55: #1 total tags in treatment: 1022009 INFO @ Sat, 11 Dec 2021 09:45:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:45:55: #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 09:45:55: #1 tags after filtering in treatment: 963224 INFO @ Sat, 11 Dec 2021 09:45:55: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:45:55: #1 finished! INFO @ Sat, 11 Dec 2021 09:45:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:45:55: #2 number of paired peaks: 7997 INFO @ Sat, 11 Dec 2021 09:45:55: start model_add_line... INFO @ Sat, 11 Dec 2021 09:45:55: start X-correlation... INFO @ Sat, 11 Dec 2021 09:45:55: end of X-cor INFO @ Sat, 11 Dec 2021 09:45:55: #2 finished! INFO @ Sat, 11 Dec 2021 09:45:55: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 09:45:55: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 09:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.10_model.r INFO @ Sat, 11 Dec 2021 09:45:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:45:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.10_summits.bed INFO @ Sat, 11 Dec 2021 09:45:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (297 records, 4 fields): 1 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 09:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.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 09:46:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:46:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:46:19: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:46:23: 2000000 INFO @ Sat, 11 Dec 2021 09:46:25: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:46:25: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:46:25: #1 total tags in treatment: 1022009 INFO @ Sat, 11 Dec 2021 09:46:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:25: #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 09:46:25: #1 tags after filtering in treatment: 963224 INFO @ Sat, 11 Dec 2021 09:46:25: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:46:25: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:46:25: #2 number of paired peaks: 7997 INFO @ Sat, 11 Dec 2021 09:46:25: start model_add_line... INFO @ Sat, 11 Dec 2021 09:46:25: start X-correlation... INFO @ Sat, 11 Dec 2021 09:46:25: end of X-cor INFO @ Sat, 11 Dec 2021 09:46:25: #2 finished! INFO @ Sat, 11 Dec 2021 09:46:25: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 09:46:25: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 09:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.20_model.r INFO @ Sat, 11 Dec 2021 09:46:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:46:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555307/SRX9555307.20_summits.bed INFO @ Sat, 11 Dec 2021 09:46:28: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 1 millis CompletedMACS2peakCalling