Job ID = 14167228 SRX = SRX8973511 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14581329 spots for SRR12479626/SRR12479626.sra Written 14581329 spots for SRR12479626/SRR12479626.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167785 ("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: 00:06:17 14581329 reads; of these: 14581329 (100.00%) were paired; of these: 11826163 (81.10%) aligned concordantly 0 times 2389089 (16.38%) aligned concordantly exactly 1 time 366077 (2.51%) aligned concordantly >1 times ---- 11826163 pairs aligned concordantly 0 times; of these: 80281 (0.68%) aligned discordantly 1 time ---- 11745882 pairs aligned 0 times concordantly or discordantly; of these: 23491764 mates make up the pairs; of these: 22979872 (97.82%) aligned 0 times 370520 (1.58%) aligned exactly 1 time 141372 (0.60%) aligned >1 times 21.20% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 74487 / 2834518 = 0.0263 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 @ Fri, 10 Dec 2021 11:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.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 @ Fri, 10 Dec 2021 11:17:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:17:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:17:09: 1000000 INFO @ Fri, 10 Dec 2021 11:17:15: 2000000 INFO @ Fri, 10 Dec 2021 11:17:21: 3000000 INFO @ Fri, 10 Dec 2021 11:17:28: 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 @ Fri, 10 Dec 2021 11:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.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 @ Fri, 10 Dec 2021 11:17:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:17:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:17:35: 5000000 INFO @ Fri, 10 Dec 2021 11:17:40: 1000000 INFO @ Fri, 10 Dec 2021 11:17:42: 6000000 INFO @ Fri, 10 Dec 2021 11:17:42: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:17:42: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:17:42: #1 total tags in treatment: 2681641 INFO @ Fri, 10 Dec 2021 11:17:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:17:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:17:42: #1 tags after filtering in treatment: 2639232 INFO @ Fri, 10 Dec 2021 11:17:42: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:17:42: #1 finished! INFO @ Fri, 10 Dec 2021 11:17:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:17:42: #2 number of paired peaks: 2846 INFO @ Fri, 10 Dec 2021 11:17:42: start model_add_line... INFO @ Fri, 10 Dec 2021 11:17:42: start X-correlation... INFO @ Fri, 10 Dec 2021 11:17:42: end of X-cor INFO @ Fri, 10 Dec 2021 11:17:42: #2 finished! INFO @ Fri, 10 Dec 2021 11:17:42: #2 predicted fragment length is 252 bps INFO @ Fri, 10 Dec 2021 11:17:42: #2 alternative fragment length(s) may be 252 bps INFO @ Fri, 10 Dec 2021 11:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.05_model.r INFO @ Fri, 10 Dec 2021 11:17:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:17:46: 2000000 INFO @ Fri, 10 Dec 2021 11:17:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:17:52: 3000000 INFO @ Fri, 10 Dec 2021 11:17:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:17:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:17:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.05_summits.bed INFO @ Fri, 10 Dec 2021 11:17:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1353 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:17:58: 4000000 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 @ Fri, 10 Dec 2021 11:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.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 @ Fri, 10 Dec 2021 11:18:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:18:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:18:04: 5000000 INFO @ Fri, 10 Dec 2021 11:18:10: 1000000 INFO @ Fri, 10 Dec 2021 11:18:12: 6000000 INFO @ Fri, 10 Dec 2021 11:18:12: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:18:12: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:18:12: #1 total tags in treatment: 2681641 INFO @ Fri, 10 Dec 2021 11:18:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:18:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:18:12: #1 tags after filtering in treatment: 2639232 INFO @ Fri, 10 Dec 2021 11:18:12: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:18:12: #1 finished! INFO @ Fri, 10 Dec 2021 11:18:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:18:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:18:12: #2 number of paired peaks: 2846 INFO @ Fri, 10 Dec 2021 11:18:12: start model_add_line... INFO @ Fri, 10 Dec 2021 11:18:12: start X-correlation... INFO @ Fri, 10 Dec 2021 11:18:12: end of X-cor INFO @ Fri, 10 Dec 2021 11:18:12: #2 finished! INFO @ Fri, 10 Dec 2021 11:18:12: #2 predicted fragment length is 252 bps INFO @ Fri, 10 Dec 2021 11:18:12: #2 alternative fragment length(s) may be 252 bps INFO @ Fri, 10 Dec 2021 11:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.10_model.r INFO @ Fri, 10 Dec 2021 11:18:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:18:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:18:17: 2000000 INFO @ Fri, 10 Dec 2021 11:18:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.10_summits.bed INFO @ Fri, 10 Dec 2021 11:18:23: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (322 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:18:25: 3000000 INFO @ Fri, 10 Dec 2021 11:18:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:18:40: 5000000 INFO @ Fri, 10 Dec 2021 11:18:48: 6000000 INFO @ Fri, 10 Dec 2021 11:18:49: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:18:49: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:18:49: #1 total tags in treatment: 2681641 INFO @ Fri, 10 Dec 2021 11:18:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:18:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:18:49: #1 tags after filtering in treatment: 2639232 INFO @ Fri, 10 Dec 2021 11:18:49: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:18:49: #1 finished! INFO @ Fri, 10 Dec 2021 11:18:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:18:49: #2 number of paired peaks: 2846 INFO @ Fri, 10 Dec 2021 11:18:49: start model_add_line... INFO @ Fri, 10 Dec 2021 11:18:49: start X-correlation... INFO @ Fri, 10 Dec 2021 11:18:49: end of X-cor INFO @ Fri, 10 Dec 2021 11:18:49: #2 finished! INFO @ Fri, 10 Dec 2021 11:18:49: #2 predicted fragment length is 252 bps INFO @ Fri, 10 Dec 2021 11:18:49: #2 alternative fragment length(s) may be 252 bps INFO @ Fri, 10 Dec 2021 11:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.20_model.r INFO @ Fri, 10 Dec 2021 11:18:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:18:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:18:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:19:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:19:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:19:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973511/SRX8973511.20_summits.bed INFO @ Fri, 10 Dec 2021 11:19:00: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 31 millis CompletedMACS2peakCalling