Job ID = 12265190 SRX = SRX3426792 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3837874 spots for SRR6327143/SRR6327143.sra Written 3837874 spots for SRR6327143/SRR6327143.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265338 ("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: 00:02:59 3837874 reads; of these: 3837874 (100.00%) were paired; of these: 2026325 (52.80%) aligned concordantly 0 times 1479898 (38.56%) aligned concordantly exactly 1 time 331651 (8.64%) aligned concordantly >1 times ---- 2026325 pairs aligned concordantly 0 times; of these: 234279 (11.56%) aligned discordantly 1 time ---- 1792046 pairs aligned 0 times concordantly or discordantly; of these: 3584092 mates make up the pairs; of these: 1954216 (54.52%) aligned 0 times 1128812 (31.50%) aligned exactly 1 time 501064 (13.98%) aligned >1 times 74.54% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 126178 / 2033236 = 0.0621 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.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, 03 Apr 2021 06:16:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:16:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:17:01: 1000000 INFO @ Sat, 03 Apr 2021 06:17:06: 2000000 INFO @ Sat, 03 Apr 2021 06:17:11: 3000000 INFO @ Sat, 03 Apr 2021 06:17:16: 4000000 INFO @ Sat, 03 Apr 2021 06:17:21: 5000000 INFO @ Sat, 03 Apr 2021 06:17:23: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 06:17:23: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 06:17:23: #1 total tags in treatment: 1695844 INFO @ Sat, 03 Apr 2021 06:17:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:17:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:17:23: #1 tags after filtering in treatment: 1464696 INFO @ Sat, 03 Apr 2021 06:17:23: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 06:17:23: #1 finished! INFO @ Sat, 03 Apr 2021 06:17:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:17:24: #2 number of paired peaks: 5027 INFO @ Sat, 03 Apr 2021 06:17:24: start model_add_line... INFO @ Sat, 03 Apr 2021 06:17:24: start X-correlation... INFO @ Sat, 03 Apr 2021 06:17:24: end of X-cor INFO @ Sat, 03 Apr 2021 06:17:24: #2 finished! INFO @ Sat, 03 Apr 2021 06:17:24: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 06:17:24: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 03 Apr 2021 06:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.05_model.r INFO @ Sat, 03 Apr 2021 06:17:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:17:24: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.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, 03 Apr 2021 06:17:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:17:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:17:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:17:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:17:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:17:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.05_summits.bed INFO @ Sat, 03 Apr 2021 06:17:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5748 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:17:30: 1000000 INFO @ Sat, 03 Apr 2021 06:17:35: 2000000 INFO @ Sat, 03 Apr 2021 06:17:40: 3000000 INFO @ Sat, 03 Apr 2021 06:17:45: 4000000 INFO @ Sat, 03 Apr 2021 06:17:50: 5000000 INFO @ Sat, 03 Apr 2021 06:17:53: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 06:17:53: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 06:17:53: #1 total tags in treatment: 1695844 INFO @ Sat, 03 Apr 2021 06:17:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:17:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:17:53: #1 tags after filtering in treatment: 1464696 INFO @ Sat, 03 Apr 2021 06:17:53: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 06:17:53: #1 finished! INFO @ Sat, 03 Apr 2021 06:17:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:17:53: #2 number of paired peaks: 5027 INFO @ Sat, 03 Apr 2021 06:17:53: start model_add_line... INFO @ Sat, 03 Apr 2021 06:17:53: start X-correlation... INFO @ Sat, 03 Apr 2021 06:17:53: end of X-cor INFO @ Sat, 03 Apr 2021 06:17:53: #2 finished! INFO @ Sat, 03 Apr 2021 06:17:53: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 06:17:53: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 03 Apr 2021 06:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.10_model.r INFO @ Sat, 03 Apr 2021 06:17:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:17:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.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, 03 Apr 2021 06:17:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:17:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:17:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:17:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:17:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:17:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.10_summits.bed INFO @ Sat, 03 Apr 2021 06:17:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2632 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:18:00: 1000000 INFO @ Sat, 03 Apr 2021 06:18:06: 2000000 INFO @ Sat, 03 Apr 2021 06:18:11: 3000000 INFO @ Sat, 03 Apr 2021 06:18:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:18:21: 5000000 INFO @ Sat, 03 Apr 2021 06:18:23: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 06:18:23: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 06:18:23: #1 total tags in treatment: 1695844 INFO @ Sat, 03 Apr 2021 06:18:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:18:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:18:23: #1 tags after filtering in treatment: 1464696 INFO @ Sat, 03 Apr 2021 06:18:23: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 06:18:23: #1 finished! INFO @ Sat, 03 Apr 2021 06:18:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:18:24: #2 number of paired peaks: 5027 INFO @ Sat, 03 Apr 2021 06:18:24: start model_add_line... INFO @ Sat, 03 Apr 2021 06:18:24: start X-correlation... INFO @ Sat, 03 Apr 2021 06:18:24: end of X-cor INFO @ Sat, 03 Apr 2021 06:18:24: #2 finished! INFO @ Sat, 03 Apr 2021 06:18:24: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 06:18:24: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 03 Apr 2021 06:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.20_model.r INFO @ Sat, 03 Apr 2021 06:18:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:18:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:18:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:18:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:18:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:18:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426792/SRX3426792.20_summits.bed INFO @ Sat, 03 Apr 2021 06:18:29: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (757 records, 4 fields): 4 millis CompletedMACS2peakCalling