Job ID = 8069807 SRX = SRX7917456 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:54:38 prefetch.2.10.7: 1) Downloading 'SRR11313037'... 2020-08-08T03:54:38 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:55:11 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:55:11 prefetch.2.10.7: 'SRR11313037' is valid 2020-08-08T03:55:11 prefetch.2.10.7: 1) 'SRR11313037' was downloaded successfully Read 1645912 spots for SRR11313037/SRR11313037.sra Written 1645912 spots for SRR11313037/SRR11313037.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070766 ("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: 00:02:24 1645912 reads; of these: 1645912 (100.00%) were paired; of these: 358180 (21.76%) aligned concordantly 0 times 1085269 (65.94%) aligned concordantly exactly 1 time 202463 (12.30%) aligned concordantly >1 times ---- 358180 pairs aligned concordantly 0 times; of these: 140777 (39.30%) aligned discordantly 1 time ---- 217403 pairs aligned 0 times concordantly or discordantly; of these: 434806 mates make up the pairs; of these: 245971 (56.57%) aligned 0 times 93897 (21.60%) aligned exactly 1 time 94938 (21.83%) aligned >1 times 92.53% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 633673 / 1423281 = 0.4452 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.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, 08 Aug 2020 12:58:51: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:58:51: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:58:56: 1000000 INFO @ Sat, 08 Aug 2020 12:59:00: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:59:00: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:59:00: #1 total tags in treatment: 681175 INFO @ Sat, 08 Aug 2020 12:59:00: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:59:00: #1 tags after filtering in treatment: 523162 INFO @ Sat, 08 Aug 2020 12:59:00: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 08 Aug 2020 12:59:00: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:00: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:00: #2 number of paired peaks: 3586 INFO @ Sat, 08 Aug 2020 12:59:00: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:00: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:00: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:00: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:00: #2 predicted fragment length is 225 bps INFO @ Sat, 08 Aug 2020 12:59:00: #2 alternative fragment length(s) may be 3,225,254 bps INFO @ Sat, 08 Aug 2020 12:59:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.05_model.r INFO @ Sat, 08 Aug 2020 12:59:00: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.05_summits.bed INFO @ Sat, 08 Aug 2020 12:59:02: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.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, 08 Aug 2020 12:59:21: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:59:21: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:59:27: 1000000 INFO @ Sat, 08 Aug 2020 12:59:32: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:59:32: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:59:32: #1 total tags in treatment: 681175 INFO @ Sat, 08 Aug 2020 12:59:32: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:59:32: #1 tags after filtering in treatment: 523162 INFO @ Sat, 08 Aug 2020 12:59:32: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 08 Aug 2020 12:59:32: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:32: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:32: #2 number of paired peaks: 3586 INFO @ Sat, 08 Aug 2020 12:59:32: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:32: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:32: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:32: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:32: #2 predicted fragment length is 225 bps INFO @ Sat, 08 Aug 2020 12:59:32: #2 alternative fragment length(s) may be 3,225,254 bps INFO @ Sat, 08 Aug 2020 12:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.10_model.r INFO @ Sat, 08 Aug 2020 12:59:32: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:33: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.10_summits.bed INFO @ Sat, 08 Aug 2020 12:59:34: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.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, 08 Aug 2020 12:59:51: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:59:51: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:59:56: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:00:00: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:00:00: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:00:00: #1 total tags in treatment: 681175 INFO @ Sat, 08 Aug 2020 13:00:00: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:00:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:00:00: #1 tags after filtering in treatment: 523162 INFO @ Sat, 08 Aug 2020 13:00:00: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 08 Aug 2020 13:00:00: #1 finished! INFO @ Sat, 08 Aug 2020 13:00:00: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:00:00: #2 number of paired peaks: 3586 INFO @ Sat, 08 Aug 2020 13:00:00: start model_add_line... INFO @ Sat, 08 Aug 2020 13:00:00: start X-correlation... INFO @ Sat, 08 Aug 2020 13:00:00: end of X-cor INFO @ Sat, 08 Aug 2020 13:00:00: #2 finished! INFO @ Sat, 08 Aug 2020 13:00:00: #2 predicted fragment length is 225 bps INFO @ Sat, 08 Aug 2020 13:00:00: #2 alternative fragment length(s) may be 3,225,254 bps INFO @ Sat, 08 Aug 2020 13:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.20_model.r INFO @ Sat, 08 Aug 2020 13:00:00: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:00:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:00:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:00:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917456/SRX7917456.20_summits.bed INFO @ Sat, 08 Aug 2020 13:00:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling