Job ID = 8071161 SRX = SRX7917514 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:21:08 prefetch.2.10.7: 1) Downloading 'SRR11313095'... 2020-08-08T04:21:08 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:21:33 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:21:33 prefetch.2.10.7: 'SRR11313095' is valid 2020-08-08T04:21:33 prefetch.2.10.7: 1) 'SRR11313095' was downloaded successfully Read 2094217 spots for SRR11313095/SRR11313095.sra Written 2094217 spots for SRR11313095/SRR11313095.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072049 ("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: 00:02:25 2094217 reads; of these: 2094217 (100.00%) were paired; of these: 532947 (25.45%) aligned concordantly 0 times 1368242 (65.33%) aligned concordantly exactly 1 time 193028 (9.22%) aligned concordantly >1 times ---- 532947 pairs aligned concordantly 0 times; of these: 180645 (33.90%) aligned discordantly 1 time ---- 352302 pairs aligned 0 times concordantly or discordantly; of these: 704604 mates make up the pairs; of these: 546789 (77.60%) aligned 0 times 84662 (12.02%) aligned exactly 1 time 73153 (10.38%) aligned >1 times 86.95% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 763652 / 1735509 = 0.4400 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 13:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.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 13:25:27: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:27: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:32: 1000000 INFO @ Sat, 08 Aug 2020 13:25:38: 2000000 INFO @ Sat, 08 Aug 2020 13:25:38: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:25:38: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:25:38: #1 total tags in treatment: 827989 INFO @ Sat, 08 Aug 2020 13:25:38: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:25:38: #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 13:25:38: #1 tags after filtering in treatment: 575347 INFO @ Sat, 08 Aug 2020 13:25:38: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 08 Aug 2020 13:25:38: #1 finished! INFO @ Sat, 08 Aug 2020 13:25:38: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:25:38: #2 number of paired peaks: 6434 INFO @ Sat, 08 Aug 2020 13:25:38: start model_add_line... INFO @ Sat, 08 Aug 2020 13:25:38: start X-correlation... INFO @ Sat, 08 Aug 2020 13:25:38: end of X-cor INFO @ Sat, 08 Aug 2020 13:25:38: #2 finished! INFO @ Sat, 08 Aug 2020 13:25:38: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 13:25:38: #2 alternative fragment length(s) may be 3,187,193 bps INFO @ Sat, 08 Aug 2020 13:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.05_model.r INFO @ Sat, 08 Aug 2020 13:25:38: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:25:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:25:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:25:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:25:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.05_summits.bed INFO @ Sat, 08 Aug 2020 13:25:40: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (21 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 13:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.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 13:25:57: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:57: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:02: 1000000 INFO @ Sat, 08 Aug 2020 13:26:08: 2000000 INFO @ Sat, 08 Aug 2020 13:26:08: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:26:08: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:26:08: #1 total tags in treatment: 827989 INFO @ Sat, 08 Aug 2020 13:26:08: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:08: #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 13:26:08: #1 tags after filtering in treatment: 575347 INFO @ Sat, 08 Aug 2020 13:26:08: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 08 Aug 2020 13:26:08: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:08: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:09: #2 number of paired peaks: 6434 INFO @ Sat, 08 Aug 2020 13:26:09: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:09: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:09: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:09: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:09: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 13:26:09: #2 alternative fragment length(s) may be 3,187,193 bps INFO @ Sat, 08 Aug 2020 13:26:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.10_model.r INFO @ Sat, 08 Aug 2020 13:26:09: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:10: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.10_summits.bed INFO @ Sat, 08 Aug 2020 13:26:10: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 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 13:26:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.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 13:26:27: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:27: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:33: 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 13:26:38: 2000000 INFO @ Sat, 08 Aug 2020 13:26:39: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:26:39: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:26:39: #1 total tags in treatment: 827989 INFO @ Sat, 08 Aug 2020 13:26:39: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:39: #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 13:26:39: #1 tags after filtering in treatment: 575347 INFO @ Sat, 08 Aug 2020 13:26:39: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 08 Aug 2020 13:26:39: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:39: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:39: #2 number of paired peaks: 6434 INFO @ Sat, 08 Aug 2020 13:26:39: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:39: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:39: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:39: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:39: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 13:26:39: #2 alternative fragment length(s) may be 3,187,193 bps INFO @ Sat, 08 Aug 2020 13:26:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.20_model.r INFO @ Sat, 08 Aug 2020 13:26:39: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917514/SRX7917514.20_summits.bed INFO @ Sat, 08 Aug 2020 13:26:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling