Job ID = 8071599 SRX = SRX7917574 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:28:58 prefetch.2.10.7: 1) Downloading 'SRR11313155'... 2020-08-08T04:28:58 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:29:39 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:29:39 prefetch.2.10.7: 'SRR11313155' is valid 2020-08-08T04:29:39 prefetch.2.10.7: 1) 'SRR11313155' was downloaded successfully Read 1927876 spots for SRR11313155/SRR11313155.sra Written 1927876 spots for SRR11313155/SRR11313155.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072467 ("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: 00:02:21 1927876 reads; of these: 1927876 (100.00%) were paired; of these: 395662 (20.52%) aligned concordantly 0 times 1324278 (68.69%) aligned concordantly exactly 1 time 207936 (10.79%) aligned concordantly >1 times ---- 395662 pairs aligned concordantly 0 times; of these: 182750 (46.19%) aligned discordantly 1 time ---- 212912 pairs aligned 0 times concordantly or discordantly; of these: 425824 mates make up the pairs; of these: 275230 (64.63%) aligned 0 times 78204 (18.37%) aligned exactly 1 time 72390 (17.00%) aligned >1 times 92.86% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 772804 / 1709988 = 0.4519 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 13:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.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 13:33:24: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:33:24: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:33:31: 1000000 INFO @ Sat, 08 Aug 2020 13:33:37: 2000000 INFO @ Sat, 08 Aug 2020 13:33:38: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:33:38: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:33:38: #1 total tags in treatment: 806168 INFO @ Sat, 08 Aug 2020 13:33:38: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:33:38: #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 13:33:38: #1 tags after filtering in treatment: 593571 INFO @ Sat, 08 Aug 2020 13:33:38: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 13:33:38: #1 finished! INFO @ Sat, 08 Aug 2020 13:33:38: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:33:38: #2 number of paired peaks: 5253 INFO @ Sat, 08 Aug 2020 13:33:38: start model_add_line... INFO @ Sat, 08 Aug 2020 13:33:38: start X-correlation... INFO @ Sat, 08 Aug 2020 13:33:38: end of X-cor INFO @ Sat, 08 Aug 2020 13:33:38: #2 finished! INFO @ Sat, 08 Aug 2020 13:33:38: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Aug 2020 13:33:38: #2 alternative fragment length(s) may be 4,172,189 bps INFO @ Sat, 08 Aug 2020 13:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.05_model.r INFO @ Sat, 08 Aug 2020 13:33:38: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:33:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:33:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:33:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:33:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.05_summits.bed INFO @ Sat, 08 Aug 2020 13:33:40: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (16 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 13:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.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 13:33:54: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:33:54: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:33:59: 1000000 INFO @ Sat, 08 Aug 2020 13:34:05: 2000000 INFO @ Sat, 08 Aug 2020 13:34:05: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:34:05: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:34:05: #1 total tags in treatment: 806168 INFO @ Sat, 08 Aug 2020 13:34:05: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:34:05: #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 13:34:05: #1 tags after filtering in treatment: 593571 INFO @ Sat, 08 Aug 2020 13:34:05: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 13:34:05: #1 finished! INFO @ Sat, 08 Aug 2020 13:34:05: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:34:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:34:05: #2 number of paired peaks: 5253 INFO @ Sat, 08 Aug 2020 13:34:05: start model_add_line... INFO @ Sat, 08 Aug 2020 13:34:05: start X-correlation... INFO @ Sat, 08 Aug 2020 13:34:05: end of X-cor INFO @ Sat, 08 Aug 2020 13:34:05: #2 finished! INFO @ Sat, 08 Aug 2020 13:34:05: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Aug 2020 13:34:05: #2 alternative fragment length(s) may be 4,172,189 bps INFO @ Sat, 08 Aug 2020 13:34:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.10_model.r INFO @ Sat, 08 Aug 2020 13:34:05: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:34:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:34:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:34:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:34:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:34:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.10_summits.bed INFO @ Sat, 08 Aug 2020 13:34:07: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 0 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 13:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.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 13:34:24: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:34:24: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:34:29: 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 13:34:35: 2000000 INFO @ Sat, 08 Aug 2020 13:34:35: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:34:35: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:34:35: #1 total tags in treatment: 806168 INFO @ Sat, 08 Aug 2020 13:34:35: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:34:35: #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 13:34:35: #1 tags after filtering in treatment: 593571 INFO @ Sat, 08 Aug 2020 13:34:35: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 13:34:35: #1 finished! INFO @ Sat, 08 Aug 2020 13:34:35: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:34:35: #2 number of paired peaks: 5253 INFO @ Sat, 08 Aug 2020 13:34:35: start model_add_line... INFO @ Sat, 08 Aug 2020 13:34:35: start X-correlation... INFO @ Sat, 08 Aug 2020 13:34:35: end of X-cor INFO @ Sat, 08 Aug 2020 13:34:35: #2 finished! INFO @ Sat, 08 Aug 2020 13:34:35: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Aug 2020 13:34:35: #2 alternative fragment length(s) may be 4,172,189 bps INFO @ Sat, 08 Aug 2020 13:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.20_model.r INFO @ Sat, 08 Aug 2020 13:34:35: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:34:36: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:34:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:34:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:34:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917574/SRX7917574.20_summits.bed INFO @ Sat, 08 Aug 2020 13:34:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling