Job ID = 8071189 SRX = SRX7917520 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:22:08 prefetch.2.10.7: 1) Downloading 'SRR11313101'... 2020-08-08T04:22:08 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:22:32 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:22:32 prefetch.2.10.7: 'SRR11313101' is valid 2020-08-08T04:22:32 prefetch.2.10.7: 1) 'SRR11313101' was downloaded successfully Read 2011238 spots for SRR11313101/SRR11313101.sra Written 2011238 spots for SRR11313101/SRR11313101.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072119 ("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: 00:02:52 2011238 reads; of these: 2011238 (100.00%) were paired; of these: 382526 (19.02%) aligned concordantly 0 times 1372356 (68.23%) aligned concordantly exactly 1 time 256356 (12.75%) aligned concordantly >1 times ---- 382526 pairs aligned concordantly 0 times; of these: 181350 (47.41%) aligned discordantly 1 time ---- 201176 pairs aligned 0 times concordantly or discordantly; of these: 402352 mates make up the pairs; of these: 160248 (39.83%) aligned 0 times 121188 (30.12%) aligned exactly 1 time 120916 (30.05%) aligned >1 times 96.02% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 845816 / 1803605 = 0.4690 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 13:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.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 13:26:50: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:50: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:55: 1000000 INFO @ Sat, 08 Aug 2020 13:27:01: 2000000 INFO @ Sat, 08 Aug 2020 13:27:02: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:27:02: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:27:02: #1 total tags in treatment: 820106 INFO @ Sat, 08 Aug 2020 13:27:02: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:02: #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 13:27:02: #1 tags after filtering in treatment: 616962 INFO @ Sat, 08 Aug 2020 13:27:02: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:27:02: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:02: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:02: #2 number of paired peaks: 2880 INFO @ Sat, 08 Aug 2020 13:27:02: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:02: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:02: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:02: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:02: #2 predicted fragment length is 205 bps INFO @ Sat, 08 Aug 2020 13:27:02: #2 alternative fragment length(s) may be 2,168,205 bps INFO @ Sat, 08 Aug 2020 13:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.05_model.r INFO @ Sat, 08 Aug 2020 13:27:02: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.05_summits.bed INFO @ Sat, 08 Aug 2020 13:27:04: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (9 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 13:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.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 13:27:20: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:20: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:24: 1000000 INFO @ Sat, 08 Aug 2020 13:27:29: 2000000 INFO @ Sat, 08 Aug 2020 13:27:30: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:27:30: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:27:30: #1 total tags in treatment: 820106 INFO @ Sat, 08 Aug 2020 13:27:30: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:30: #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 13:27:30: #1 tags after filtering in treatment: 616962 INFO @ Sat, 08 Aug 2020 13:27:30: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:27:30: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:30: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:30: #2 number of paired peaks: 2880 INFO @ Sat, 08 Aug 2020 13:27:30: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:30: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:30: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:30: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:30: #2 predicted fragment length is 205 bps INFO @ Sat, 08 Aug 2020 13:27:30: #2 alternative fragment length(s) may be 2,168,205 bps INFO @ Sat, 08 Aug 2020 13:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.10_model.r INFO @ Sat, 08 Aug 2020 13:27:30: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:31: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.10_summits.bed INFO @ Sat, 08 Aug 2020 13:27:32: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (3 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 13:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.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 13:27:50: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:50: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:55: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:27:59: 2000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:28:00: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:28:00: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:28:00: #1 total tags in treatment: 820106 INFO @ Sat, 08 Aug 2020 13:28:00: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:00: #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 13:28:00: #1 tags after filtering in treatment: 616962 INFO @ Sat, 08 Aug 2020 13:28:00: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 08 Aug 2020 13:28:00: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:00: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:00: #2 number of paired peaks: 2880 INFO @ Sat, 08 Aug 2020 13:28:00: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:00: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:00: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:00: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:00: #2 predicted fragment length is 205 bps INFO @ Sat, 08 Aug 2020 13:28:00: #2 alternative fragment length(s) may be 2,168,205 bps INFO @ Sat, 08 Aug 2020 13:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.20_model.r INFO @ Sat, 08 Aug 2020 13:28:00: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917520/SRX7917520.20_summits.bed INFO @ Sat, 08 Aug 2020 13:28:02: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling