Job ID = 6528429 SRX = SRX6441115 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T15:27:47 prefetch.2.10.7: 1) Downloading 'SRR9680913'... 2020-06-29T15:27:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:28:25 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:28:25 prefetch.2.10.7: 'SRR9680913' is valid 2020-06-29T15:28:25 prefetch.2.10.7: 1) 'SRR9680913' was downloaded successfully 2020-06-29T15:28:25 prefetch.2.10.7: 'SRR9680913' has 0 unresolved dependencies Read 1441930 spots for SRR9680913/SRR9680913.sra Written 1441930 spots for SRR9680913/SRR9680913.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:36 1441930 reads; of these: 1441930 (100.00%) were paired; of these: 391390 (27.14%) aligned concordantly 0 times 798401 (55.37%) aligned concordantly exactly 1 time 252139 (17.49%) aligned concordantly >1 times ---- 391390 pairs aligned concordantly 0 times; of these: 84356 (21.55%) aligned discordantly 1 time ---- 307034 pairs aligned 0 times concordantly or discordantly; of these: 614068 mates make up the pairs; of these: 330819 (53.87%) aligned 0 times 168022 (27.36%) aligned exactly 1 time 115227 (18.76%) aligned >1 times 88.53% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 727042 / 1133468 = 0.6414 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 @ Tue, 30 Jun 2020 00:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.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 @ Tue, 30 Jun 2020 00:34:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:34:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:35:03: 1000000 INFO @ Tue, 30 Jun 2020 00:35:03: #1 tag size is determined as 82 bps INFO @ Tue, 30 Jun 2020 00:35:03: #1 tag size = 82 INFO @ Tue, 30 Jun 2020 00:35:03: #1 total tags in treatment: 363684 INFO @ Tue, 30 Jun 2020 00:35:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:35:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:35:03: #1 tags after filtering in treatment: 295589 INFO @ Tue, 30 Jun 2020 00:35:03: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 30 Jun 2020 00:35:03: #1 finished! INFO @ Tue, 30 Jun 2020 00:35:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:35:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:35:03: #2 number of paired peaks: 4735 INFO @ Tue, 30 Jun 2020 00:35:03: start model_add_line... INFO @ Tue, 30 Jun 2020 00:35:03: start X-correlation... INFO @ Tue, 30 Jun 2020 00:35:03: end of X-cor INFO @ Tue, 30 Jun 2020 00:35:03: #2 finished! INFO @ Tue, 30 Jun 2020 00:35:03: #2 predicted fragment length is 300 bps INFO @ Tue, 30 Jun 2020 00:35:03: #2 alternative fragment length(s) may be 9,248,300 bps INFO @ Tue, 30 Jun 2020 00:35:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.05_model.r INFO @ Tue, 30 Jun 2020 00:35:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:35:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.05_summits.bed INFO @ Tue, 30 Jun 2020 00:35:04: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (82 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 @ Tue, 30 Jun 2020 00:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.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 @ Tue, 30 Jun 2020 00:35:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:35:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:35:34: 1000000 INFO @ Tue, 30 Jun 2020 00:35:34: #1 tag size is determined as 82 bps INFO @ Tue, 30 Jun 2020 00:35:34: #1 tag size = 82 INFO @ Tue, 30 Jun 2020 00:35:34: #1 total tags in treatment: 363684 INFO @ Tue, 30 Jun 2020 00:35:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:35:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:35:34: #1 tags after filtering in treatment: 295589 INFO @ Tue, 30 Jun 2020 00:35:34: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 30 Jun 2020 00:35:34: #1 finished! INFO @ Tue, 30 Jun 2020 00:35:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:35:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:35:35: #2 number of paired peaks: 4735 INFO @ Tue, 30 Jun 2020 00:35:35: start model_add_line... INFO @ Tue, 30 Jun 2020 00:35:35: start X-correlation... INFO @ Tue, 30 Jun 2020 00:35:35: end of X-cor INFO @ Tue, 30 Jun 2020 00:35:35: #2 finished! INFO @ Tue, 30 Jun 2020 00:35:35: #2 predicted fragment length is 300 bps INFO @ Tue, 30 Jun 2020 00:35:35: #2 alternative fragment length(s) may be 9,248,300 bps INFO @ Tue, 30 Jun 2020 00:35:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.10_model.r INFO @ Tue, 30 Jun 2020 00:35:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:35:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:35:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:35:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.10_summits.bed INFO @ Tue, 30 Jun 2020 00:35:36: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 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 @ Tue, 30 Jun 2020 00:35:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.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 @ Tue, 30 Jun 2020 00:35:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:35:55: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:36:03: 1000000 INFO @ Tue, 30 Jun 2020 00:36:04: #1 tag size is determined as 82 bps INFO @ Tue, 30 Jun 2020 00:36:04: #1 tag size = 82 INFO @ Tue, 30 Jun 2020 00:36:04: #1 total tags in treatment: 363684 INFO @ Tue, 30 Jun 2020 00:36:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:36:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:36:04: #1 tags after filtering in treatment: 295589 INFO @ Tue, 30 Jun 2020 00:36:04: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 30 Jun 2020 00:36:04: #1 finished! INFO @ Tue, 30 Jun 2020 00:36:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:36:04: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:36:04: #2 number of paired peaks: 4735 INFO @ Tue, 30 Jun 2020 00:36:04: start model_add_line... INFO @ Tue, 30 Jun 2020 00:36:04: start X-correlation... INFO @ Tue, 30 Jun 2020 00:36:04: end of X-cor INFO @ Tue, 30 Jun 2020 00:36:04: #2 finished! INFO @ Tue, 30 Jun 2020 00:36:04: #2 predicted fragment length is 300 bps INFO @ Tue, 30 Jun 2020 00:36:04: #2 alternative fragment length(s) may be 9,248,300 bps INFO @ Tue, 30 Jun 2020 00:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.20_model.r INFO @ Tue, 30 Jun 2020 00:36:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:36:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:36:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441115/SRX6441115.20_summits.bed INFO @ Tue, 30 Jun 2020 00:36:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling