Job ID = 5721181 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,726,962 reads read : 7,453,924 reads written : 7,453,924 spots read : 3,685,503 reads read : 7,371,006 reads written : 7,371,006 spots read : 3,655,658 reads read : 7,311,316 reads written : 7,311,316 spots read : 3,659,823 reads read : 7,319,646 reads written : 7,319,646 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: 00:03:09 14727946 reads; of these: 14727946 (100.00%) were paired; of these: 14169870 (96.21%) aligned concordantly 0 times 401937 (2.73%) aligned concordantly exactly 1 time 156139 (1.06%) aligned concordantly >1 times ---- 14169870 pairs aligned concordantly 0 times; of these: 1312 (0.01%) aligned discordantly 1 time ---- 14168558 pairs aligned 0 times concordantly or discordantly; of these: 28337116 mates make up the pairs; of these: 27969643 (98.70%) aligned 0 times 77112 (0.27%) aligned exactly 1 time 290361 (1.02%) aligned >1 times 5.05% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 9423 / 558407 = 0.0169 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 @ Thu, 16 Apr 2020 05:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.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 @ Thu, 16 Apr 2020 05:42:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:42:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:42:37: 1000000 INFO @ Thu, 16 Apr 2020 05:42:39: #1 tag size is determined as 38 bps INFO @ Thu, 16 Apr 2020 05:42:39: #1 tag size = 38 INFO @ Thu, 16 Apr 2020 05:42:39: #1 total tags in treatment: 548661 INFO @ Thu, 16 Apr 2020 05:42:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:42:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:42:39: #1 tags after filtering in treatment: 541133 INFO @ Thu, 16 Apr 2020 05:42:39: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 16 Apr 2020 05:42:39: #1 finished! INFO @ Thu, 16 Apr 2020 05:42:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:42:39: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 05:42:39: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 05:42:39: start model_add_line... INFO @ Thu, 16 Apr 2020 05:42:39: start X-correlation... INFO @ Thu, 16 Apr 2020 05:42:39: end of X-cor INFO @ Thu, 16 Apr 2020 05:42:39: #2 finished! INFO @ Thu, 16 Apr 2020 05:42:39: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 05:42:39: #2 alternative fragment length(s) may be 78,567,596,598 bps INFO @ Thu, 16 Apr 2020 05:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.05_model.r INFO @ Thu, 16 Apr 2020 05:42:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:42:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:42:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:42:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:42:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.05_summits.bed INFO @ Thu, 16 Apr 2020 05:42:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 0 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 @ Thu, 16 Apr 2020 05:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.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 @ Thu, 16 Apr 2020 05:43:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:43:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:43:07: 1000000 INFO @ Thu, 16 Apr 2020 05:43:09: #1 tag size is determined as 38 bps INFO @ Thu, 16 Apr 2020 05:43:09: #1 tag size = 38 INFO @ Thu, 16 Apr 2020 05:43:09: #1 total tags in treatment: 548661 INFO @ Thu, 16 Apr 2020 05:43:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:43:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:43:09: #1 tags after filtering in treatment: 541133 INFO @ Thu, 16 Apr 2020 05:43:09: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 16 Apr 2020 05:43:09: #1 finished! INFO @ Thu, 16 Apr 2020 05:43:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:43:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:43:09: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 05:43:09: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 05:43:09: start model_add_line... INFO @ Thu, 16 Apr 2020 05:43:09: start X-correlation... INFO @ Thu, 16 Apr 2020 05:43:09: end of X-cor INFO @ Thu, 16 Apr 2020 05:43:09: #2 finished! INFO @ Thu, 16 Apr 2020 05:43:09: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 05:43:09: #2 alternative fragment length(s) may be 78,567,596,598 bps INFO @ Thu, 16 Apr 2020 05:43:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.10_model.r INFO @ Thu, 16 Apr 2020 05:43:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:43:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:43:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:43:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:43:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:43:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.10_summits.bed INFO @ Thu, 16 Apr 2020 05:43:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (56 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 @ Thu, 16 Apr 2020 05:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.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 @ Thu, 16 Apr 2020 05:43:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:43:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:43:37: 1000000 INFO @ Thu, 16 Apr 2020 05:43:39: #1 tag size is determined as 38 bps INFO @ Thu, 16 Apr 2020 05:43:39: #1 tag size = 38 INFO @ Thu, 16 Apr 2020 05:43:39: #1 total tags in treatment: 548661 INFO @ Thu, 16 Apr 2020 05:43:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:43:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:43:39: #1 tags after filtering in treatment: 541133 INFO @ Thu, 16 Apr 2020 05:43:39: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 16 Apr 2020 05:43:39: #1 finished! INFO @ Thu, 16 Apr 2020 05:43:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:43:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:43:39: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 05:43:39: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 05:43:39: start model_add_line... INFO @ Thu, 16 Apr 2020 05:43:39: start X-correlation... INFO @ Thu, 16 Apr 2020 05:43:39: end of X-cor INFO @ Thu, 16 Apr 2020 05:43:39: #2 finished! INFO @ Thu, 16 Apr 2020 05:43:39: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 05:43:39: #2 alternative fragment length(s) may be 78,567,596,598 bps INFO @ Thu, 16 Apr 2020 05:43:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.20_model.r INFO @ Thu, 16 Apr 2020 05:43:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:43:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762290/SRX6762290.20_summits.bed INFO @ Thu, 16 Apr 2020 05:43:41: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (41 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。