Job ID = 5721180 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,545,640 reads read : 7,091,280 reads written : 7,091,280 spots read : 3,516,588 reads read : 7,033,176 reads written : 7,033,176 spots read : 3,475,612 reads read : 6,951,224 reads written : 6,951,224 spots read : 3,480,440 reads read : 6,960,880 reads written : 6,960,880 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: 00:02:49 14018280 reads; of these: 14018280 (100.00%) were paired; of these: 13541430 (96.60%) aligned concordantly 0 times 329027 (2.35%) aligned concordantly exactly 1 time 147823 (1.05%) aligned concordantly >1 times ---- 13541430 pairs aligned concordantly 0 times; of these: 1169 (0.01%) aligned discordantly 1 time ---- 13540261 pairs aligned 0 times concordantly or discordantly; of these: 27080522 mates make up the pairs; of these: 26770126 (98.85%) aligned 0 times 55167 (0.20%) aligned exactly 1 time 255229 (0.94%) aligned >1 times 4.52% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 8771 / 477343 = 0.0184 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 05:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.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 05:39:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:39:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:40:03: 1000000 INFO @ Thu, 16 Apr 2020 05:40:04: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:40:04: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:40:04: #1 total tags in treatment: 468085 INFO @ Thu, 16 Apr 2020 05:40:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:40:04: #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 05:40:04: #1 tags after filtering in treatment: 459176 INFO @ Thu, 16 Apr 2020 05:40:04: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:40:04: #1 finished! INFO @ Thu, 16 Apr 2020 05:40:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:40:04: #2 number of paired peaks: 870 WARNING @ Thu, 16 Apr 2020 05:40:04: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Thu, 16 Apr 2020 05:40:04: start model_add_line... INFO @ Thu, 16 Apr 2020 05:40:04: start X-correlation... INFO @ Thu, 16 Apr 2020 05:40:04: end of X-cor INFO @ Thu, 16 Apr 2020 05:40:04: #2 finished! INFO @ Thu, 16 Apr 2020 05:40:04: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 05:40:04: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 05:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.05_model.r INFO @ Thu, 16 Apr 2020 05:40:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:40:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:40:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:40:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:40:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.05_summits.bed INFO @ Thu, 16 Apr 2020 05:40:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (87 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 @ Thu, 16 Apr 2020 05:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.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 05:40:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:40:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:40:34: 1000000 INFO @ Thu, 16 Apr 2020 05:40:35: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:40:35: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:40:35: #1 total tags in treatment: 468085 INFO @ Thu, 16 Apr 2020 05:40:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:40:35: #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 05:40:35: #1 tags after filtering in treatment: 459176 INFO @ Thu, 16 Apr 2020 05:40:35: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:40:35: #1 finished! INFO @ Thu, 16 Apr 2020 05:40:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:40:35: #2 number of paired peaks: 870 WARNING @ Thu, 16 Apr 2020 05:40:35: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Thu, 16 Apr 2020 05:40:35: start model_add_line... INFO @ Thu, 16 Apr 2020 05:40:35: start X-correlation... INFO @ Thu, 16 Apr 2020 05:40:35: end of X-cor INFO @ Thu, 16 Apr 2020 05:40:35: #2 finished! INFO @ Thu, 16 Apr 2020 05:40:35: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 05:40:35: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 05:40:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.10_model.r INFO @ Thu, 16 Apr 2020 05:40:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:40:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:40:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:40:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:40:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:40:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.10_summits.bed INFO @ Thu, 16 Apr 2020 05:40:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (58 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 05:40:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.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 05:40:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:40:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:41:03: 1000000 INFO @ Thu, 16 Apr 2020 05:41:04: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:41:04: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:41:04: #1 total tags in treatment: 468085 INFO @ Thu, 16 Apr 2020 05:41:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:41:04: #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 05:41:04: #1 tags after filtering in treatment: 459176 INFO @ Thu, 16 Apr 2020 05:41:04: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:41:04: #1 finished! INFO @ Thu, 16 Apr 2020 05:41:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:41:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:41:04: #2 number of paired peaks: 870 WARNING @ Thu, 16 Apr 2020 05:41:04: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Thu, 16 Apr 2020 05:41:04: start model_add_line... INFO @ Thu, 16 Apr 2020 05:41:04: start X-correlation... INFO @ Thu, 16 Apr 2020 05:41:04: end of X-cor INFO @ Thu, 16 Apr 2020 05:41:04: #2 finished! INFO @ Thu, 16 Apr 2020 05:41:04: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 05:41:04: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 05:41:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.20_model.r INFO @ Thu, 16 Apr 2020 05:41:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:41:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762289/SRX6762289.20_summits.bed INFO @ Thu, 16 Apr 2020 05:41:05: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 0 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。