Job ID = 5721184 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,334,886 reads read : 8,669,772 reads written : 8,669,772 spots read : 4,255,088 reads read : 8,510,176 reads written : 8,510,176 spots read : 4,180,771 reads read : 8,361,542 reads written : 8,361,542 spots read : 4,178,092 reads read : 8,356,184 reads written : 8,356,184 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: 00:03:18 16948837 reads; of these: 16948837 (100.00%) were paired; of these: 16433630 (96.96%) aligned concordantly 0 times 344662 (2.03%) aligned concordantly exactly 1 time 170545 (1.01%) aligned concordantly >1 times ---- 16433630 pairs aligned concordantly 0 times; of these: 983 (0.01%) aligned discordantly 1 time ---- 16432647 pairs aligned 0 times concordantly or discordantly; of these: 32865294 mates make up the pairs; of these: 32503959 (98.90%) aligned 0 times 51451 (0.16%) aligned exactly 1 time 309884 (0.94%) aligned >1 times 4.11% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 10584 / 515587 = 0.0205 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 05:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.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 05:44:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:44:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:44:20: 1000000 INFO @ Thu, 16 Apr 2020 05:44:22: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:44:22: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:44:22: #1 total tags in treatment: 504627 INFO @ Thu, 16 Apr 2020 05:44:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:44:22: #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 05:44:22: #1 tags after filtering in treatment: 491850 INFO @ Thu, 16 Apr 2020 05:44:22: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:44:22: #1 finished! INFO @ Thu, 16 Apr 2020 05:44:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:44:22: #2 number of paired peaks: 1093 INFO @ Thu, 16 Apr 2020 05:44:22: start model_add_line... INFO @ Thu, 16 Apr 2020 05:44:22: start X-correlation... INFO @ Thu, 16 Apr 2020 05:44:22: end of X-cor INFO @ Thu, 16 Apr 2020 05:44:22: #2 finished! INFO @ Thu, 16 Apr 2020 05:44:22: #2 predicted fragment length is 95 bps INFO @ Thu, 16 Apr 2020 05:44:22: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 16 Apr 2020 05:44:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.05_model.r INFO @ Thu, 16 Apr 2020 05:44:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:44:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:44:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.05_summits.bed INFO @ Thu, 16 Apr 2020 05:44:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (114 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 05:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.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 05:44:45: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:44:45: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:44:50: 1000000 INFO @ Thu, 16 Apr 2020 05:44:52: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:44:52: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:44:52: #1 total tags in treatment: 504627 INFO @ Thu, 16 Apr 2020 05:44:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:44:52: #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 05:44:52: #1 tags after filtering in treatment: 491850 INFO @ Thu, 16 Apr 2020 05:44:52: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:44:52: #1 finished! INFO @ Thu, 16 Apr 2020 05:44:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:44:52: #2 number of paired peaks: 1093 INFO @ Thu, 16 Apr 2020 05:44:52: start model_add_line... INFO @ Thu, 16 Apr 2020 05:44:52: start X-correlation... INFO @ Thu, 16 Apr 2020 05:44:52: end of X-cor INFO @ Thu, 16 Apr 2020 05:44:52: #2 finished! INFO @ Thu, 16 Apr 2020 05:44:52: #2 predicted fragment length is 95 bps INFO @ Thu, 16 Apr 2020 05:44:52: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 16 Apr 2020 05:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.10_model.r INFO @ Thu, 16 Apr 2020 05:44:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:44:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:44:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:44:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:44:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.10_summits.bed INFO @ Thu, 16 Apr 2020 05:44:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (65 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 05:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.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 05:45:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:45:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:45:21: 1000000 INFO @ Thu, 16 Apr 2020 05:45:23: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:45:23: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:45:23: #1 total tags in treatment: 504627 INFO @ Thu, 16 Apr 2020 05:45:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:45:23: #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 05:45:23: #1 tags after filtering in treatment: 491850 INFO @ Thu, 16 Apr 2020 05:45:23: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:45:23: #1 finished! INFO @ Thu, 16 Apr 2020 05:45:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:45:23: #2 number of paired peaks: 1093 INFO @ Thu, 16 Apr 2020 05:45:23: start model_add_line... INFO @ Thu, 16 Apr 2020 05:45:23: start X-correlation... INFO @ Thu, 16 Apr 2020 05:45:23: end of X-cor INFO @ Thu, 16 Apr 2020 05:45:23: #2 finished! INFO @ Thu, 16 Apr 2020 05:45:23: #2 predicted fragment length is 95 bps INFO @ Thu, 16 Apr 2020 05:45:23: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 16 Apr 2020 05:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.20_model.r INFO @ Thu, 16 Apr 2020 05:45:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:45:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762293/SRX6762293.20_summits.bed INFO @ Thu, 16 Apr 2020 05:45:24: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (45 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。