Job ID = 5721185 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,121,877 reads read : 6,243,754 reads written : 6,243,754 spots read : 3,088,649 reads read : 6,177,298 reads written : 6,177,298 spots read : 3,069,089 reads read : 6,138,178 reads written : 6,138,178 spots read : 3,061,941 reads read : 6,123,882 reads written : 6,123,882 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: 00:04:51 12341556 reads; of these: 12341556 (100.00%) were paired; of these: 10643396 (86.24%) aligned concordantly 0 times 1223016 (9.91%) aligned concordantly exactly 1 time 475144 (3.85%) aligned concordantly >1 times ---- 10643396 pairs aligned concordantly 0 times; of these: 6860 (0.06%) aligned discordantly 1 time ---- 10636536 pairs aligned 0 times concordantly or discordantly; of these: 21273072 mates make up the pairs; of these: 20789454 (97.73%) aligned 0 times 183977 (0.86%) aligned exactly 1 time 299641 (1.41%) aligned >1 times 15.77% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 32781 / 1699850 = 0.0193 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 05:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.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 05:45:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:45:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:45:28: 1000000 INFO @ Thu, 16 Apr 2020 05:45:33: 2000000 INFO @ Thu, 16 Apr 2020 05:45:37: 3000000 INFO @ Thu, 16 Apr 2020 05:45:41: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:45:41: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:45:41: #1 total tags in treatment: 1665409 INFO @ Thu, 16 Apr 2020 05:45:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:45:41: #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 05:45:41: #1 tags after filtering in treatment: 1620740 INFO @ Thu, 16 Apr 2020 05:45:41: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:45:41: #1 finished! INFO @ Thu, 16 Apr 2020 05:45:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:45:42: #2 number of paired peaks: 725 WARNING @ Thu, 16 Apr 2020 05:45:42: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Thu, 16 Apr 2020 05:45:42: start model_add_line... INFO @ Thu, 16 Apr 2020 05:45:42: start X-correlation... INFO @ Thu, 16 Apr 2020 05:45:42: end of X-cor INFO @ Thu, 16 Apr 2020 05:45:42: #2 finished! INFO @ Thu, 16 Apr 2020 05:45:42: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 05:45:42: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 05:45:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.05_model.r INFO @ Thu, 16 Apr 2020 05:45:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:45:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:45:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.05_summits.bed INFO @ Thu, 16 Apr 2020 05:45:47: Done! 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 pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (293 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.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 05:45:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:45:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:45:57: 1000000 INFO @ Thu, 16 Apr 2020 05:46:02: 2000000 INFO @ Thu, 16 Apr 2020 05:46:07: 3000000 INFO @ Thu, 16 Apr 2020 05:46:11: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:46:11: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:46:11: #1 total tags in treatment: 1665409 INFO @ Thu, 16 Apr 2020 05:46:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:46:11: #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 05:46:11: #1 tags after filtering in treatment: 1620740 INFO @ Thu, 16 Apr 2020 05:46:11: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:46:11: #1 finished! INFO @ Thu, 16 Apr 2020 05:46:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:46:11: #2 number of paired peaks: 725 WARNING @ Thu, 16 Apr 2020 05:46:11: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Thu, 16 Apr 2020 05:46:11: start model_add_line... INFO @ Thu, 16 Apr 2020 05:46:11: start X-correlation... INFO @ Thu, 16 Apr 2020 05:46:11: end of X-cor INFO @ Thu, 16 Apr 2020 05:46:11: #2 finished! INFO @ Thu, 16 Apr 2020 05:46:11: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 05:46:11: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 05:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.10_model.r INFO @ Thu, 16 Apr 2020 05:46:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:46:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.10_summits.bed INFO @ Thu, 16 Apr 2020 05:46:16: Done! 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 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.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 05:46:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:46:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:46:28: 1000000 INFO @ Thu, 16 Apr 2020 05:46:33: 2000000 INFO @ Thu, 16 Apr 2020 05:46:37: 3000000 INFO @ Thu, 16 Apr 2020 05:46:41: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:46:41: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:46:41: #1 total tags in treatment: 1665409 INFO @ Thu, 16 Apr 2020 05:46:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:46:41: #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 05:46:41: #1 tags after filtering in treatment: 1620740 INFO @ Thu, 16 Apr 2020 05:46:41: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:46:41: #1 finished! INFO @ Thu, 16 Apr 2020 05:46:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:46:41: #2 number of paired peaks: 725 WARNING @ Thu, 16 Apr 2020 05:46:41: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Thu, 16 Apr 2020 05:46:41: start model_add_line... INFO @ Thu, 16 Apr 2020 05:46:41: start X-correlation... INFO @ Thu, 16 Apr 2020 05:46:41: end of X-cor INFO @ Thu, 16 Apr 2020 05:46:41: #2 finished! INFO @ Thu, 16 Apr 2020 05:46:41: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 05:46:41: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 05:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.20_model.r INFO @ Thu, 16 Apr 2020 05:46:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:46:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:46:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:46:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:46:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762294/SRX6762294.20_summits.bed INFO @ Thu, 16 Apr 2020 05:46:47: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (51 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。