Job ID = 5721135 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,436,138 reads read : 2,872,276 reads written : 2,872,276 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:01:57 1436138 reads; of these: 1436138 (100.00%) were paired; of these: 163156 (11.36%) aligned concordantly 0 times 1107023 (77.08%) aligned concordantly exactly 1 time 165959 (11.56%) aligned concordantly >1 times ---- 163156 pairs aligned concordantly 0 times; of these: 63099 (38.67%) aligned discordantly 1 time ---- 100057 pairs aligned 0 times concordantly or discordantly; of these: 200114 mates make up the pairs; of these: 119973 (59.95%) aligned 0 times 47087 (23.53%) aligned exactly 1 time 33054 (16.52%) aligned >1 times 95.82% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 51399 / 1333316 = 0.0385 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 05:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.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 05:14:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:14:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:14:23: 1000000 INFO @ Thu, 16 Apr 2020 05:14:31: 2000000 INFO @ Thu, 16 Apr 2020 05:14:35: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:14:35: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:14:35: #1 total tags in treatment: 1223434 INFO @ Thu, 16 Apr 2020 05:14:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:14:35: #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 05:14:35: #1 tags after filtering in treatment: 1204153 INFO @ Thu, 16 Apr 2020 05:14:35: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:14:35: #1 finished! INFO @ Thu, 16 Apr 2020 05:14:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:14:36: #2 number of paired peaks: 4638 INFO @ Thu, 16 Apr 2020 05:14:36: start model_add_line... INFO @ Thu, 16 Apr 2020 05:14:36: start X-correlation... INFO @ Thu, 16 Apr 2020 05:14:36: end of X-cor INFO @ Thu, 16 Apr 2020 05:14:36: #2 finished! INFO @ Thu, 16 Apr 2020 05:14:36: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 05:14:36: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 05:14:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.05_model.r INFO @ Thu, 16 Apr 2020 05:14:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:14:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:14:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:14:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:14:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.05_summits.bed INFO @ Thu, 16 Apr 2020 05:14:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (780 records, 4 fields): 2 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 05:14:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.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 05:14:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:14:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:14:53: 1000000 INFO @ Thu, 16 Apr 2020 05:15:00: 2000000 INFO @ Thu, 16 Apr 2020 05:15:05: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:15:05: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:15:05: #1 total tags in treatment: 1223434 INFO @ Thu, 16 Apr 2020 05:15:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:15:05: #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 05:15:05: #1 tags after filtering in treatment: 1204153 INFO @ Thu, 16 Apr 2020 05:15:05: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:15:05: #1 finished! INFO @ Thu, 16 Apr 2020 05:15:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:15:05: #2 number of paired peaks: 4638 INFO @ Thu, 16 Apr 2020 05:15:05: start model_add_line... INFO @ Thu, 16 Apr 2020 05:15:05: start X-correlation... INFO @ Thu, 16 Apr 2020 05:15:05: end of X-cor INFO @ Thu, 16 Apr 2020 05:15:05: #2 finished! INFO @ Thu, 16 Apr 2020 05:15:05: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 05:15:05: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 05:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.10_model.r INFO @ Thu, 16 Apr 2020 05:15:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:15:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:15:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.10_summits.bed INFO @ Thu, 16 Apr 2020 05:15:10: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (239 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 @ Thu, 16 Apr 2020 05:15:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.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 05:15:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:15:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:15:23: 1000000 INFO @ Thu, 16 Apr 2020 05:15:31: 2000000 INFO @ Thu, 16 Apr 2020 05:15:35: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:15:35: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:15:35: #1 total tags in treatment: 1223434 INFO @ Thu, 16 Apr 2020 05:15:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:15:35: #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 05:15:35: #1 tags after filtering in treatment: 1204153 INFO @ Thu, 16 Apr 2020 05:15:35: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:15:35: #1 finished! INFO @ Thu, 16 Apr 2020 05:15:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:15:35: #2 number of paired peaks: 4638 INFO @ Thu, 16 Apr 2020 05:15:35: start model_add_line... INFO @ Thu, 16 Apr 2020 05:15:35: start X-correlation... INFO @ Thu, 16 Apr 2020 05:15:35: end of X-cor INFO @ Thu, 16 Apr 2020 05:15:35: #2 finished! INFO @ Thu, 16 Apr 2020 05:15:35: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 05:15:35: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 05:15:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.20_model.r INFO @ Thu, 16 Apr 2020 05:15:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:15:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:15:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:15:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708276/SRX6708276.20_summits.bed INFO @ Thu, 16 Apr 2020 05:15:40: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (91 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。