Job ID = 5720584 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,095,293 reads read : 10,095,293 reads written : 10,095,293 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289714.sra.cache’: 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: 00:02:41 10095293 reads; of these: 10095293 (100.00%) were unpaired; of these: 944574 (9.36%) aligned 0 times 8131741 (80.55%) aligned exactly 1 time 1018978 (10.09%) aligned >1 times 90.64% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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_rmdupse_core] 4779600 / 9150719 = 0.5223 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 00:40:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.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 00:40:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:06: 1000000 INFO @ Thu, 16 Apr 2020 00:40:12: 2000000 INFO @ Thu, 16 Apr 2020 00:40:17: 3000000 INFO @ Thu, 16 Apr 2020 00:40:22: 4000000 INFO @ Thu, 16 Apr 2020 00:40:24: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:40:24: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:40:24: #1 total tags in treatment: 4371119 INFO @ Thu, 16 Apr 2020 00:40:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:24: #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 00:40:24: #1 tags after filtering in treatment: 4371119 INFO @ Thu, 16 Apr 2020 00:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:24: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:25: #2 number of paired peaks: 320 WARNING @ Thu, 16 Apr 2020 00:40:25: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 16 Apr 2020 00:40:25: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:25: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:25: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:25: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:25: #2 predicted fragment length is 215 bps INFO @ Thu, 16 Apr 2020 00:40:25: #2 alternative fragment length(s) may be 215 bps INFO @ Thu, 16 Apr 2020 00:40:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.05_model.r INFO @ Thu, 16 Apr 2020 00:40:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:25: #3 Pre-compute pvalue-qvalue table... 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 00:40:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.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 00:40:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:36: 1000000 INFO @ Thu, 16 Apr 2020 00:40:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:40:42: 2000000 INFO @ Thu, 16 Apr 2020 00:40:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:40:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:40:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.05_summits.bed INFO @ Thu, 16 Apr 2020 00:40:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14823 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:40:47: 3000000 INFO @ Thu, 16 Apr 2020 00:40:53: 4000000 INFO @ Thu, 16 Apr 2020 00:40:55: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:40:55: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:40:55: #1 total tags in treatment: 4371119 INFO @ Thu, 16 Apr 2020 00:40:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:55: #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 00:40:55: #1 tags after filtering in treatment: 4371119 INFO @ Thu, 16 Apr 2020 00:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:55: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:56: #2 number of paired peaks: 320 WARNING @ Thu, 16 Apr 2020 00:40:56: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 16 Apr 2020 00:40:56: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:56: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:56: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:56: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:56: #2 predicted fragment length is 215 bps INFO @ Thu, 16 Apr 2020 00:40:56: #2 alternative fragment length(s) may be 215 bps INFO @ Thu, 16 Apr 2020 00:40:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.10_model.r INFO @ Thu, 16 Apr 2020 00:40:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:56: #3 Pre-compute pvalue-qvalue table... 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 00:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.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 00:41:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:41:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:41:07: 1000000 INFO @ Thu, 16 Apr 2020 00:41:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:12: 2000000 INFO @ Thu, 16 Apr 2020 00:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.10_summits.bed INFO @ Thu, 16 Apr 2020 00:41:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (12549 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:41:18: 3000000 INFO @ Thu, 16 Apr 2020 00:41:23: 4000000 INFO @ Thu, 16 Apr 2020 00:41:25: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:41:25: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:41:25: #1 total tags in treatment: 4371119 INFO @ Thu, 16 Apr 2020 00:41:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:25: #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 00:41:25: #1 tags after filtering in treatment: 4371119 INFO @ Thu, 16 Apr 2020 00:41:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:25: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:26: #2 number of paired peaks: 320 WARNING @ Thu, 16 Apr 2020 00:41:26: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:26: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:26: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:26: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:26: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:26: #2 predicted fragment length is 215 bps INFO @ Thu, 16 Apr 2020 00:41:26: #2 alternative fragment length(s) may be 215 bps INFO @ Thu, 16 Apr 2020 00:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.20_model.r INFO @ Thu, 16 Apr 2020 00:41:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:38: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592437/SRX2592437.20_summits.bed INFO @ Thu, 16 Apr 2020 00:41:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9779 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。