Job ID = 5720570 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,980,849 reads read : 13,980,849 reads written : 13,980,849 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289707.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: 00:04:14 13980849 reads; of these: 13980849 (100.00%) were unpaired; of these: 1057076 (7.56%) aligned 0 times 10340548 (73.96%) aligned exactly 1 time 2583225 (18.48%) aligned >1 times 92.44% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2867249 / 12923773 = 0.2219 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 00:40:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.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 00:40:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:36: 1000000 INFO @ Thu, 16 Apr 2020 00:40:42: 2000000 INFO @ Thu, 16 Apr 2020 00:40:47: 3000000 INFO @ Thu, 16 Apr 2020 00:40:52: 4000000 INFO @ Thu, 16 Apr 2020 00:40:58: 5000000 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/SRX2592430/SRX2592430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.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 00:41:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:41:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:41:03: 6000000 INFO @ Thu, 16 Apr 2020 00:41:07: 1000000 INFO @ Thu, 16 Apr 2020 00:41:09: 7000000 INFO @ Thu, 16 Apr 2020 00:41:13: 2000000 INFO @ Thu, 16 Apr 2020 00:41:15: 8000000 INFO @ Thu, 16 Apr 2020 00:41:19: 3000000 INFO @ Thu, 16 Apr 2020 00:41:20: 9000000 INFO @ Thu, 16 Apr 2020 00:41:25: 4000000 INFO @ Thu, 16 Apr 2020 00:41:26: 10000000 INFO @ Thu, 16 Apr 2020 00:41:26: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:41:26: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:41:26: #1 total tags in treatment: 10056524 INFO @ Thu, 16 Apr 2020 00:41:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:26: #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 00:41:26: #1 tags after filtering in treatment: 10056524 INFO @ Thu, 16 Apr 2020 00:41:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:26: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:27: #2 number of paired peaks: 114 WARNING @ Thu, 16 Apr 2020 00:41:27: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:27: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:27: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:27: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:27: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:27: #2 predicted fragment length is 298 bps INFO @ Thu, 16 Apr 2020 00:41:27: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 16 Apr 2020 00:41:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.05_model.r INFO @ Thu, 16 Apr 2020 00:41:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:27: #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 00:41:31: 5000000 INFO @ Thu, 16 Apr 2020 00:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.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 00:41:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:41:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:41:36: 1000000 INFO @ Thu, 16 Apr 2020 00:41:37: 6000000 INFO @ Thu, 16 Apr 2020 00:41:42: 2000000 INFO @ Thu, 16 Apr 2020 00:41:43: 7000000 INFO @ Thu, 16 Apr 2020 00:41:47: 3000000 INFO @ Thu, 16 Apr 2020 00:41:49: 8000000 INFO @ Thu, 16 Apr 2020 00:41:52: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:53: 4000000 INFO @ Thu, 16 Apr 2020 00:41:54: 9000000 INFO @ Thu, 16 Apr 2020 00:41:58: 5000000 INFO @ Thu, 16 Apr 2020 00:42:00: 10000000 INFO @ Thu, 16 Apr 2020 00:42:01: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:42:01: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:42:01: #1 total tags in treatment: 10056524 INFO @ Thu, 16 Apr 2020 00:42:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:42:01: #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 00:42:01: #1 tags after filtering in treatment: 10056524 INFO @ Thu, 16 Apr 2020 00:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:42:01: #1 finished! INFO @ Thu, 16 Apr 2020 00:42:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:42:02: #2 number of paired peaks: 114 WARNING @ Thu, 16 Apr 2020 00:42:02: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Thu, 16 Apr 2020 00:42:02: start model_add_line... INFO @ Thu, 16 Apr 2020 00:42:02: start X-correlation... INFO @ Thu, 16 Apr 2020 00:42:02: end of X-cor INFO @ Thu, 16 Apr 2020 00:42:02: #2 finished! INFO @ Thu, 16 Apr 2020 00:42:02: #2 predicted fragment length is 298 bps INFO @ Thu, 16 Apr 2020 00:42:02: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 16 Apr 2020 00:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.10_model.r INFO @ Thu, 16 Apr 2020 00:42:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:42:04: 6000000 INFO @ Thu, 16 Apr 2020 00:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.05_summits.bed INFO @ Thu, 16 Apr 2020 00:42:05: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12778 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:42:09: 7000000 INFO @ Thu, 16 Apr 2020 00:42:14: 8000000 INFO @ Thu, 16 Apr 2020 00:42:19: 9000000 INFO @ Thu, 16 Apr 2020 00:42:24: 10000000 INFO @ Thu, 16 Apr 2020 00:42:24: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:42:24: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:42:24: #1 total tags in treatment: 10056524 INFO @ Thu, 16 Apr 2020 00:42:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:42:24: #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 00:42:24: #1 tags after filtering in treatment: 10056524 INFO @ Thu, 16 Apr 2020 00:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:42:24: #1 finished! INFO @ Thu, 16 Apr 2020 00:42:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:42:25: #2 number of paired peaks: 114 WARNING @ Thu, 16 Apr 2020 00:42:25: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Thu, 16 Apr 2020 00:42:25: start model_add_line... INFO @ Thu, 16 Apr 2020 00:42:25: start X-correlation... INFO @ Thu, 16 Apr 2020 00:42:25: end of X-cor INFO @ Thu, 16 Apr 2020 00:42:25: #2 finished! INFO @ Thu, 16 Apr 2020 00:42:25: #2 predicted fragment length is 298 bps INFO @ Thu, 16 Apr 2020 00:42:25: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 16 Apr 2020 00:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.20_model.r INFO @ Thu, 16 Apr 2020 00:42:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:42:26: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.10_summits.bed INFO @ Thu, 16 Apr 2020 00:42:40: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8475 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:42:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:43:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:43:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:43:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592430/SRX2592430.20_summits.bed INFO @ Thu, 16 Apr 2020 00:43:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4814 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。