Job ID = 5721287 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,310,459 reads read : 38,620,918 reads written : 19,310,459 reads 0-length : 19,310,459 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: 00:05:56 19310459 reads; of these: 19310459 (100.00%) were unpaired; of these: 714374 (3.70%) aligned 0 times 14822406 (76.76%) aligned exactly 1 time 3773679 (19.54%) aligned >1 times 96.30% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 2855512 / 18596085 = 0.1536 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 06:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.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 06:27:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:27:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:28:04: 1000000 INFO @ Thu, 16 Apr 2020 06:28:10: 2000000 INFO @ Thu, 16 Apr 2020 06:28:15: 3000000 INFO @ Thu, 16 Apr 2020 06:28:21: 4000000 INFO @ Thu, 16 Apr 2020 06:28:27: 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 06:28:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.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 06:28:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:28:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:28:33: 6000000 INFO @ Thu, 16 Apr 2020 06:28:36: 1000000 INFO @ Thu, 16 Apr 2020 06:28:40: 7000000 INFO @ Thu, 16 Apr 2020 06:28:43: 2000000 INFO @ Thu, 16 Apr 2020 06:28:46: 8000000 INFO @ Thu, 16 Apr 2020 06:28:49: 3000000 INFO @ Thu, 16 Apr 2020 06:28:53: 9000000 INFO @ Thu, 16 Apr 2020 06:28:56: 4000000 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 06:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.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 06:28:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:28:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:28:59: 10000000 INFO @ Thu, 16 Apr 2020 06:29:03: 5000000 INFO @ Thu, 16 Apr 2020 06:29:06: 11000000 INFO @ Thu, 16 Apr 2020 06:29:06: 1000000 INFO @ Thu, 16 Apr 2020 06:29:10: 6000000 INFO @ Thu, 16 Apr 2020 06:29:13: 12000000 INFO @ Thu, 16 Apr 2020 06:29:14: 2000000 INFO @ Thu, 16 Apr 2020 06:29:17: 7000000 INFO @ Thu, 16 Apr 2020 06:29:20: 13000000 INFO @ Thu, 16 Apr 2020 06:29:22: 3000000 INFO @ Thu, 16 Apr 2020 06:29:24: 8000000 INFO @ Thu, 16 Apr 2020 06:29:27: 14000000 INFO @ Thu, 16 Apr 2020 06:29:29: 4000000 INFO @ Thu, 16 Apr 2020 06:29:31: 9000000 INFO @ Thu, 16 Apr 2020 06:29:34: 15000000 INFO @ Thu, 16 Apr 2020 06:29:37: 5000000 INFO @ Thu, 16 Apr 2020 06:29:38: 10000000 INFO @ Thu, 16 Apr 2020 06:29:39: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:29:39: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:29:39: #1 total tags in treatment: 15740573 INFO @ Thu, 16 Apr 2020 06:29:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:29:39: #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 06:29:40: #1 tags after filtering in treatment: 15740573 INFO @ Thu, 16 Apr 2020 06:29:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:29:40: #1 finished! INFO @ Thu, 16 Apr 2020 06:29:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:29:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:29:41: #2 number of paired peaks: 276 WARNING @ Thu, 16 Apr 2020 06:29:41: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Thu, 16 Apr 2020 06:29:41: start model_add_line... INFO @ Thu, 16 Apr 2020 06:29:41: start X-correlation... INFO @ Thu, 16 Apr 2020 06:29:41: end of X-cor INFO @ Thu, 16 Apr 2020 06:29:41: #2 finished! INFO @ Thu, 16 Apr 2020 06:29:41: #2 predicted fragment length is 162 bps INFO @ Thu, 16 Apr 2020 06:29:41: #2 alternative fragment length(s) may be 162 bps INFO @ Thu, 16 Apr 2020 06:29:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.05_model.r INFO @ Thu, 16 Apr 2020 06:29:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:29:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:29:44: 11000000 INFO @ Thu, 16 Apr 2020 06:29:45: 6000000 INFO @ Thu, 16 Apr 2020 06:29:51: 12000000 INFO @ Thu, 16 Apr 2020 06:29:53: 7000000 INFO @ Thu, 16 Apr 2020 06:29:58: 13000000 INFO @ Thu, 16 Apr 2020 06:30:00: 8000000 INFO @ Thu, 16 Apr 2020 06:30:04: 14000000 INFO @ Thu, 16 Apr 2020 06:30:08: 9000000 INFO @ Thu, 16 Apr 2020 06:30:11: 15000000 INFO @ Thu, 16 Apr 2020 06:30:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:30:15: 10000000 INFO @ Thu, 16 Apr 2020 06:30:16: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:30:16: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:30:16: #1 total tags in treatment: 15740573 INFO @ Thu, 16 Apr 2020 06:30:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:30:16: #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 06:30:16: #1 tags after filtering in treatment: 15740573 INFO @ Thu, 16 Apr 2020 06:30:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:30:16: #1 finished! INFO @ Thu, 16 Apr 2020 06:30:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:30:17: #2 number of paired peaks: 276 WARNING @ Thu, 16 Apr 2020 06:30:17: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Thu, 16 Apr 2020 06:30:17: start model_add_line... INFO @ Thu, 16 Apr 2020 06:30:17: start X-correlation... INFO @ Thu, 16 Apr 2020 06:30:17: end of X-cor INFO @ Thu, 16 Apr 2020 06:30:17: #2 finished! INFO @ Thu, 16 Apr 2020 06:30:17: #2 predicted fragment length is 162 bps INFO @ Thu, 16 Apr 2020 06:30:17: #2 alternative fragment length(s) may be 162 bps INFO @ Thu, 16 Apr 2020 06:30:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.10_model.r INFO @ Thu, 16 Apr 2020 06:30:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:30:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:30:22: 11000000 INFO @ Thu, 16 Apr 2020 06:30:29: 12000000 INFO @ Thu, 16 Apr 2020 06:30:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:30:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:30:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.05_summits.bed INFO @ Thu, 16 Apr 2020 06:30:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5250 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:30:36: 13000000 INFO @ Thu, 16 Apr 2020 06:30:43: 14000000 INFO @ Thu, 16 Apr 2020 06:30:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:30:50: 15000000 INFO @ Thu, 16 Apr 2020 06:30:55: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:30:55: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:30:55: #1 total tags in treatment: 15740573 INFO @ Thu, 16 Apr 2020 06:30:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:30:55: #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 06:30:55: #1 tags after filtering in treatment: 15740573 INFO @ Thu, 16 Apr 2020 06:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:30:55: #1 finished! INFO @ Thu, 16 Apr 2020 06:30:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:30:56: #2 number of paired peaks: 276 WARNING @ Thu, 16 Apr 2020 06:30:56: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Thu, 16 Apr 2020 06:30:56: start model_add_line... INFO @ Thu, 16 Apr 2020 06:30:56: start X-correlation... INFO @ Thu, 16 Apr 2020 06:30:56: end of X-cor INFO @ Thu, 16 Apr 2020 06:30:56: #2 finished! INFO @ Thu, 16 Apr 2020 06:30:56: #2 predicted fragment length is 162 bps INFO @ Thu, 16 Apr 2020 06:30:56: #2 alternative fragment length(s) may be 162 bps INFO @ Thu, 16 Apr 2020 06:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.20_model.r INFO @ Thu, 16 Apr 2020 06:30:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.10_summits.bed INFO @ Thu, 16 Apr 2020 06:31:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3115 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:31:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:31:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:31:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299243/SRX7299243.20_summits.bed INFO @ Thu, 16 Apr 2020 06:31:47: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1613 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。