Job ID = 5720627 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,401,785 reads read : 14,401,785 reads written : 14,401,785 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289733.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:41 14401785 reads; of these: 14401785 (100.00%) were unpaired; of these: 1560798 (10.84%) aligned 0 times 7298989 (50.68%) aligned exactly 1 time 5541998 (38.48%) aligned >1 times 89.16% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 3837267 / 12840987 = 0.2988 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 00:54:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.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 00:54:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:04: 1000000 INFO @ Thu, 16 Apr 2020 00:55:10: 2000000 INFO @ Thu, 16 Apr 2020 00:55:16: 3000000 INFO @ Thu, 16 Apr 2020 00:55:21: 4000000 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 00:55:27: 5000000 INFO @ Thu, 16 Apr 2020 00:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.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 00:55:29: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:29: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:33: 6000000 INFO @ Thu, 16 Apr 2020 00:55:36: 1000000 INFO @ Thu, 16 Apr 2020 00:55:40: 7000000 INFO @ Thu, 16 Apr 2020 00:55:43: 2000000 INFO @ Thu, 16 Apr 2020 00:55:46: 8000000 INFO @ Thu, 16 Apr 2020 00:55:50: 3000000 INFO @ Thu, 16 Apr 2020 00:55:52: 9000000 INFO @ Thu, 16 Apr 2020 00:55:52: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:52: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:52: #1 total tags in treatment: 9003720 INFO @ Thu, 16 Apr 2020 00:55:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:52: #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 00:55:53: #1 tags after filtering in treatment: 9003720 INFO @ Thu, 16 Apr 2020 00:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:53: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:53: #2 number of paired peaks: 420 WARNING @ Thu, 16 Apr 2020 00:55:53: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 16 Apr 2020 00:55:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:53: #2 predicted fragment length is 114 bps INFO @ Thu, 16 Apr 2020 00:55:53: #2 alternative fragment length(s) may be 114 bps INFO @ Thu, 16 Apr 2020 00:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.05_model.r INFO @ Thu, 16 Apr 2020 00:55:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:53: #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 00:55:57: 4000000 INFO @ Thu, 16 Apr 2020 00:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.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 00:55:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:56:04: 5000000 INFO @ Thu, 16 Apr 2020 00:56:06: 1000000 INFO @ Thu, 16 Apr 2020 00:56:11: 6000000 INFO @ Thu, 16 Apr 2020 00:56:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:13: 2000000 INFO @ Thu, 16 Apr 2020 00:56:19: 7000000 INFO @ Thu, 16 Apr 2020 00:56:20: 3000000 INFO @ Thu, 16 Apr 2020 00:56:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.05_summits.bed INFO @ Thu, 16 Apr 2020 00:56:24: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (17676 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:56:26: 8000000 INFO @ Thu, 16 Apr 2020 00:56:27: 4000000 INFO @ Thu, 16 Apr 2020 00:56:33: 9000000 INFO @ Thu, 16 Apr 2020 00:56:33: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:33: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:33: #1 total tags in treatment: 9003720 INFO @ Thu, 16 Apr 2020 00:56:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:33: #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 00:56:33: #1 tags after filtering in treatment: 9003720 INFO @ Thu, 16 Apr 2020 00:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:33: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:34: 5000000 INFO @ Thu, 16 Apr 2020 00:56:34: #2 number of paired peaks: 420 WARNING @ Thu, 16 Apr 2020 00:56:34: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 16 Apr 2020 00:56:34: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:34: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:34: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:34: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:34: #2 predicted fragment length is 114 bps INFO @ Thu, 16 Apr 2020 00:56:34: #2 alternative fragment length(s) may be 114 bps INFO @ Thu, 16 Apr 2020 00:56:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.10_model.r INFO @ Thu, 16 Apr 2020 00:56:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:41: 6000000 INFO @ Thu, 16 Apr 2020 00:56:47: 7000000 INFO @ Thu, 16 Apr 2020 00:56:54: 8000000 INFO @ Thu, 16 Apr 2020 00:56:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:00: 9000000 INFO @ Thu, 16 Apr 2020 00:57:00: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:57:00: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:57:00: #1 total tags in treatment: 9003720 INFO @ Thu, 16 Apr 2020 00:57:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:57:00: #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 00:57:00: #1 tags after filtering in treatment: 9003720 INFO @ Thu, 16 Apr 2020 00:57:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:57:00: #1 finished! INFO @ Thu, 16 Apr 2020 00:57:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:57:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:57:01: #2 number of paired peaks: 420 WARNING @ Thu, 16 Apr 2020 00:57:01: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 16 Apr 2020 00:57:01: start model_add_line... INFO @ Thu, 16 Apr 2020 00:57:01: start X-correlation... INFO @ Thu, 16 Apr 2020 00:57:01: end of X-cor INFO @ Thu, 16 Apr 2020 00:57:01: #2 finished! INFO @ Thu, 16 Apr 2020 00:57:01: #2 predicted fragment length is 114 bps INFO @ Thu, 16 Apr 2020 00:57:01: #2 alternative fragment length(s) may be 114 bps INFO @ Thu, 16 Apr 2020 00:57:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.20_model.r INFO @ Thu, 16 Apr 2020 00:57:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:57:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.10_summits.bed INFO @ Thu, 16 Apr 2020 00:57:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11483 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:57:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592456/SRX2592456.20_summits.bed INFO @ Thu, 16 Apr 2020 00:57:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6634 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。