Job ID = 5720967 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,915,615 reads read : 21,915,615 reads written : 21,915,615 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: 00:07:06 21915615 reads; of these: 21915615 (100.00%) were unpaired; of these: 2982735 (13.61%) aligned 0 times 13835329 (63.13%) aligned exactly 1 time 5097551 (23.26%) aligned >1 times 86.39% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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] 6041981 / 18932880 = 0.3191 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 03:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.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 03:51:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:51:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:51:48: 1000000 INFO @ Thu, 16 Apr 2020 03:51:54: 2000000 INFO @ Thu, 16 Apr 2020 03:51:59: 3000000 INFO @ Thu, 16 Apr 2020 03:52:05: 4000000 INFO @ Thu, 16 Apr 2020 03:52:10: 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 03:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.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 03:52:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:52:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:52:16: 6000000 INFO @ Thu, 16 Apr 2020 03:52:19: 1000000 INFO @ Thu, 16 Apr 2020 03:52:22: 7000000 INFO @ Thu, 16 Apr 2020 03:52:25: 2000000 INFO @ Thu, 16 Apr 2020 03:52:28: 8000000 INFO @ Thu, 16 Apr 2020 03:52:32: 3000000 INFO @ Thu, 16 Apr 2020 03:52:34: 9000000 INFO @ Thu, 16 Apr 2020 03:52:38: 4000000 INFO @ Thu, 16 Apr 2020 03:52:41: 10000000 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 03:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.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 03:52:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:52:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:52:44: 5000000 INFO @ Thu, 16 Apr 2020 03:52:47: 11000000 INFO @ Thu, 16 Apr 2020 03:52:50: 1000000 INFO @ Thu, 16 Apr 2020 03:52:51: 6000000 INFO @ Thu, 16 Apr 2020 03:52:54: 12000000 INFO @ Thu, 16 Apr 2020 03:52:57: 2000000 INFO @ Thu, 16 Apr 2020 03:52:58: 7000000 INFO @ Thu, 16 Apr 2020 03:53:00: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:53:00: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:53:00: #1 total tags in treatment: 12890899 INFO @ Thu, 16 Apr 2020 03:53:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:53:00: #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 03:53:00: #1 tags after filtering in treatment: 12890899 INFO @ Thu, 16 Apr 2020 03:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:53:00: #1 finished! INFO @ Thu, 16 Apr 2020 03:53:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:53:01: #2 number of paired peaks: 303 WARNING @ Thu, 16 Apr 2020 03:53:01: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 16 Apr 2020 03:53:01: start model_add_line... INFO @ Thu, 16 Apr 2020 03:53:01: start X-correlation... INFO @ Thu, 16 Apr 2020 03:53:01: end of X-cor INFO @ Thu, 16 Apr 2020 03:53:01: #2 finished! INFO @ Thu, 16 Apr 2020 03:53:01: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 03:53:01: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 03:53:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.05_model.r INFO @ Thu, 16 Apr 2020 03:53:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:53:04: 3000000 INFO @ Thu, 16 Apr 2020 03:53:04: 8000000 INFO @ Thu, 16 Apr 2020 03:53:11: 9000000 INFO @ Thu, 16 Apr 2020 03:53:11: 4000000 INFO @ Thu, 16 Apr 2020 03:53:17: 10000000 INFO @ Thu, 16 Apr 2020 03:53:19: 5000000 INFO @ Thu, 16 Apr 2020 03:53:24: 11000000 INFO @ Thu, 16 Apr 2020 03:53:26: 6000000 INFO @ Thu, 16 Apr 2020 03:53:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:53:30: 12000000 INFO @ Thu, 16 Apr 2020 03:53:33: 7000000 INFO @ Thu, 16 Apr 2020 03:53:36: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:53:36: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:53:36: #1 total tags in treatment: 12890899 INFO @ Thu, 16 Apr 2020 03:53:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:53:36: #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 03:53:36: #1 tags after filtering in treatment: 12890899 INFO @ Thu, 16 Apr 2020 03:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:53:36: #1 finished! INFO @ Thu, 16 Apr 2020 03:53:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:53:37: #2 number of paired peaks: 303 WARNING @ Thu, 16 Apr 2020 03:53:37: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 16 Apr 2020 03:53:37: start model_add_line... INFO @ Thu, 16 Apr 2020 03:53:37: start X-correlation... INFO @ Thu, 16 Apr 2020 03:53:37: end of X-cor INFO @ Thu, 16 Apr 2020 03:53:37: #2 finished! INFO @ Thu, 16 Apr 2020 03:53:37: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 03:53:37: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 03:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.10_model.r INFO @ Thu, 16 Apr 2020 03:53:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.05_summits.bed INFO @ Thu, 16 Apr 2020 03:53:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4171 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:53:40: 8000000 INFO @ Thu, 16 Apr 2020 03:53:47: 9000000 INFO @ Thu, 16 Apr 2020 03:53:53: 10000000 INFO @ Thu, 16 Apr 2020 03:54:00: 11000000 INFO @ Thu, 16 Apr 2020 03:54:02: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:54:07: 12000000 INFO @ Thu, 16 Apr 2020 03:54:12: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:54:12: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:54:12: #1 total tags in treatment: 12890899 INFO @ Thu, 16 Apr 2020 03:54:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:54:12: #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 03:54:13: #1 tags after filtering in treatment: 12890899 INFO @ Thu, 16 Apr 2020 03:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:54:13: #1 finished! INFO @ Thu, 16 Apr 2020 03:54:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:54:13: #2 number of paired peaks: 303 WARNING @ Thu, 16 Apr 2020 03:54:13: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 16 Apr 2020 03:54:13: start model_add_line... INFO @ Thu, 16 Apr 2020 03:54:13: start X-correlation... INFO @ Thu, 16 Apr 2020 03:54:14: end of X-cor INFO @ Thu, 16 Apr 2020 03:54:14: #2 finished! INFO @ Thu, 16 Apr 2020 03:54:14: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 03:54:14: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 03:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.20_model.r INFO @ Thu, 16 Apr 2020 03:54:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.10_summits.bed INFO @ Thu, 16 Apr 2020 03:54:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2564 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:54:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:54:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:54:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:54:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386760/SRX6386760.20_summits.bed INFO @ Thu, 16 Apr 2020 03:54:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1331 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。