Job ID = 14170422 SRX = SRX8784754 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5885452 spots for SRR12280884/SRR12280884.sra Written 5885452 spots for SRR12280884/SRR12280884.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170820 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:50 5885452 reads; of these: 5885452 (100.00%) were unpaired; of these: 371077 (6.30%) aligned 0 times 4937212 (83.89%) aligned exactly 1 time 577163 (9.81%) aligned >1 times 93.70% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 303920 / 5514375 = 0.0551 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.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 @ Sat, 11 Dec 2021 06:51:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:51:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:51:51: 1000000 INFO @ Sat, 11 Dec 2021 06:52:03: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.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 @ Sat, 11 Dec 2021 06:52:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:52:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:52:15: 3000000 INFO @ Sat, 11 Dec 2021 06:52:22: 1000000 INFO @ Sat, 11 Dec 2021 06:52:27: 4000000 INFO @ Sat, 11 Dec 2021 06:52:34: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.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 @ Sat, 11 Dec 2021 06:52:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:52:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:52:40: 5000000 INFO @ Sat, 11 Dec 2021 06:52:42: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:52:42: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:52:42: #1 total tags in treatment: 5210455 INFO @ Sat, 11 Dec 2021 06:52:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:52:42: #1 tags after filtering in treatment: 5210455 INFO @ Sat, 11 Dec 2021 06:52:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:42: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:42: #2 number of paired peaks: 583 WARNING @ Sat, 11 Dec 2021 06:52:42: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:42: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:43: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:43: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:43: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:43: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 06:52:43: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 06:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.05_model.r INFO @ Sat, 11 Dec 2021 06:52:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:52:47: 3000000 INFO @ Sat, 11 Dec 2021 06:52:52: 1000000 INFO @ Sat, 11 Dec 2021 06:52:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:52:59: 4000000 INFO @ Sat, 11 Dec 2021 06:53:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.05_summits.bed INFO @ Sat, 11 Dec 2021 06:53:02: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7202 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:53:04: 2000000 INFO @ Sat, 11 Dec 2021 06:53:12: 5000000 INFO @ Sat, 11 Dec 2021 06:53:14: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:53:14: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:53:14: #1 total tags in treatment: 5210455 INFO @ Sat, 11 Dec 2021 06:53:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:53:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:53:15: #1 tags after filtering in treatment: 5210455 INFO @ Sat, 11 Dec 2021 06:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:53:15: #1 finished! INFO @ Sat, 11 Dec 2021 06:53:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:53:15: #2 number of paired peaks: 583 WARNING @ Sat, 11 Dec 2021 06:53:15: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sat, 11 Dec 2021 06:53:15: start model_add_line... INFO @ Sat, 11 Dec 2021 06:53:15: start X-correlation... INFO @ Sat, 11 Dec 2021 06:53:15: end of X-cor INFO @ Sat, 11 Dec 2021 06:53:15: #2 finished! INFO @ Sat, 11 Dec 2021 06:53:15: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 06:53:15: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 06:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.10_model.r INFO @ Sat, 11 Dec 2021 06:53:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:53:17: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:53:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:29: 4000000 INFO @ Sat, 11 Dec 2021 06:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.10_summits.bed INFO @ Sat, 11 Dec 2021 06:53:34: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1856 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:53:41: 5000000 INFO @ Sat, 11 Dec 2021 06:53:43: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:53:43: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:53:43: #1 total tags in treatment: 5210455 INFO @ Sat, 11 Dec 2021 06:53:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:53:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:53:43: #1 tags after filtering in treatment: 5210455 INFO @ Sat, 11 Dec 2021 06:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:53:43: #1 finished! INFO @ Sat, 11 Dec 2021 06:53:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:53:43: #2 number of paired peaks: 583 WARNING @ Sat, 11 Dec 2021 06:53:43: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sat, 11 Dec 2021 06:53:43: start model_add_line... INFO @ Sat, 11 Dec 2021 06:53:43: start X-correlation... INFO @ Sat, 11 Dec 2021 06:53:43: end of X-cor INFO @ Sat, 11 Dec 2021 06:53:43: #2 finished! INFO @ Sat, 11 Dec 2021 06:53:43: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 06:53:43: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 06:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.20_model.r INFO @ Sat, 11 Dec 2021 06:53:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:53:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784754/SRX8784754.20_summits.bed INFO @ Sat, 11 Dec 2021 06:54:02: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling