Job ID = 14170430 SRX = SRX8784759 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6804801 spots for SRR12280889/SRR12280889.sra Written 6804801 spots for SRR12280889/SRR12280889.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170836 ("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: 00:03:07 6804801 reads; of these: 6804801 (100.00%) were unpaired; of these: 303098 (4.45%) aligned 0 times 6155883 (90.46%) aligned exactly 1 time 345820 (5.08%) aligned >1 times 95.55% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 383036 / 6501703 = 0.0589 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 06:53:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.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 06:53:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:53:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:53:58: 1000000 INFO @ Sat, 11 Dec 2021 06:54:10: 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 06:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.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 06:54:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:54:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:54:22: 3000000 INFO @ Sat, 11 Dec 2021 06:54:26: 1000000 INFO @ Sat, 11 Dec 2021 06:54:34: 4000000 INFO @ Sat, 11 Dec 2021 06:54:35: 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 06:54:44: 3000000 INFO @ Sat, 11 Dec 2021 06:54:45: 5000000 INFO @ Sat, 11 Dec 2021 06:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.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 06:54:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:54:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:54:53: 4000000 INFO @ Sat, 11 Dec 2021 06:54:57: 6000000 INFO @ Sat, 11 Dec 2021 06:54:59: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:54:59: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:54:59: #1 total tags in treatment: 6118667 INFO @ Sat, 11 Dec 2021 06:54:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:54:59: #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 06:54:59: 1000000 INFO @ Sat, 11 Dec 2021 06:54:59: #1 tags after filtering in treatment: 6118667 INFO @ Sat, 11 Dec 2021 06:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:54:59: #1 finished! INFO @ Sat, 11 Dec 2021 06:54:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:54:59: #2 number of paired peaks: 651 WARNING @ Sat, 11 Dec 2021 06:54:59: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Sat, 11 Dec 2021 06:54:59: start model_add_line... INFO @ Sat, 11 Dec 2021 06:55:00: start X-correlation... INFO @ Sat, 11 Dec 2021 06:55:00: end of X-cor INFO @ Sat, 11 Dec 2021 06:55:00: #2 finished! INFO @ Sat, 11 Dec 2021 06:55:00: #2 predicted fragment length is 242 bps INFO @ Sat, 11 Dec 2021 06:55:00: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 11 Dec 2021 06:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.05_model.r INFO @ Sat, 11 Dec 2021 06:55:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:55:02: 5000000 INFO @ Sat, 11 Dec 2021 06:55:11: 2000000 INFO @ Sat, 11 Dec 2021 06:55:11: 6000000 INFO @ Sat, 11 Dec 2021 06:55:13: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:55:13: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:55:13: #1 total tags in treatment: 6118667 INFO @ Sat, 11 Dec 2021 06:55:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:55:13: #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 06:55:13: #1 tags after filtering in treatment: 6118667 INFO @ Sat, 11 Dec 2021 06:55:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:55:13: #1 finished! INFO @ Sat, 11 Dec 2021 06:55:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:55:13: #2 number of paired peaks: 651 WARNING @ Sat, 11 Dec 2021 06:55:13: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Sat, 11 Dec 2021 06:55:13: start model_add_line... INFO @ Sat, 11 Dec 2021 06:55:13: start X-correlation... INFO @ Sat, 11 Dec 2021 06:55:13: end of X-cor INFO @ Sat, 11 Dec 2021 06:55:13: #2 finished! INFO @ Sat, 11 Dec 2021 06:55:13: #2 predicted fragment length is 242 bps INFO @ Sat, 11 Dec 2021 06:55:13: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 11 Dec 2021 06:55:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.10_model.r INFO @ Sat, 11 Dec 2021 06:55:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:55:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:55:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:55:23: 3000000 INFO @ Sat, 11 Dec 2021 06:55:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:55:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:55:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.05_summits.bed INFO @ Sat, 11 Dec 2021 06:55:29: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (4072 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:55:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:55:34: 4000000 INFO @ Sat, 11 Dec 2021 06:55:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:55:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.10_summits.bed INFO @ Sat, 11 Dec 2021 06:55:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1697 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:55:46: 5000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:55:57: 6000000 INFO @ Sat, 11 Dec 2021 06:55:59: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:55:59: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:55:59: #1 total tags in treatment: 6118667 INFO @ Sat, 11 Dec 2021 06:55:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:55:59: #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 06:55:59: #1 tags after filtering in treatment: 6118667 INFO @ Sat, 11 Dec 2021 06:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:55:59: #1 finished! INFO @ Sat, 11 Dec 2021 06:55:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:55:59: #2 number of paired peaks: 651 WARNING @ Sat, 11 Dec 2021 06:55:59: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Sat, 11 Dec 2021 06:55:59: start model_add_line... INFO @ Sat, 11 Dec 2021 06:55:59: start X-correlation... INFO @ Sat, 11 Dec 2021 06:55:59: end of X-cor INFO @ Sat, 11 Dec 2021 06:55:59: #2 finished! INFO @ Sat, 11 Dec 2021 06:55:59: #2 predicted fragment length is 242 bps INFO @ Sat, 11 Dec 2021 06:55:59: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 11 Dec 2021 06:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.20_model.r INFO @ Sat, 11 Dec 2021 06:56:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:56:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784759/SRX8784759.20_summits.bed INFO @ Sat, 11 Dec 2021 06:56:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 3 millis CompletedMACS2peakCalling