Job ID = 14171369 SRX = SRX9986160 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13300114 spots for SRR13591515/SRR13591515.sra Written 13300114 spots for SRR13591515/SRR13591515.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171828 ("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 13300114 reads; of these: 13300114 (100.00%) were unpaired; of these: 3835047 (28.83%) aligned 0 times 7589425 (57.06%) aligned exactly 1 time 1875642 (14.10%) aligned >1 times 71.17% 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] 1672195 / 9465067 = 0.1767 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 11:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.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 11:32:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:32:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:32:08: 1000000 INFO @ Sat, 11 Dec 2021 11:32:13: 2000000 INFO @ Sat, 11 Dec 2021 11:32:18: 3000000 INFO @ Sat, 11 Dec 2021 11:32:24: 4000000 INFO @ Sat, 11 Dec 2021 11:32:29: 5000000 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 11:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.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 11:32:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:32:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:32:34: 6000000 INFO @ Sat, 11 Dec 2021 11:32:38: 1000000 INFO @ Sat, 11 Dec 2021 11:32:40: 7000000 INFO @ Sat, 11 Dec 2021 11:32:43: 2000000 INFO @ Sat, 11 Dec 2021 11:32:45: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:32:45: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:32:45: #1 total tags in treatment: 7792872 INFO @ Sat, 11 Dec 2021 11:32:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:32:45: #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 11:32:45: #1 tags after filtering in treatment: 7792872 INFO @ Sat, 11 Dec 2021 11:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:32:45: #1 finished! INFO @ Sat, 11 Dec 2021 11:32:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:32:45: #2 number of paired peaks: 687 WARNING @ Sat, 11 Dec 2021 11:32:45: Fewer paired peaks (687) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 687 pairs to build model! INFO @ Sat, 11 Dec 2021 11:32:45: start model_add_line... INFO @ Sat, 11 Dec 2021 11:32:45: start X-correlation... INFO @ Sat, 11 Dec 2021 11:32:45: end of X-cor INFO @ Sat, 11 Dec 2021 11:32:45: #2 finished! INFO @ Sat, 11 Dec 2021 11:32:45: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 11:32:45: #2 alternative fragment length(s) may be 1,170,195,247 bps INFO @ Sat, 11 Dec 2021 11:32:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.05_model.r INFO @ Sat, 11 Dec 2021 11:32:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:32:49: 3000000 INFO @ Sat, 11 Dec 2021 11:32:54: 4000000 INFO @ Sat, 11 Dec 2021 11:33:00: 5000000 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 11:33:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.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 11:33:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:33:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:33:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:33:05: 6000000 INFO @ Sat, 11 Dec 2021 11:33:07: 1000000 INFO @ Sat, 11 Dec 2021 11:33:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:33:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:33:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.05_summits.bed INFO @ Sat, 11 Dec 2021 11:33:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1923 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:33:11: 7000000 INFO @ Sat, 11 Dec 2021 11:33:12: 2000000 INFO @ Sat, 11 Dec 2021 11:33:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:33:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:33:15: #1 total tags in treatment: 7792872 INFO @ Sat, 11 Dec 2021 11:33:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:33:15: #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 11:33:15: #1 tags after filtering in treatment: 7792872 INFO @ Sat, 11 Dec 2021 11:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:33:15: #1 finished! INFO @ Sat, 11 Dec 2021 11:33:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:33:16: #2 number of paired peaks: 687 WARNING @ Sat, 11 Dec 2021 11:33:16: Fewer paired peaks (687) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 687 pairs to build model! INFO @ Sat, 11 Dec 2021 11:33:16: start model_add_line... INFO @ Sat, 11 Dec 2021 11:33:16: start X-correlation... INFO @ Sat, 11 Dec 2021 11:33:16: end of X-cor INFO @ Sat, 11 Dec 2021 11:33:16: #2 finished! INFO @ Sat, 11 Dec 2021 11:33:16: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 11:33:16: #2 alternative fragment length(s) may be 1,170,195,247 bps INFO @ Sat, 11 Dec 2021 11:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.10_model.r INFO @ Sat, 11 Dec 2021 11:33:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:33:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:33:18: 3000000 INFO @ Sat, 11 Dec 2021 11:33:23: 4000000 INFO @ Sat, 11 Dec 2021 11:33:28: 5000000 INFO @ Sat, 11 Dec 2021 11:33:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:33:33: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:33:39: 7000000 INFO @ Sat, 11 Dec 2021 11:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.10_summits.bed INFO @ Sat, 11 Dec 2021 11:33:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:33:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:33:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:33:43: #1 total tags in treatment: 7792872 INFO @ Sat, 11 Dec 2021 11:33:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:33:43: #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 11:33:43: #1 tags after filtering in treatment: 7792872 INFO @ Sat, 11 Dec 2021 11:33:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:33:43: #1 finished! INFO @ Sat, 11 Dec 2021 11:33:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:33:44: #2 number of paired peaks: 687 WARNING @ Sat, 11 Dec 2021 11:33:44: Fewer paired peaks (687) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 687 pairs to build model! INFO @ Sat, 11 Dec 2021 11:33:44: start model_add_line... INFO @ Sat, 11 Dec 2021 11:33:44: start X-correlation... INFO @ Sat, 11 Dec 2021 11:33:44: end of X-cor INFO @ Sat, 11 Dec 2021 11:33:44: #2 finished! INFO @ Sat, 11 Dec 2021 11:33:44: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 11:33:44: #2 alternative fragment length(s) may be 1,170,195,247 bps INFO @ Sat, 11 Dec 2021 11:33:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.20_model.r INFO @ Sat, 11 Dec 2021 11:33:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:33:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:34:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:34:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:34:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:34:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986160/SRX9986160.20_summits.bed INFO @ Sat, 11 Dec 2021 11:34:09: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (121 records, 4 fields): 2 millis CompletedMACS2peakCalling