Job ID = 14170570 SRX = SRX9720891 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9389970 spots for SRR13291881/SRR13291881.sra Written 9389970 spots for SRR13291881/SRR13291881.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170978 ("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: 00:02:42 9389970 reads; of these: 9389970 (100.00%) were unpaired; of these: 1516419 (16.15%) aligned 0 times 5226578 (55.66%) aligned exactly 1 time 2646973 (28.19%) aligned >1 times 83.85% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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_rmdupse_core] 734274 / 7873551 = 0.0933 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 07:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.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 07:22:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:22:35: 1000000 INFO @ Sat, 11 Dec 2021 07:22:40: 2000000 INFO @ Sat, 11 Dec 2021 07:22:45: 3000000 INFO @ Sat, 11 Dec 2021 07:22:50: 4000000 INFO @ Sat, 11 Dec 2021 07:22:55: 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 07:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.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 07:22:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:23:01: 6000000 INFO @ Sat, 11 Dec 2021 07:23:06: 1000000 INFO @ Sat, 11 Dec 2021 07:23:06: 7000000 INFO @ Sat, 11 Dec 2021 07:23:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:23:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:23:07: #1 total tags in treatment: 7139277 INFO @ Sat, 11 Dec 2021 07:23:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:23:07: #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 07:23:07: #1 tags after filtering in treatment: 7139277 INFO @ Sat, 11 Dec 2021 07:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:23:07: #1 finished! INFO @ Sat, 11 Dec 2021 07:23:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:23:08: #2 number of paired peaks: 481 WARNING @ Sat, 11 Dec 2021 07:23:08: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sat, 11 Dec 2021 07:23:08: start model_add_line... INFO @ Sat, 11 Dec 2021 07:23:08: start X-correlation... INFO @ Sat, 11 Dec 2021 07:23:08: end of X-cor INFO @ Sat, 11 Dec 2021 07:23:08: #2 finished! INFO @ Sat, 11 Dec 2021 07:23:08: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 07:23:08: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 07:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.05_model.r INFO @ Sat, 11 Dec 2021 07:23:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:23:13: 2000000 INFO @ Sat, 11 Dec 2021 07:23:19: 3000000 INFO @ Sat, 11 Dec 2021 07:23:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:23:25: 4000000 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 07:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.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 07:23:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:23:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:23:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.05_summits.bed INFO @ Sat, 11 Dec 2021 07:23:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2597 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:23:32: 5000000 INFO @ Sat, 11 Dec 2021 07:23:36: 1000000 INFO @ Sat, 11 Dec 2021 07:23:38: 6000000 INFO @ Sat, 11 Dec 2021 07:23:43: 2000000 INFO @ Sat, 11 Dec 2021 07:23:45: 7000000 INFO @ Sat, 11 Dec 2021 07:23:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:23:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:23:46: #1 total tags in treatment: 7139277 INFO @ Sat, 11 Dec 2021 07:23:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:23:46: #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 07:23:46: #1 tags after filtering in treatment: 7139277 INFO @ Sat, 11 Dec 2021 07:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:23:46: #1 finished! INFO @ Sat, 11 Dec 2021 07:23:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:23:46: #2 number of paired peaks: 481 WARNING @ Sat, 11 Dec 2021 07:23:46: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sat, 11 Dec 2021 07:23:46: start model_add_line... INFO @ Sat, 11 Dec 2021 07:23:46: start X-correlation... INFO @ Sat, 11 Dec 2021 07:23:46: end of X-cor INFO @ Sat, 11 Dec 2021 07:23:46: #2 finished! INFO @ Sat, 11 Dec 2021 07:23:46: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 07:23:46: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 07:23:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.10_model.r INFO @ Sat, 11 Dec 2021 07:23:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:23:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:23:49: 3000000 INFO @ Sat, 11 Dec 2021 07:23:55: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:24:02: 5000000 INFO @ Sat, 11 Dec 2021 07:24:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:24:08: 6000000 INFO @ Sat, 11 Dec 2021 07:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.10_summits.bed INFO @ Sat, 11 Dec 2021 07:24:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1687 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:24:14: 7000000 INFO @ Sat, 11 Dec 2021 07:24:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:24:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:24:15: #1 total tags in treatment: 7139277 INFO @ Sat, 11 Dec 2021 07:24:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:24:15: #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 07:24:15: #1 tags after filtering in treatment: 7139277 INFO @ Sat, 11 Dec 2021 07:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:24:15: #1 finished! INFO @ Sat, 11 Dec 2021 07:24:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:24:15: #2 number of paired peaks: 481 WARNING @ Sat, 11 Dec 2021 07:24:15: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sat, 11 Dec 2021 07:24:15: start model_add_line... INFO @ Sat, 11 Dec 2021 07:24:15: start X-correlation... INFO @ Sat, 11 Dec 2021 07:24:15: end of X-cor INFO @ Sat, 11 Dec 2021 07:24:15: #2 finished! INFO @ Sat, 11 Dec 2021 07:24:15: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 07:24:15: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 07:24:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.20_model.r INFO @ Sat, 11 Dec 2021 07:24:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:24:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:24:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720891/SRX9720891.20_summits.bed INFO @ Sat, 11 Dec 2021 07:24:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (956 records, 4 fields): 3 millis CompletedMACS2peakCalling