Job ID = 16437446 SRX = SRX12764397 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 37727297 spots for SRR16562273/SRR16562273.sra Written 37727297 spots for SRR16562273/SRR16562273.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437579 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:25 37727297 reads; of these: 37727297 (100.00%) were unpaired; of these: 26022990 (68.98%) aligned 0 times 8565027 (22.70%) aligned exactly 1 time 3139280 (8.32%) aligned >1 times 31.02% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 2112674 / 11704307 = 0.1805 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.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 @ Tue, 02 Aug 2022 12:45:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:45:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:45:26: 1000000 INFO @ Tue, 02 Aug 2022 12:45:32: 2000000 INFO @ Tue, 02 Aug 2022 12:45:39: 3000000 INFO @ Tue, 02 Aug 2022 12:45:45: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.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 @ Tue, 02 Aug 2022 12:45:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:45:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:45:52: 5000000 INFO @ Tue, 02 Aug 2022 12:45:56: 1000000 INFO @ Tue, 02 Aug 2022 12:45:59: 6000000 INFO @ Tue, 02 Aug 2022 12:46:03: 2000000 INFO @ Tue, 02 Aug 2022 12:46:07: 7000000 INFO @ Tue, 02 Aug 2022 12:46:10: 3000000 INFO @ Tue, 02 Aug 2022 12:46:14: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:46:18: 4000000 INFO @ Tue, 02 Aug 2022 12:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.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 @ Tue, 02 Aug 2022 12:46:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:46:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:46:21: 9000000 INFO @ Tue, 02 Aug 2022 12:46:25: 5000000 INFO @ Tue, 02 Aug 2022 12:46:25: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:46:25: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:46:25: #1 total tags in treatment: 9591633 INFO @ Tue, 02 Aug 2022 12:46:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:46:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:46:25: #1 tags after filtering in treatment: 9591633 INFO @ Tue, 02 Aug 2022 12:46:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:46:25: #1 finished! INFO @ Tue, 02 Aug 2022 12:46:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:46:26: #2 number of paired peaks: 655 WARNING @ Tue, 02 Aug 2022 12:46:26: Fewer paired peaks (655) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 655 pairs to build model! INFO @ Tue, 02 Aug 2022 12:46:26: start model_add_line... INFO @ Tue, 02 Aug 2022 12:46:26: start X-correlation... INFO @ Tue, 02 Aug 2022 12:46:26: end of X-cor INFO @ Tue, 02 Aug 2022 12:46:26: #2 finished! INFO @ Tue, 02 Aug 2022 12:46:26: #2 predicted fragment length is 130 bps INFO @ Tue, 02 Aug 2022 12:46:26: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 02 Aug 2022 12:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.05_model.r INFO @ Tue, 02 Aug 2022 12:46:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:46:27: 1000000 INFO @ Tue, 02 Aug 2022 12:46:31: 6000000 INFO @ Tue, 02 Aug 2022 12:46:34: 2000000 INFO @ Tue, 02 Aug 2022 12:46:38: 7000000 INFO @ Tue, 02 Aug 2022 12:46:42: 3000000 INFO @ Tue, 02 Aug 2022 12:46:44: 8000000 INFO @ Tue, 02 Aug 2022 12:46:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:46:49: 4000000 INFO @ Tue, 02 Aug 2022 12:46:51: 9000000 INFO @ Tue, 02 Aug 2022 12:46:55: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:46:55: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:46:55: #1 total tags in treatment: 9591633 INFO @ Tue, 02 Aug 2022 12:46:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:46:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:46:55: #1 tags after filtering in treatment: 9591633 INFO @ Tue, 02 Aug 2022 12:46:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:46:55: #1 finished! INFO @ Tue, 02 Aug 2022 12:46:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:46:56: #2 number of paired peaks: 655 WARNING @ Tue, 02 Aug 2022 12:46:56: Fewer paired peaks (655) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 655 pairs to build model! INFO @ Tue, 02 Aug 2022 12:46:56: start model_add_line... INFO @ Tue, 02 Aug 2022 12:46:56: 5000000 INFO @ Tue, 02 Aug 2022 12:46:56: start X-correlation... INFO @ Tue, 02 Aug 2022 12:46:56: end of X-cor INFO @ Tue, 02 Aug 2022 12:46:56: #2 finished! INFO @ Tue, 02 Aug 2022 12:46:56: #2 predicted fragment length is 130 bps INFO @ Tue, 02 Aug 2022 12:46:56: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 02 Aug 2022 12:46:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.10_model.r INFO @ Tue, 02 Aug 2022 12:46:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:46:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:46:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:46:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:46:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.05_summits.bed INFO @ Tue, 02 Aug 2022 12:46:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3263 records, 4 fields): 558 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:47:03: 6000000 INFO @ Tue, 02 Aug 2022 12:47:11: 7000000 INFO @ Tue, 02 Aug 2022 12:47:17: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:47:20: 8000000 INFO @ Tue, 02 Aug 2022 12:47:28: 9000000 INFO @ Tue, 02 Aug 2022 12:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.10_summits.bed INFO @ Tue, 02 Aug 2022 12:47:28: Done! pass1 - making usageList (14 chroms): 17 millis pass2 - checking and writing primary data (1219 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:47:32: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:47:32: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:47:32: #1 total tags in treatment: 9591633 INFO @ Tue, 02 Aug 2022 12:47:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:47:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:47:32: #1 tags after filtering in treatment: 9591633 INFO @ Tue, 02 Aug 2022 12:47:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:47:32: #1 finished! INFO @ Tue, 02 Aug 2022 12:47:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:47:33: #2 number of paired peaks: 655 WARNING @ Tue, 02 Aug 2022 12:47:33: Fewer paired peaks (655) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 655 pairs to build model! INFO @ Tue, 02 Aug 2022 12:47:33: start model_add_line... INFO @ Tue, 02 Aug 2022 12:47:33: start X-correlation... INFO @ Tue, 02 Aug 2022 12:47:33: end of X-cor INFO @ Tue, 02 Aug 2022 12:47:33: #2 finished! INFO @ Tue, 02 Aug 2022 12:47:33: #2 predicted fragment length is 130 bps INFO @ Tue, 02 Aug 2022 12:47:33: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 02 Aug 2022 12:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.20_model.r INFO @ Tue, 02 Aug 2022 12:47:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:47:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:47:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764397/SRX12764397.20_summits.bed INFO @ Tue, 02 Aug 2022 12:48:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (399 records, 4 fields): 17 millis CompletedMACS2peakCalling