Job ID = 16437426 SRX = SRX12764390 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34500713 spots for SRR16562266/SRR16562266.sra Written 34500713 spots for SRR16562266/SRR16562266.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437464 ("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: 00:03:31 34500713 reads; of these: 34500713 (100.00%) were unpaired; of these: 33222606 (96.30%) aligned 0 times 882892 (2.56%) aligned exactly 1 time 395215 (1.15%) aligned >1 times 3.70% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 156244 / 1278107 = 0.1222 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 12:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.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 12:33:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:33:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:33:43: 1000000 INFO @ Tue, 02 Aug 2022 12:33:43: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:33:43: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:33:43: #1 total tags in treatment: 1121863 INFO @ Tue, 02 Aug 2022 12:33:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:33:43: #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 12:33:43: #1 tags after filtering in treatment: 1121863 INFO @ Tue, 02 Aug 2022 12:33:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:33:43: #1 finished! INFO @ Tue, 02 Aug 2022 12:33:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:33:44: #2 number of paired peaks: 5287 INFO @ Tue, 02 Aug 2022 12:33:44: start model_add_line... INFO @ Tue, 02 Aug 2022 12:33:44: start X-correlation... INFO @ Tue, 02 Aug 2022 12:33:44: end of X-cor INFO @ Tue, 02 Aug 2022 12:33:44: #2 finished! INFO @ Tue, 02 Aug 2022 12:33:44: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 12:33:44: #2 alternative fragment length(s) may be 56,148 bps INFO @ Tue, 02 Aug 2022 12:33:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.05_model.r INFO @ Tue, 02 Aug 2022 12:33:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:33:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:33:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:33:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:33:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:33:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.05_summits.bed INFO @ Tue, 02 Aug 2022 12:33:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1899 records, 4 fields): 18 millis CompletedMACS2peakCalling 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 12:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.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 12:34:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:34:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:34:13: 1000000 INFO @ Tue, 02 Aug 2022 12:34:14: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:34:14: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:34:14: #1 total tags in treatment: 1121863 INFO @ Tue, 02 Aug 2022 12:34:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:34:14: #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 12:34:14: #1 tags after filtering in treatment: 1121863 INFO @ Tue, 02 Aug 2022 12:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:34:14: #1 finished! INFO @ Tue, 02 Aug 2022 12:34:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:34:14: #2 number of paired peaks: 5287 INFO @ Tue, 02 Aug 2022 12:34:14: start model_add_line... INFO @ Tue, 02 Aug 2022 12:34:14: start X-correlation... INFO @ Tue, 02 Aug 2022 12:34:14: end of X-cor INFO @ Tue, 02 Aug 2022 12:34:14: #2 finished! INFO @ Tue, 02 Aug 2022 12:34:14: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 12:34:14: #2 alternative fragment length(s) may be 56,148 bps INFO @ Tue, 02 Aug 2022 12:34:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.10_model.r INFO @ Tue, 02 Aug 2022 12:34:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:34:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:34:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:34:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:34:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:34:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.10_summits.bed INFO @ Tue, 02 Aug 2022 12:34:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (667 records, 4 fields): 86 millis CompletedMACS2peakCalling 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 12:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.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 12:34:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:34:37: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:34:43: 1000000 INFO @ Tue, 02 Aug 2022 12:34:44: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:34:44: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:34:44: #1 total tags in treatment: 1121863 INFO @ Tue, 02 Aug 2022 12:34:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:34:44: #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 12:34:44: #1 tags after filtering in treatment: 1121863 INFO @ Tue, 02 Aug 2022 12:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:34:44: #1 finished! INFO @ Tue, 02 Aug 2022 12:34:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:34:44: #2 number of paired peaks: 5287 INFO @ Tue, 02 Aug 2022 12:34:44: start model_add_line... INFO @ Tue, 02 Aug 2022 12:34:44: start X-correlation... INFO @ Tue, 02 Aug 2022 12:34:44: end of X-cor INFO @ Tue, 02 Aug 2022 12:34:44: #2 finished! INFO @ Tue, 02 Aug 2022 12:34:44: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 12:34:44: #2 alternative fragment length(s) may be 56,148 bps INFO @ Tue, 02 Aug 2022 12:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.20_model.r INFO @ Tue, 02 Aug 2022 12:34:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:34:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:34:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:34:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:34:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764390/SRX12764390.20_summits.bed INFO @ Tue, 02 Aug 2022 12:34:48: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 4 millis CompletedMACS2peakCalling