Job ID = 14167273 SRX = SRX8688927 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6638702 spots for SRR12174214/SRR12174214.sra Written 6638702 spots for SRR12174214/SRR12174214.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167880 ("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: 00:01:47 6638702 reads; of these: 6638702 (100.00%) were unpaired; of these: 531995 (8.01%) aligned 0 times 5152894 (77.62%) aligned exactly 1 time 953813 (14.37%) aligned >1 times 91.99% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 226428 / 6106707 = 0.0371 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 @ Fri, 10 Dec 2021 11:32:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.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 @ Fri, 10 Dec 2021 11:32:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:32:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:32:15: 1000000 INFO @ Fri, 10 Dec 2021 11:32:21: 2000000 INFO @ Fri, 10 Dec 2021 11:32:26: 3000000 INFO @ Fri, 10 Dec 2021 11:32:31: 4000000 INFO @ Fri, 10 Dec 2021 11:32:37: 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 @ Fri, 10 Dec 2021 11:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.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 @ Fri, 10 Dec 2021 11:32:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:32:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:32:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:32:41: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:32:41: #1 total tags in treatment: 5880279 INFO @ Fri, 10 Dec 2021 11:32:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:32:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:32:42: #1 tags after filtering in treatment: 5880279 INFO @ Fri, 10 Dec 2021 11:32:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:32:42: #1 finished! INFO @ Fri, 10 Dec 2021 11:32:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:32:42: #2 number of paired peaks: 292 WARNING @ Fri, 10 Dec 2021 11:32:42: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Fri, 10 Dec 2021 11:32:42: start model_add_line... INFO @ Fri, 10 Dec 2021 11:32:42: start X-correlation... INFO @ Fri, 10 Dec 2021 11:32:42: end of X-cor INFO @ Fri, 10 Dec 2021 11:32:42: #2 finished! INFO @ Fri, 10 Dec 2021 11:32:42: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 11:32:42: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 11:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.05_model.r INFO @ Fri, 10 Dec 2021 11:32:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:32:46: 1000000 INFO @ Fri, 10 Dec 2021 11:32:52: 2000000 INFO @ Fri, 10 Dec 2021 11:32:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:32:58: 3000000 INFO @ Fri, 10 Dec 2021 11:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.05_summits.bed INFO @ Fri, 10 Dec 2021 11:33:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3501 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:33:03: 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 @ Fri, 10 Dec 2021 11:33:09: 5000000 INFO @ Fri, 10 Dec 2021 11:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.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 @ Fri, 10 Dec 2021 11:33:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:33:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:33:15: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:33:15: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:33:15: #1 total tags in treatment: 5880279 INFO @ Fri, 10 Dec 2021 11:33:15: #1 user defined the maximum tags... INFO @ Fri, 10 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 @ Fri, 10 Dec 2021 11:33:15: #1 tags after filtering in treatment: 5880279 INFO @ Fri, 10 Dec 2021 11:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:33:15: #1 finished! INFO @ Fri, 10 Dec 2021 11:33:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:33:15: #2 number of paired peaks: 292 WARNING @ Fri, 10 Dec 2021 11:33:15: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Fri, 10 Dec 2021 11:33:15: start model_add_line... INFO @ Fri, 10 Dec 2021 11:33:15: start X-correlation... INFO @ Fri, 10 Dec 2021 11:33:15: end of X-cor INFO @ Fri, 10 Dec 2021 11:33:15: #2 finished! INFO @ Fri, 10 Dec 2021 11:33:15: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 11:33:15: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 11:33:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.10_model.r INFO @ Fri, 10 Dec 2021 11:33:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:33:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:33:16: 1000000 INFO @ Fri, 10 Dec 2021 11:33:21: 2000000 INFO @ Fri, 10 Dec 2021 11:33:27: 3000000 INFO @ Fri, 10 Dec 2021 11:33:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:33:32: 4000000 INFO @ Fri, 10 Dec 2021 11:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.10_summits.bed INFO @ Fri, 10 Dec 2021 11:33:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:33:38: 5000000 INFO @ Fri, 10 Dec 2021 11:33:43: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:33:43: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:33:43: #1 total tags in treatment: 5880279 INFO @ Fri, 10 Dec 2021 11:33:43: #1 user defined the maximum tags... INFO @ Fri, 10 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 @ Fri, 10 Dec 2021 11:33:43: #1 tags after filtering in treatment: 5880279 INFO @ Fri, 10 Dec 2021 11:33:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:33:43: #1 finished! INFO @ Fri, 10 Dec 2021 11:33:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:33:43: #2 number of paired peaks: 292 WARNING @ Fri, 10 Dec 2021 11:33:43: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Fri, 10 Dec 2021 11:33:43: start model_add_line... INFO @ Fri, 10 Dec 2021 11:33:43: start X-correlation... INFO @ Fri, 10 Dec 2021 11:33:43: end of X-cor INFO @ Fri, 10 Dec 2021 11:33:43: #2 finished! INFO @ Fri, 10 Dec 2021 11:33:43: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 11:33:43: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 11:33:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.20_model.r INFO @ Fri, 10 Dec 2021 11:33:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:33:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:33:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:34:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:34:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:34:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688927/SRX8688927.20_summits.bed INFO @ Fri, 10 Dec 2021 11:34:01: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (360 records, 4 fields): 13 millis CompletedMACS2peakCalling