Job ID = 14171715 SRX = SRX9986127 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:34 27241297 reads; of these: 27241297 (100.00%) were unpaired; of these: 2218483 (8.14%) aligned 0 times 21292773 (78.16%) aligned exactly 1 time 3730041 (13.69%) aligned >1 times 91.86% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9520990 / 25022814 = 0.3805 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 12:45:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.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 12:45:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:45:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:45:27: 1000000 INFO @ Sat, 11 Dec 2021 12:45:33: 2000000 INFO @ Sat, 11 Dec 2021 12:45:40: 3000000 INFO @ Sat, 11 Dec 2021 12:45:46: 4000000 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 12:45:51: 5000000 INFO @ Sat, 11 Dec 2021 12:45:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.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 12:45:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:45:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:45:58: 6000000 INFO @ Sat, 11 Dec 2021 12:45:59: 1000000 INFO @ Sat, 11 Dec 2021 12:46:05: 7000000 INFO @ Sat, 11 Dec 2021 12:46:05: 2000000 INFO @ Sat, 11 Dec 2021 12:46:11: 8000000 INFO @ Sat, 11 Dec 2021 12:46:12: 3000000 BedGraph に変換中... INFO @ Sat, 11 Dec 2021 12:46:18: 9000000 INFO @ Sat, 11 Dec 2021 12:46:18: 4000000 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 12:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.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 12:46:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:46:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:46:24: 10000000 INFO @ Sat, 11 Dec 2021 12:46:25: 5000000 INFO @ Sat, 11 Dec 2021 12:46:26: 1000000 INFO @ Sat, 11 Dec 2021 12:46:30: 11000000 INFO @ Sat, 11 Dec 2021 12:46:31: 2000000 INFO @ Sat, 11 Dec 2021 12:46:31: 6000000 INFO @ Sat, 11 Dec 2021 12:46:36: 3000000 INFO @ Sat, 11 Dec 2021 12:46:37: 12000000 INFO @ Sat, 11 Dec 2021 12:46:37: 7000000 INFO @ Sat, 11 Dec 2021 12:46:41: 4000000 INFO @ Sat, 11 Dec 2021 12:46:43: 8000000 INFO @ Sat, 11 Dec 2021 12:46:43: 13000000 INFO @ Sat, 11 Dec 2021 12:46:46: 5000000 INFO @ Sat, 11 Dec 2021 12:46:48: 14000000 INFO @ Sat, 11 Dec 2021 12:46:48: 9000000 INFO @ Sat, 11 Dec 2021 12:46:50: 6000000 INFO @ Sat, 11 Dec 2021 12:46:54: 15000000 INFO @ Sat, 11 Dec 2021 12:46:54: 10000000 INFO @ Sat, 11 Dec 2021 12:46:55: 7000000 INFO @ Sat, 11 Dec 2021 12:46:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:46:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:46:57: #1 total tags in treatment: 15501824 INFO @ Sat, 11 Dec 2021 12:46:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:46:57: #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 12:46:57: #1 tags after filtering in treatment: 15501724 INFO @ Sat, 11 Dec 2021 12:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:46:57: #1 finished! INFO @ Sat, 11 Dec 2021 12:46:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:46:58: #2 number of paired peaks: 146 WARNING @ Sat, 11 Dec 2021 12:46:58: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 11 Dec 2021 12:46:58: start model_add_line... INFO @ Sat, 11 Dec 2021 12:46:58: start X-correlation... INFO @ Sat, 11 Dec 2021 12:46:58: end of X-cor INFO @ Sat, 11 Dec 2021 12:46:58: #2 finished! INFO @ Sat, 11 Dec 2021 12:46:58: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 12:46:58: #2 alternative fragment length(s) may be 2,93,131,154,187,207,220,228,257,276,304 bps INFO @ Sat, 11 Dec 2021 12:46:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.05_model.r INFO @ Sat, 11 Dec 2021 12:46:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:46:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:47:00: 11000000 INFO @ Sat, 11 Dec 2021 12:47:00: 8000000 INFO @ Sat, 11 Dec 2021 12:47:05: 9000000 INFO @ Sat, 11 Dec 2021 12:47:06: 12000000 INFO @ Sat, 11 Dec 2021 12:47:10: 10000000 INFO @ Sat, 11 Dec 2021 12:47:12: 13000000 INFO @ Sat, 11 Dec 2021 12:47:15: 11000000 INFO @ Sat, 11 Dec 2021 12:47:17: 14000000 INFO @ Sat, 11 Dec 2021 12:47:19: 12000000 INFO @ Sat, 11 Dec 2021 12:47:23: 15000000 INFO @ Sat, 11 Dec 2021 12:47:25: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:47:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:47:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:47:26: #1 total tags in treatment: 15501824 INFO @ Sat, 11 Dec 2021 12:47:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:47:26: #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 12:47:26: #1 tags after filtering in treatment: 15501724 INFO @ Sat, 11 Dec 2021 12:47:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:47:26: #1 finished! INFO @ Sat, 11 Dec 2021 12:47:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:47:27: #2 number of paired peaks: 146 WARNING @ Sat, 11 Dec 2021 12:47:27: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 11 Dec 2021 12:47:27: start model_add_line... INFO @ Sat, 11 Dec 2021 12:47:27: start X-correlation... INFO @ Sat, 11 Dec 2021 12:47:27: end of X-cor INFO @ Sat, 11 Dec 2021 12:47:27: #2 finished! INFO @ Sat, 11 Dec 2021 12:47:27: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 12:47:27: #2 alternative fragment length(s) may be 2,93,131,154,187,207,220,228,257,276,304 bps INFO @ Sat, 11 Dec 2021 12:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.10_model.r INFO @ Sat, 11 Dec 2021 12:47:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:47:29: 14000000 INFO @ Sat, 11 Dec 2021 12:47:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:47:34: 15000000 INFO @ Sat, 11 Dec 2021 12:47:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:47:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:47:36: #1 total tags in treatment: 15501824 INFO @ Sat, 11 Dec 2021 12:47:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:47:36: #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 12:47:37: #1 tags after filtering in treatment: 15501724 INFO @ Sat, 11 Dec 2021 12:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:47:37: #1 finished! INFO @ Sat, 11 Dec 2021 12:47:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:47:38: #2 number of paired peaks: 146 WARNING @ Sat, 11 Dec 2021 12:47:38: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 11 Dec 2021 12:47:38: start model_add_line... INFO @ Sat, 11 Dec 2021 12:47:38: start X-correlation... INFO @ Sat, 11 Dec 2021 12:47:38: end of X-cor INFO @ Sat, 11 Dec 2021 12:47:38: #2 finished! INFO @ Sat, 11 Dec 2021 12:47:38: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 12:47:38: #2 alternative fragment length(s) may be 2,93,131,154,187,207,220,228,257,276,304 bps INFO @ Sat, 11 Dec 2021 12:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.20_model.r INFO @ Sat, 11 Dec 2021 12:47:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:47:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.05_summits.bed INFO @ Sat, 11 Dec 2021 12:47:46: Done! pass1 - making usageList (99 chroms): 1 millis pass2 - checking and writing primary data (5649 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:47:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:48:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:48:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:48:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:48:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.10_summits.bed INFO @ Sat, 11 Dec 2021 12:48:12: Done! pass1 - making usageList (65 chroms): 1 millis pass2 - checking and writing primary data (1446 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:48:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:48:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:48:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986127/SRX9986127.20_summits.bed INFO @ Sat, 11 Dec 2021 12:48:24: Done! pass1 - making usageList (38 chroms): 0 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling