Job ID = 6529458 SRX = SRX287604 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: 00:03:40 17229279 reads; of these: 17229279 (100.00%) were unpaired; of these: 1056050 (6.13%) aligned 0 times 14725740 (85.47%) aligned exactly 1 time 1447489 (8.40%) aligned >1 times 93.87% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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 8 files... [bam_rmdupse_core] 4264272 / 16173229 = 0.2637 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.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, 30 Jun 2020 02:12:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:12:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:12:15: 1000000 INFO @ Tue, 30 Jun 2020 02:12:21: 2000000 INFO @ Tue, 30 Jun 2020 02:12:26: 3000000 INFO @ Tue, 30 Jun 2020 02:12:33: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:12:39: 5000000 INFO @ Tue, 30 Jun 2020 02:12:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.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, 30 Jun 2020 02:12:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:12:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:12:44: 1000000 INFO @ Tue, 30 Jun 2020 02:12:45: 6000000 INFO @ Tue, 30 Jun 2020 02:12:50: 2000000 INFO @ Tue, 30 Jun 2020 02:12:51: 7000000 INFO @ Tue, 30 Jun 2020 02:12:55: 3000000 INFO @ Tue, 30 Jun 2020 02:12:57: 8000000 INFO @ Tue, 30 Jun 2020 02:13:01: 4000000 INFO @ Tue, 30 Jun 2020 02:13:03: 9000000 INFO @ Tue, 30 Jun 2020 02:13:06: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.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, 30 Jun 2020 02:13:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:13:10: 10000000 INFO @ Tue, 30 Jun 2020 02:13:12: 6000000 INFO @ Tue, 30 Jun 2020 02:13:14: 1000000 INFO @ Tue, 30 Jun 2020 02:13:16: 11000000 INFO @ Tue, 30 Jun 2020 02:13:17: 7000000 INFO @ Tue, 30 Jun 2020 02:13:20: 2000000 INFO @ Tue, 30 Jun 2020 02:13:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:13:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:13:21: #1 total tags in treatment: 11908957 INFO @ Tue, 30 Jun 2020 02:13:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:13:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:13:22: #1 tags after filtering in treatment: 11908919 INFO @ Tue, 30 Jun 2020 02:13:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:23: 8000000 INFO @ Tue, 30 Jun 2020 02:13:23: #2 number of paired peaks: 207 WARNING @ Tue, 30 Jun 2020 02:13:23: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:23: #2 predicted fragment length is 120 bps INFO @ Tue, 30 Jun 2020 02:13:23: #2 alternative fragment length(s) may be 4,96,120,544,559 bps INFO @ Tue, 30 Jun 2020 02:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.05_model.r INFO @ Tue, 30 Jun 2020 02:13:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:26: 3000000 INFO @ Tue, 30 Jun 2020 02:13:28: 9000000 INFO @ Tue, 30 Jun 2020 02:13:32: 4000000 INFO @ Tue, 30 Jun 2020 02:13:34: 10000000 INFO @ Tue, 30 Jun 2020 02:13:38: 5000000 INFO @ Tue, 30 Jun 2020 02:13:39: 11000000 INFO @ Tue, 30 Jun 2020 02:13:44: 6000000 INFO @ Tue, 30 Jun 2020 02:13:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:13:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:13:44: #1 total tags in treatment: 11908957 INFO @ Tue, 30 Jun 2020 02:13:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:13:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:13:45: #1 tags after filtering in treatment: 11908919 INFO @ Tue, 30 Jun 2020 02:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:45: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:45: #2 number of paired peaks: 207 WARNING @ Tue, 30 Jun 2020 02:13:45: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:45: #2 predicted fragment length is 120 bps INFO @ Tue, 30 Jun 2020 02:13:45: #2 alternative fragment length(s) may be 4,96,120,544,559 bps INFO @ Tue, 30 Jun 2020 02:13:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.10_model.r INFO @ Tue, 30 Jun 2020 02:13:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:49: 7000000 INFO @ Tue, 30 Jun 2020 02:13:55: 8000000 INFO @ Tue, 30 Jun 2020 02:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.05_summits.bed INFO @ Tue, 30 Jun 2020 02:13:57: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:14:00: 9000000 INFO @ Tue, 30 Jun 2020 02:14:06: 10000000 INFO @ Tue, 30 Jun 2020 02:14:08: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:14:12: 11000000 INFO @ Tue, 30 Jun 2020 02:14:17: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:14:17: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:14:17: #1 total tags in treatment: 11908957 INFO @ Tue, 30 Jun 2020 02:14:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:14:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:14:17: #1 tags after filtering in treatment: 11908919 INFO @ Tue, 30 Jun 2020 02:14:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:14:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:14:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:14:18: #2 number of paired peaks: 207 WARNING @ Tue, 30 Jun 2020 02:14:18: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 30 Jun 2020 02:14:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:14:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:14:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:14:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:14:18: #2 predicted fragment length is 120 bps INFO @ Tue, 30 Jun 2020 02:14:18: #2 alternative fragment length(s) may be 4,96,120,544,559 bps INFO @ Tue, 30 Jun 2020 02:14:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.20_model.r INFO @ Tue, 30 Jun 2020 02:14:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:14:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:14:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:14:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:14:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.10_summits.bed INFO @ Tue, 30 Jun 2020 02:14:20: Done! pass1 - making usageList (55 chroms): 0 millis pass2 - checking and writing primary data (137 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:14:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:14:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287604/SRX287604.20_summits.bed INFO @ Tue, 30 Jun 2020 02:14:58: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling