Job ID = 6529530 SRX = SRX287954 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: 00:03:47 17177634 reads; of these: 17177634 (100.00%) were unpaired; of these: 889654 (5.18%) aligned 0 times 14282930 (83.15%) aligned exactly 1 time 2005050 (11.67%) aligned >1 times 94.82% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1762438 / 16287980 = 0.1082 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 02:18:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.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 02:18:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:26: 1000000 INFO @ Tue, 30 Jun 2020 02:18:33: 2000000 INFO @ Tue, 30 Jun 2020 02:18:40: 3000000 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 02:18:48: 4000000 INFO @ Tue, 30 Jun 2020 02:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.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 02:18:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:56: 1000000 INFO @ Tue, 30 Jun 2020 02:18:56: 5000000 INFO @ Tue, 30 Jun 2020 02:19:04: 6000000 INFO @ Tue, 30 Jun 2020 02:19:04: 2000000 INFO @ Tue, 30 Jun 2020 02:19:12: 7000000 INFO @ Tue, 30 Jun 2020 02:19:12: 3000000 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 02:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.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 02:19:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:20: 8000000 INFO @ Tue, 30 Jun 2020 02:19:20: 4000000 INFO @ Tue, 30 Jun 2020 02:19:26: 1000000 INFO @ Tue, 30 Jun 2020 02:19:28: 9000000 INFO @ Tue, 30 Jun 2020 02:19:28: 5000000 INFO @ Tue, 30 Jun 2020 02:19:35: 2000000 INFO @ Tue, 30 Jun 2020 02:19:36: 10000000 INFO @ Tue, 30 Jun 2020 02:19:36: 6000000 INFO @ Tue, 30 Jun 2020 02:19:43: 3000000 INFO @ Tue, 30 Jun 2020 02:19:44: 11000000 INFO @ Tue, 30 Jun 2020 02:19:45: 7000000 INFO @ Tue, 30 Jun 2020 02:19:51: 4000000 INFO @ Tue, 30 Jun 2020 02:19:52: 12000000 INFO @ Tue, 30 Jun 2020 02:19:53: 8000000 INFO @ Tue, 30 Jun 2020 02:19:59: 5000000 INFO @ Tue, 30 Jun 2020 02:20:01: 9000000 INFO @ Tue, 30 Jun 2020 02:20:01: 13000000 INFO @ Tue, 30 Jun 2020 02:20:08: 6000000 INFO @ Tue, 30 Jun 2020 02:20:08: 10000000 INFO @ Tue, 30 Jun 2020 02:20:09: 14000000 INFO @ Tue, 30 Jun 2020 02:20:14: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:20:14: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:20:14: #1 total tags in treatment: 14525542 INFO @ Tue, 30 Jun 2020 02:20:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:14: #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 02:20:15: #1 tags after filtering in treatment: 14525537 INFO @ Tue, 30 Jun 2020 02:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:15: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:16: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 02:20:16: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:16: #2 predicted fragment length is 138 bps INFO @ Tue, 30 Jun 2020 02:20:16: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 30 Jun 2020 02:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.05_model.r INFO @ Tue, 30 Jun 2020 02:20:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:16: 7000000 INFO @ Tue, 30 Jun 2020 02:20:16: 11000000 INFO @ Tue, 30 Jun 2020 02:20:24: 8000000 INFO @ Tue, 30 Jun 2020 02:20:24: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:20:32: 9000000 INFO @ Tue, 30 Jun 2020 02:20:32: 13000000 INFO @ Tue, 30 Jun 2020 02:20:39: 10000000 INFO @ Tue, 30 Jun 2020 02:20:40: 14000000 INFO @ Tue, 30 Jun 2020 02:20:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:20:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:20:44: #1 total tags in treatment: 14525542 INFO @ Tue, 30 Jun 2020 02:20:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:44: #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 02:20:45: #1 tags after filtering in treatment: 14525537 INFO @ Tue, 30 Jun 2020 02:20:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:45: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:46: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 02:20:46: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:46: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:46: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:46: #2 predicted fragment length is 138 bps INFO @ Tue, 30 Jun 2020 02:20:46: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 30 Jun 2020 02:20:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.10_model.r INFO @ Tue, 30 Jun 2020 02:20:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:47: 11000000 INFO @ Tue, 30 Jun 2020 02:20:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:20:54: 12000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:21:02: 13000000 INFO @ Tue, 30 Jun 2020 02:21:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.05_summits.bed INFO @ Tue, 30 Jun 2020 02:21:09: Done! pass1 - making usageList (390 chroms): 1 millis pass2 - checking and writing primary data (3461 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:09: 14000000 INFO @ Tue, 30 Jun 2020 02:21:13: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:21:13: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:21:13: #1 total tags in treatment: 14525542 INFO @ Tue, 30 Jun 2020 02:21:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:13: #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 02:21:14: #1 tags after filtering in treatment: 14525537 INFO @ Tue, 30 Jun 2020 02:21:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:14: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:15: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 02:21:15: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:15: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:15: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:15: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:15: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:15: #2 predicted fragment length is 138 bps INFO @ Tue, 30 Jun 2020 02:21:15: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 30 Jun 2020 02:21:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.20_model.r INFO @ Tue, 30 Jun 2020 02:21:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.10_summits.bed INFO @ Tue, 30 Jun 2020 02:21:37: Done! pass1 - making usageList (305 chroms): 2 millis pass2 - checking and writing primary data (1428 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287954/SRX287954.20_summits.bed INFO @ Tue, 30 Jun 2020 02:22:06: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 5 millis CompletedMACS2peakCalling