Job ID = 6529148 SRX = SRX013057 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: 00:00:54 4718133 reads; of these: 4718133 (100.00%) were unpaired; of these: 374446 (7.94%) aligned 0 times 3875217 (82.13%) aligned exactly 1 time 468470 (9.93%) aligned >1 times 92.06% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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_rmdupse_core] 1242653 / 4343687 = 0.2861 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 01:35:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.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 01:35:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:35:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:35:35: 1000000 INFO @ Tue, 30 Jun 2020 01:35:41: 2000000 INFO @ Tue, 30 Jun 2020 01:35:47: 3000000 INFO @ Tue, 30 Jun 2020 01:35:48: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:35:48: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:35:48: #1 total tags in treatment: 3101034 INFO @ Tue, 30 Jun 2020 01:35:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:35:48: #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 01:35:48: #1 tags after filtering in treatment: 3100806 INFO @ Tue, 30 Jun 2020 01:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:35:48: #1 finished! INFO @ Tue, 30 Jun 2020 01:35:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:35:49: #2 number of paired peaks: 211 WARNING @ Tue, 30 Jun 2020 01:35:49: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 30 Jun 2020 01:35:49: start model_add_line... INFO @ Tue, 30 Jun 2020 01:35:49: start X-correlation... INFO @ Tue, 30 Jun 2020 01:35:49: end of X-cor INFO @ Tue, 30 Jun 2020 01:35:49: #2 finished! INFO @ Tue, 30 Jun 2020 01:35:49: #2 predicted fragment length is 85 bps INFO @ Tue, 30 Jun 2020 01:35:49: #2 alternative fragment length(s) may be 4,85,576 bps INFO @ Tue, 30 Jun 2020 01:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.05_model.r INFO @ Tue, 30 Jun 2020 01:35:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:35:49: #3 Pre-compute pvalue-qvalue table... 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 01:35:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:35:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.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 01:35:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:35:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:36:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:36:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.05_summits.bed INFO @ Tue, 30 Jun 2020 01:36:01: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:36:04: 1000000 INFO @ Tue, 30 Jun 2020 01:36:10: 2000000 INFO @ Tue, 30 Jun 2020 01:36:16: 3000000 INFO @ Tue, 30 Jun 2020 01:36:17: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:36:17: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:36:17: #1 total tags in treatment: 3101034 INFO @ Tue, 30 Jun 2020 01:36:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:36:17: #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 01:36:17: #1 tags after filtering in treatment: 3100806 INFO @ Tue, 30 Jun 2020 01:36:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:36:17: #1 finished! INFO @ Tue, 30 Jun 2020 01:36:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:36:18: #2 number of paired peaks: 211 WARNING @ Tue, 30 Jun 2020 01:36:18: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 30 Jun 2020 01:36:18: start model_add_line... INFO @ Tue, 30 Jun 2020 01:36:18: start X-correlation... INFO @ Tue, 30 Jun 2020 01:36:18: end of X-cor INFO @ Tue, 30 Jun 2020 01:36:18: #2 finished! INFO @ Tue, 30 Jun 2020 01:36:18: #2 predicted fragment length is 85 bps INFO @ Tue, 30 Jun 2020 01:36:18: #2 alternative fragment length(s) may be 4,85,576 bps INFO @ Tue, 30 Jun 2020 01:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.10_model.r INFO @ Tue, 30 Jun 2020 01:36:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:36:26: #3 Call peaks for each chromosome... 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 01:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.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 01:36:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.10_summits.bed INFO @ Tue, 30 Jun 2020 01:36:30: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:36:34: 1000000 INFO @ Tue, 30 Jun 2020 01:36:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:36:46: 3000000 INFO @ Tue, 30 Jun 2020 01:36:47: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:36:47: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:36:47: #1 total tags in treatment: 3101034 INFO @ Tue, 30 Jun 2020 01:36:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:36:47: #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 01:36:48: #1 tags after filtering in treatment: 3100806 INFO @ Tue, 30 Jun 2020 01:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:36:48: #1 finished! INFO @ Tue, 30 Jun 2020 01:36:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:36:48: #2 number of paired peaks: 211 WARNING @ Tue, 30 Jun 2020 01:36:48: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 30 Jun 2020 01:36:48: start model_add_line... INFO @ Tue, 30 Jun 2020 01:36:48: start X-correlation... INFO @ Tue, 30 Jun 2020 01:36:48: end of X-cor INFO @ Tue, 30 Jun 2020 01:36:48: #2 finished! INFO @ Tue, 30 Jun 2020 01:36:48: #2 predicted fragment length is 85 bps INFO @ Tue, 30 Jun 2020 01:36:48: #2 alternative fragment length(s) may be 4,85,576 bps INFO @ Tue, 30 Jun 2020 01:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.20_model.r INFO @ Tue, 30 Jun 2020 01:36:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:36:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:36:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013057/SRX013057.20_summits.bed INFO @ Tue, 30 Jun 2020 01:37:00: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis CompletedMACS2peakCalling