Job ID = 6454834 SRX = SRX2592430 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:44:40 prefetch.2.10.7: 1) Downloading 'SRR5289707'... 2020-06-21T09:44:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:33 prefetch.2.10.7: 'SRR5289707' is valid 2020-06-21T09:46:33 prefetch.2.10.7: 1) 'SRR5289707' was downloaded successfully Read 13980849 spots for SRR5289707/SRR5289707.sra Written 13980849 spots for SRR5289707/SRR5289707.sra 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: 00:04:10 13980849 reads; of these: 13980849 (100.00%) were unpaired; of these: 1095008 (7.83%) aligned 0 times 10375256 (74.21%) aligned exactly 1 time 2510585 (17.96%) aligned >1 times 92.17% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 2966631 / 12885841 = 0.2302 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 @ Sun, 21 Jun 2020 18:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.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 @ Sun, 21 Jun 2020 18:55:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:22: 1000000 INFO @ Sun, 21 Jun 2020 18:55:28: 2000000 INFO @ Sun, 21 Jun 2020 18:55:34: 3000000 INFO @ Sun, 21 Jun 2020 18:55:40: 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 @ Sun, 21 Jun 2020 18:55:46: 5000000 INFO @ Sun, 21 Jun 2020 18:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.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 @ Sun, 21 Jun 2020 18:55:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:53: 6000000 INFO @ Sun, 21 Jun 2020 18:55:53: 1000000 INFO @ Sun, 21 Jun 2020 18:56:00: 7000000 INFO @ Sun, 21 Jun 2020 18:56:00: 2000000 INFO @ Sun, 21 Jun 2020 18:56:07: 3000000 INFO @ Sun, 21 Jun 2020 18:56:07: 8000000 INFO @ Sun, 21 Jun 2020 18:56:13: 4000000 INFO @ Sun, 21 Jun 2020 18:56:14: 9000000 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 @ Sun, 21 Jun 2020 18:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.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 @ Sun, 21 Jun 2020 18:56:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:20: 5000000 INFO @ Sun, 21 Jun 2020 18:56:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:56:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:56:21: #1 total tags in treatment: 9919210 INFO @ Sun, 21 Jun 2020 18:56:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:56:21: #1 tags after filtering in treatment: 9919089 INFO @ Sun, 21 Jun 2020 18:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:22: #2 number of paired peaks: 209 WARNING @ Sun, 21 Jun 2020 18:56:22: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 21 Jun 2020 18:56:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:22: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:56:22: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 18:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.05_model.r INFO @ Sun, 21 Jun 2020 18:56:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:23: 1000000 INFO @ Sun, 21 Jun 2020 18:56:28: 6000000 INFO @ Sun, 21 Jun 2020 18:56:30: 2000000 INFO @ Sun, 21 Jun 2020 18:56:35: 7000000 INFO @ Sun, 21 Jun 2020 18:56:37: 3000000 INFO @ Sun, 21 Jun 2020 18:56:42: 8000000 INFO @ Sun, 21 Jun 2020 18:56:44: 4000000 INFO @ Sun, 21 Jun 2020 18:56:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:49: 9000000 INFO @ Sun, 21 Jun 2020 18:56:51: 5000000 INFO @ Sun, 21 Jun 2020 18:56:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:56:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:56:56: #1 total tags in treatment: 9919210 INFO @ Sun, 21 Jun 2020 18:56:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:56:56: #1 tags after filtering in treatment: 9919089 INFO @ Sun, 21 Jun 2020 18:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:57: #2 number of paired peaks: 209 WARNING @ Sun, 21 Jun 2020 18:56:57: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 21 Jun 2020 18:56:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:57: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:56:57: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 18:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.10_model.r INFO @ Sun, 21 Jun 2020 18:56:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:58: 6000000 INFO @ Sun, 21 Jun 2020 18:56:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.05_summits.bed INFO @ Sun, 21 Jun 2020 18:56:59: Done! pass1 - making usageList (344 chroms): 3 millis pass2 - checking and writing primary data (14869 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:05: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:57:11: 8000000 INFO @ Sun, 21 Jun 2020 18:57:18: 9000000 INFO @ Sun, 21 Jun 2020 18:57:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:57:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:57:23: #1 total tags in treatment: 9919210 INFO @ Sun, 21 Jun 2020 18:57:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:57:24: #1 tags after filtering in treatment: 9919089 INFO @ Sun, 21 Jun 2020 18:57:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:25: #2 number of paired peaks: 209 WARNING @ Sun, 21 Jun 2020 18:57:25: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 21 Jun 2020 18:57:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:25: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:57:25: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 18:57:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.20_model.r INFO @ Sun, 21 Jun 2020 18:57:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.10_summits.bed INFO @ Sun, 21 Jun 2020 18:57:30: Done! pass1 - making usageList (229 chroms): 2 millis pass2 - checking and writing primary data (10240 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:57:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592430/SRX2592430.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:00: Done! pass1 - making usageList (139 chroms): 2 millis pass2 - checking and writing primary data (6420 records, 4 fields): 11 millis CompletedMACS2peakCalling