Job ID = 6454860 SRX = SRX2592452 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:10 prefetch.2.10.7: 1) Downloading 'SRR5289729'... 2020-06-21T09:48:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:01 prefetch.2.10.7: 'SRR5289729' is valid 2020-06-21T09:50:01 prefetch.2.10.7: 1) 'SRR5289729' was downloaded successfully Read 14625252 spots for SRR5289729/SRR5289729.sra Written 14625252 spots for SRR5289729/SRR5289729.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: 00:05:18 14625252 reads; of these: 14625252 (100.00%) were unpaired; of these: 1674302 (11.45%) aligned 0 times 8754443 (59.86%) aligned exactly 1 time 4196507 (28.69%) aligned >1 times 88.55% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 4935655 / 12950950 = 0.3811 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 18:59:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.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 18:59:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:46: 1000000 INFO @ Sun, 21 Jun 2020 18:59:53: 2000000 INFO @ Sun, 21 Jun 2020 18:59:59: 3000000 INFO @ Sun, 21 Jun 2020 19:00:05: 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 19:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.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 19:00:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:12: 5000000 INFO @ Sun, 21 Jun 2020 19:00:18: 1000000 INFO @ Sun, 21 Jun 2020 19:00:20: 6000000 INFO @ Sun, 21 Jun 2020 19:00:26: 2000000 INFO @ Sun, 21 Jun 2020 19:00:27: 7000000 INFO @ Sun, 21 Jun 2020 19:00:34: 3000000 INFO @ Sun, 21 Jun 2020 19:00:35: 8000000 INFO @ Sun, 21 Jun 2020 19:00:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:00:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:00:35: #1 total tags in treatment: 8015295 INFO @ Sun, 21 Jun 2020 19:00:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:35: #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 19:00:35: #1 tags after filtering in treatment: 8015192 INFO @ Sun, 21 Jun 2020 19:00:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:36: #2 number of paired peaks: 944 WARNING @ Sun, 21 Jun 2020 19:00:36: Fewer paired peaks (944) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 944 pairs to build model! INFO @ Sun, 21 Jun 2020 19:00:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:36: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 19:00:36: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 19:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.05_model.r INFO @ Sun, 21 Jun 2020 19:00:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:36: #3 Pre-compute pvalue-qvalue table... 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 19:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.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 19:00:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:42: 4000000 INFO @ Sun, 21 Jun 2020 19:00:48: 1000000 INFO @ Sun, 21 Jun 2020 19:00:50: 5000000 INFO @ Sun, 21 Jun 2020 19:00:56: 2000000 INFO @ Sun, 21 Jun 2020 19:00:58: 6000000 INFO @ Sun, 21 Jun 2020 19:00:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:04: 3000000 INFO @ Sun, 21 Jun 2020 19:01:06: 7000000 INFO @ Sun, 21 Jun 2020 19:01:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.05_summits.bed INFO @ Sun, 21 Jun 2020 19:01:11: Done! pass1 - making usageList (758 chroms): 2 millis pass2 - checking and writing primary data (15204 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:01:12: 4000000 INFO @ Sun, 21 Jun 2020 19:01:15: 8000000 INFO @ Sun, 21 Jun 2020 19:01:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:01:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:01:15: #1 total tags in treatment: 8015295 INFO @ Sun, 21 Jun 2020 19:01:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:15: #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 19:01:15: #1 tags after filtering in treatment: 8015192 INFO @ Sun, 21 Jun 2020 19:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:15: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:01:16: #2 number of paired peaks: 944 WARNING @ Sun, 21 Jun 2020 19:01:16: Fewer paired peaks (944) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 944 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:16: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 19:01:16: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 19:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.10_model.r INFO @ Sun, 21 Jun 2020 19:01:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:20: 5000000 INFO @ Sun, 21 Jun 2020 19:01:28: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:01:35: 7000000 INFO @ Sun, 21 Jun 2020 19:01:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:43: 8000000 INFO @ Sun, 21 Jun 2020 19:01:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:01:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:01:43: #1 total tags in treatment: 8015295 INFO @ Sun, 21 Jun 2020 19:01:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:43: #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 19:01:44: #1 tags after filtering in treatment: 8015192 INFO @ Sun, 21 Jun 2020 19:01:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:45: #2 number of paired peaks: 944 WARNING @ Sun, 21 Jun 2020 19:01:45: Fewer paired peaks (944) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 944 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:45: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 19:01:45: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 19:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.20_model.r INFO @ Sun, 21 Jun 2020 19:01:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.10_summits.bed INFO @ Sun, 21 Jun 2020 19:01:49: Done! pass1 - making usageList (614 chroms): 3 millis pass2 - checking and writing primary data (12170 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:02:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592452/SRX2592452.20_summits.bed INFO @ Sun, 21 Jun 2020 19:02:19: Done! pass1 - making usageList (436 chroms): 3 millis pass2 - checking and writing primary data (8773 records, 4 fields): 24 millis CompletedMACS2peakCalling