Job ID = 6454804 SRX = SRX2592404 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:41:55 prefetch.2.10.7: 1) Downloading 'SRR5289681'... 2020-06-21T09:41:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:44:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:44:18 prefetch.2.10.7: 'SRR5289681' is valid 2020-06-21T09:44:18 prefetch.2.10.7: 1) 'SRR5289681' was downloaded successfully Read 11377851 spots for SRR5289681/SRR5289681.sra Written 11377851 spots for SRR5289681/SRR5289681.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: 00:02:28 11377851 reads; of these: 11377851 (100.00%) were unpaired; of these: 3277725 (28.81%) aligned 0 times 6410544 (56.34%) aligned exactly 1 time 1689582 (14.85%) aligned >1 times 71.19% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 833726 / 8100126 = 0.1029 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 18:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.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 18:50:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:11: 1000000 INFO @ Sun, 21 Jun 2020 18:50:17: 2000000 INFO @ Sun, 21 Jun 2020 18:50:23: 3000000 INFO @ Sun, 21 Jun 2020 18:50:29: 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 18:50:35: 5000000 INFO @ Sun, 21 Jun 2020 18:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.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 18:50:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:42: 6000000 INFO @ Sun, 21 Jun 2020 18:50:42: 1000000 INFO @ Sun, 21 Jun 2020 18:50:48: 7000000 INFO @ Sun, 21 Jun 2020 18:50:48: 2000000 INFO @ Sun, 21 Jun 2020 18:50:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:50:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:50:50: #1 total tags in treatment: 7266400 INFO @ Sun, 21 Jun 2020 18:50:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:50: #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 18:50:50: #1 tags after filtering in treatment: 7266202 INFO @ Sun, 21 Jun 2020 18:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:51: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 18:50:51: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 18:50:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:51: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 18:50:51: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 18:50:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.05_model.r INFO @ Sun, 21 Jun 2020 18:50:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:54: 3000000 INFO @ Sun, 21 Jun 2020 18:51:00: 4000000 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 18:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.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 18:51:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:06: 5000000 INFO @ Sun, 21 Jun 2020 18:51:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:11: 1000000 INFO @ Sun, 21 Jun 2020 18:51:13: 6000000 INFO @ Sun, 21 Jun 2020 18:51:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:14: Done! pass1 - making usageList (341 chroms): 1 millis pass2 - checking and writing primary data (2543 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:17: 2000000 INFO @ Sun, 21 Jun 2020 18:51:19: 7000000 INFO @ Sun, 21 Jun 2020 18:51:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:51:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:51:21: #1 total tags in treatment: 7266400 INFO @ Sun, 21 Jun 2020 18:51:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:21: #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 18:51:21: #1 tags after filtering in treatment: 7266202 INFO @ Sun, 21 Jun 2020 18:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:21: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 18:51:21: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:22: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 18:51:22: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 18:51:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.10_model.r INFO @ Sun, 21 Jun 2020 18:51:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:23: 3000000 INFO @ Sun, 21 Jun 2020 18:51:28: 4000000 INFO @ Sun, 21 Jun 2020 18:51:34: 5000000 INFO @ Sun, 21 Jun 2020 18:51:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:40: 6000000 INFO @ Sun, 21 Jun 2020 18:51:45: 7000000 INFO @ Sun, 21 Jun 2020 18:51:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:46: Done! pass1 - making usageList (210 chroms): 1 millis pass2 - checking and writing primary data (701 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:51:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:51:47: #1 total tags in treatment: 7266400 INFO @ Sun, 21 Jun 2020 18:51:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:47: #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 18:51:47: #1 tags after filtering in treatment: 7266202 INFO @ Sun, 21 Jun 2020 18:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:47: #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 18:51:48: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 18:51:48: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:48: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 18:51:48: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 18:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.20_model.r INFO @ Sun, 21 Jun 2020 18:51:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592404/SRX2592404.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:14: Done! pass1 - making usageList (82 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 5 millis CompletedMACS2peakCalling