Job ID = 6454140 SRX = SRX183886 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:53:49 prefetch.2.10.7: 1) Downloading 'SRR557681'... 2020-06-21T08:53:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:54:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:54:43 prefetch.2.10.7: 'SRR557681' is valid 2020-06-21T08:54:43 prefetch.2.10.7: 1) 'SRR557681' was downloaded successfully Read 6868536 spots for SRR557681/SRR557681.sra Written 6868536 spots for SRR557681/SRR557681.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: 00:02:16 6868536 reads; of these: 6868536 (100.00%) were unpaired; of these: 317979 (4.63%) aligned 0 times 3097720 (45.10%) aligned exactly 1 time 3452837 (50.27%) aligned >1 times 95.37% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 1317885 / 6550557 = 0.2012 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 17:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.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 17:58:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:45: 1000000 INFO @ Sun, 21 Jun 2020 17:58:49: 2000000 INFO @ Sun, 21 Jun 2020 17:58:53: 3000000 INFO @ Sun, 21 Jun 2020 17:58:58: 4000000 INFO @ Sun, 21 Jun 2020 17:59:02: 5000000 INFO @ Sun, 21 Jun 2020 17:59:03: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:59:03: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:59:03: #1 total tags in treatment: 5232672 INFO @ Sun, 21 Jun 2020 17:59:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:03: #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 17:59:04: #1 tags after filtering in treatment: 5232667 INFO @ Sun, 21 Jun 2020 17:59:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:04: #2 number of paired peaks: 916 WARNING @ Sun, 21 Jun 2020 17:59:04: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Sun, 21 Jun 2020 17:59:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:04: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:59:04: #2 alternative fragment length(s) may be 4,22,46,583 bps INFO @ Sun, 21 Jun 2020 17:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.05_model.r INFO @ Sun, 21 Jun 2020 17:59:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:04: #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 @ Sun, 21 Jun 2020 17:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.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 17:59:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:15: 1000000 INFO @ Sun, 21 Jun 2020 17:59:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:19: 2000000 INFO @ Sun, 21 Jun 2020 17:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.05_summits.bed INFO @ Sun, 21 Jun 2020 17:59:21: Done! pass1 - making usageList (468 chroms): 1 millis pass2 - checking and writing primary data (2041 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:59:24: 3000000 INFO @ Sun, 21 Jun 2020 17:59:28: 4000000 INFO @ Sun, 21 Jun 2020 17:59:33: 5000000 INFO @ Sun, 21 Jun 2020 17:59:34: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:59:34: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:59:34: #1 total tags in treatment: 5232672 INFO @ Sun, 21 Jun 2020 17:59:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:34: #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 17:59:34: #1 tags after filtering in treatment: 5232667 INFO @ Sun, 21 Jun 2020 17:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:35: #2 number of paired peaks: 916 WARNING @ Sun, 21 Jun 2020 17:59:35: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Sun, 21 Jun 2020 17:59:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:35: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:59:35: #2 alternative fragment length(s) may be 4,22,46,583 bps INFO @ Sun, 21 Jun 2020 17:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.10_model.r INFO @ Sun, 21 Jun 2020 17:59:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:35: #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 17:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.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 17:59:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:46: 1000000 INFO @ Sun, 21 Jun 2020 17:59:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:51: 2000000 INFO @ Sun, 21 Jun 2020 17:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.10_summits.bed INFO @ Sun, 21 Jun 2020 17:59:51: Done! pass1 - making usageList (284 chroms): 1 millis pass2 - checking and writing primary data (643 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:59:56: 3000000 INFO @ Sun, 21 Jun 2020 18:00:01: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:00:06: 5000000 INFO @ Sun, 21 Jun 2020 18:00:07: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 18:00:07: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 18:00:07: #1 total tags in treatment: 5232672 INFO @ Sun, 21 Jun 2020 18:00:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:07: #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 18:00:07: #1 tags after filtering in treatment: 5232667 INFO @ Sun, 21 Jun 2020 18:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:08: #2 number of paired peaks: 916 WARNING @ Sun, 21 Jun 2020 18:00:08: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Sun, 21 Jun 2020 18:00:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:08: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 18:00:08: #2 alternative fragment length(s) may be 4,22,46,583 bps INFO @ Sun, 21 Jun 2020 18:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.20_model.r INFO @ Sun, 21 Jun 2020 18:00:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:00:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183886/SRX183886.20_summits.bed INFO @ Sun, 21 Jun 2020 18:00:25: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 4 millis CompletedMACS2peakCalling