Job ID = 6459891 SRX = SRX969923 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:51:34 prefetch.2.10.7: 1) Downloading 'SRR1931639'... 2020-06-21T13:51:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:53:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:53:37 prefetch.2.10.7: 'SRR1931639' is valid 2020-06-21T13:53:37 prefetch.2.10.7: 1) 'SRR1931639' was downloaded successfully Read 22516723 spots for SRR1931639/SRR1931639.sra Written 22516723 spots for SRR1931639/SRR1931639.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: 00:06:28 22516723 reads; of these: 22516723 (100.00%) were unpaired; of these: 702968 (3.12%) aligned 0 times 16330870 (72.53%) aligned exactly 1 time 5482885 (24.35%) aligned >1 times 96.88% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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_sort_core] merging from 12 files... [bam_rmdupse_core] 4676572 / 21813755 = 0.2144 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 23:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.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 23:05:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:05:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:05:24: 1000000 INFO @ Sun, 21 Jun 2020 23:05:29: 2000000 INFO @ Sun, 21 Jun 2020 23:05:34: 3000000 INFO @ Sun, 21 Jun 2020 23:05:39: 4000000 INFO @ Sun, 21 Jun 2020 23:05:44: 5000000 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 23:05:48: 6000000 INFO @ Sun, 21 Jun 2020 23:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.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 23:05:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:05:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:05:53: 7000000 INFO @ Sun, 21 Jun 2020 23:05:55: 1000000 INFO @ Sun, 21 Jun 2020 23:05:59: 8000000 INFO @ Sun, 21 Jun 2020 23:06:00: 2000000 INFO @ Sun, 21 Jun 2020 23:06:04: 9000000 INFO @ Sun, 21 Jun 2020 23:06:06: 3000000 INFO @ Sun, 21 Jun 2020 23:06:09: 10000000 INFO @ Sun, 21 Jun 2020 23:06:11: 4000000 INFO @ Sun, 21 Jun 2020 23:06:15: 11000000 INFO @ Sun, 21 Jun 2020 23:06:16: 5000000 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 23:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.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 23:06:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:06:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:06:20: 12000000 INFO @ Sun, 21 Jun 2020 23:06:22: 6000000 INFO @ Sun, 21 Jun 2020 23:06:25: 1000000 INFO @ Sun, 21 Jun 2020 23:06:25: 13000000 INFO @ Sun, 21 Jun 2020 23:06:27: 7000000 INFO @ Sun, 21 Jun 2020 23:06:30: 2000000 INFO @ Sun, 21 Jun 2020 23:06:31: 14000000 INFO @ Sun, 21 Jun 2020 23:06:32: 8000000 INFO @ Sun, 21 Jun 2020 23:06:36: 3000000 INFO @ Sun, 21 Jun 2020 23:06:36: 15000000 INFO @ Sun, 21 Jun 2020 23:06:37: 9000000 INFO @ Sun, 21 Jun 2020 23:06:41: 4000000 INFO @ Sun, 21 Jun 2020 23:06:41: 16000000 INFO @ Sun, 21 Jun 2020 23:06:43: 10000000 INFO @ Sun, 21 Jun 2020 23:06:46: 5000000 INFO @ Sun, 21 Jun 2020 23:06:47: 17000000 INFO @ Sun, 21 Jun 2020 23:06:48: 11000000 INFO @ Sun, 21 Jun 2020 23:06:48: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 23:06:48: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 23:06:48: #1 total tags in treatment: 17137183 INFO @ Sun, 21 Jun 2020 23:06:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:06:48: #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 23:06:48: #1 tags after filtering in treatment: 17137181 INFO @ Sun, 21 Jun 2020 23:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:06:48: #1 finished! INFO @ Sun, 21 Jun 2020 23:06:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:06:50: #2 number of paired peaks: 511 WARNING @ Sun, 21 Jun 2020 23:06:50: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Sun, 21 Jun 2020 23:06:50: start model_add_line... INFO @ Sun, 21 Jun 2020 23:06:50: start X-correlation... INFO @ Sun, 21 Jun 2020 23:06:50: end of X-cor INFO @ Sun, 21 Jun 2020 23:06:50: #2 finished! INFO @ Sun, 21 Jun 2020 23:06:50: #2 predicted fragment length is 197 bps INFO @ Sun, 21 Jun 2020 23:06:50: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 21 Jun 2020 23:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.05_model.r INFO @ Sun, 21 Jun 2020 23:06:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:06:52: 6000000 INFO @ Sun, 21 Jun 2020 23:06:53: 12000000 INFO @ Sun, 21 Jun 2020 23:06:57: 7000000 INFO @ Sun, 21 Jun 2020 23:06:58: 13000000 INFO @ Sun, 21 Jun 2020 23:07:02: 8000000 INFO @ Sun, 21 Jun 2020 23:07:04: 14000000 INFO @ Sun, 21 Jun 2020 23:07:07: 9000000 INFO @ Sun, 21 Jun 2020 23:07:09: 15000000 INFO @ Sun, 21 Jun 2020 23:07:12: 10000000 INFO @ Sun, 21 Jun 2020 23:07:14: 16000000 INFO @ Sun, 21 Jun 2020 23:07:17: 11000000 INFO @ Sun, 21 Jun 2020 23:07:20: 17000000 INFO @ Sun, 21 Jun 2020 23:07:21: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 23:07:21: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 23:07:21: #1 total tags in treatment: 17137183 INFO @ Sun, 21 Jun 2020 23:07:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:07:21: #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 23:07:21: #1 tags after filtering in treatment: 17137181 INFO @ Sun, 21 Jun 2020 23:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:07:21: #1 finished! INFO @ Sun, 21 Jun 2020 23:07:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:07:22: #2 number of paired peaks: 511 WARNING @ Sun, 21 Jun 2020 23:07:22: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Sun, 21 Jun 2020 23:07:22: start model_add_line... INFO @ Sun, 21 Jun 2020 23:07:22: start X-correlation... INFO @ Sun, 21 Jun 2020 23:07:22: end of X-cor INFO @ Sun, 21 Jun 2020 23:07:22: #2 finished! INFO @ Sun, 21 Jun 2020 23:07:22: #2 predicted fragment length is 197 bps INFO @ Sun, 21 Jun 2020 23:07:22: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 21 Jun 2020 23:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.10_model.r INFO @ Sun, 21 Jun 2020 23:07:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:07:23: 12000000 INFO @ Sun, 21 Jun 2020 23:07:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:07:28: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:07:33: 14000000 INFO @ Sun, 21 Jun 2020 23:07:38: 15000000 INFO @ Sun, 21 Jun 2020 23:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.05_summits.bed INFO @ Sun, 21 Jun 2020 23:07:39: Done! pass1 - making usageList (733 chroms): 2 millis pass2 - checking and writing primary data (5657 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:07:43: 16000000 INFO @ Sun, 21 Jun 2020 23:07:48: 17000000 INFO @ Sun, 21 Jun 2020 23:07:49: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 23:07:49: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 23:07:49: #1 total tags in treatment: 17137183 INFO @ Sun, 21 Jun 2020 23:07:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:07:49: #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 23:07:49: #1 tags after filtering in treatment: 17137181 INFO @ Sun, 21 Jun 2020 23:07:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:07:49: #1 finished! INFO @ Sun, 21 Jun 2020 23:07:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:07:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:07:50: #2 number of paired peaks: 511 WARNING @ Sun, 21 Jun 2020 23:07:50: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Sun, 21 Jun 2020 23:07:50: start model_add_line... INFO @ Sun, 21 Jun 2020 23:07:50: start X-correlation... INFO @ Sun, 21 Jun 2020 23:07:50: end of X-cor INFO @ Sun, 21 Jun 2020 23:07:50: #2 finished! INFO @ Sun, 21 Jun 2020 23:07:50: #2 predicted fragment length is 197 bps INFO @ Sun, 21 Jun 2020 23:07:50: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 21 Jun 2020 23:07:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.20_model.r INFO @ Sun, 21 Jun 2020 23:07:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:07:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:07:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:08:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:08:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:08:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.10_summits.bed INFO @ Sun, 21 Jun 2020 23:08:12: Done! pass1 - making usageList (655 chroms): 2 millis pass2 - checking and writing primary data (4301 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:08:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:08:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:08:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:08:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969923/SRX969923.20_summits.bed INFO @ Sun, 21 Jun 2020 23:08:42: Done! pass1 - making usageList (514 chroms): 2 millis pass2 - checking and writing primary data (2910 records, 4 fields): 15 millis CompletedMACS2peakCalling