Job ID = 6457534 SRX = SRX4669026 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:38:25 prefetch.2.10.7: 1) Downloading 'SRR7817551'... 2020-06-21T11:38:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:39:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:39:53 prefetch.2.10.7: 'SRR7817551' is valid 2020-06-21T11:39:53 prefetch.2.10.7: 1) 'SRR7817551' was downloaded successfully 2020-06-21T11:39:53 prefetch.2.10.7: 'SRR7817551' has 0 unresolved dependencies Read 19191421 spots for SRR7817551/SRR7817551.sra Written 19191421 spots for SRR7817551/SRR7817551.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: 00:04:03 19191421 reads; of these: 19191421 (100.00%) were unpaired; of these: 698760 (3.64%) aligned 0 times 16828186 (87.69%) aligned exactly 1 time 1664475 (8.67%) aligned >1 times 96.36% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 3878240 / 18492661 = 0.2097 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 20:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.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 20:48:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:48:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:48:38: 1000000 INFO @ Sun, 21 Jun 2020 20:48:42: 2000000 INFO @ Sun, 21 Jun 2020 20:48:47: 3000000 INFO @ Sun, 21 Jun 2020 20:48:51: 4000000 INFO @ Sun, 21 Jun 2020 20:48:56: 5000000 INFO @ Sun, 21 Jun 2020 20:49:01: 6000000 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 20:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.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 20:49:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:49:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:49:05: 7000000 INFO @ Sun, 21 Jun 2020 20:49:09: 1000000 INFO @ Sun, 21 Jun 2020 20:49:10: 8000000 INFO @ Sun, 21 Jun 2020 20:49:14: 2000000 INFO @ Sun, 21 Jun 2020 20:49:15: 9000000 INFO @ Sun, 21 Jun 2020 20:49:20: 10000000 INFO @ Sun, 21 Jun 2020 20:49:20: 3000000 INFO @ Sun, 21 Jun 2020 20:49:25: 11000000 INFO @ Sun, 21 Jun 2020 20:49:26: 4000000 INFO @ Sun, 21 Jun 2020 20:49:29: 12000000 INFO @ Sun, 21 Jun 2020 20:49:31: 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 20:49:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.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 20:49:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:49:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:49:35: 13000000 INFO @ Sun, 21 Jun 2020 20:49:37: 6000000 INFO @ Sun, 21 Jun 2020 20:49:38: 1000000 INFO @ Sun, 21 Jun 2020 20:49:40: 14000000 INFO @ Sun, 21 Jun 2020 20:49:43: 7000000 INFO @ Sun, 21 Jun 2020 20:49:43: 2000000 INFO @ Sun, 21 Jun 2020 20:49:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:49:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:49:43: #1 total tags in treatment: 14614421 INFO @ Sun, 21 Jun 2020 20:49:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:49:43: #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 20:49:44: #1 tags after filtering in treatment: 14614347 INFO @ Sun, 21 Jun 2020 20:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:49:44: #1 finished! INFO @ Sun, 21 Jun 2020 20:49:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:49:45: #2 number of paired peaks: 721 WARNING @ Sun, 21 Jun 2020 20:49:45: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 21 Jun 2020 20:49:45: start model_add_line... INFO @ Sun, 21 Jun 2020 20:49:45: start X-correlation... INFO @ Sun, 21 Jun 2020 20:49:45: end of X-cor INFO @ Sun, 21 Jun 2020 20:49:45: #2 finished! INFO @ Sun, 21 Jun 2020 20:49:45: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 20:49:45: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 21 Jun 2020 20:49:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.05_model.r INFO @ Sun, 21 Jun 2020 20:49:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:49:48: 3000000 INFO @ Sun, 21 Jun 2020 20:49:48: 8000000 INFO @ Sun, 21 Jun 2020 20:49:53: 4000000 INFO @ Sun, 21 Jun 2020 20:49:54: 9000000 INFO @ Sun, 21 Jun 2020 20:49:58: 5000000 INFO @ Sun, 21 Jun 2020 20:50:00: 10000000 INFO @ Sun, 21 Jun 2020 20:50:03: 6000000 INFO @ Sun, 21 Jun 2020 20:50:05: 11000000 INFO @ Sun, 21 Jun 2020 20:50:08: 7000000 INFO @ Sun, 21 Jun 2020 20:50:11: 12000000 INFO @ Sun, 21 Jun 2020 20:50:13: 8000000 INFO @ Sun, 21 Jun 2020 20:50:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:50:17: 13000000 INFO @ Sun, 21 Jun 2020 20:50:17: 9000000 INFO @ Sun, 21 Jun 2020 20:50:22: 10000000 INFO @ Sun, 21 Jun 2020 20:50:23: 14000000 INFO @ Sun, 21 Jun 2020 20:50:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:50:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:50:26: #1 total tags in treatment: 14614421 INFO @ Sun, 21 Jun 2020 20:50:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:50:26: #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 20:50:27: #1 tags after filtering in treatment: 14614347 INFO @ Sun, 21 Jun 2020 20:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:50:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:50:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:50:27: 11000000 INFO @ Sun, 21 Jun 2020 20:50:28: #2 number of paired peaks: 721 WARNING @ Sun, 21 Jun 2020 20:50:28: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 21 Jun 2020 20:50:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:50:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:50:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:50:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:50:28: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 20:50:28: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 21 Jun 2020 20:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.10_model.r INFO @ Sun, 21 Jun 2020 20:50:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.05_summits.bed INFO @ Sun, 21 Jun 2020 20:50:31: Done! pass1 - making usageList (244 chroms): 2 millis pass2 - checking and writing primary data (10092 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:50:32: 12000000 INFO @ Sun, 21 Jun 2020 20:50:37: 13000000 INFO @ Sun, 21 Jun 2020 20:50:42: 14000000 INFO @ Sun, 21 Jun 2020 20:50:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:50:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:50:45: #1 total tags in treatment: 14614421 INFO @ Sun, 21 Jun 2020 20:50:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:50:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:50:45: #1 tags after filtering in treatment: 14614347 INFO @ Sun, 21 Jun 2020 20:50:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:50:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:50:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:50:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:50:46: #2 number of paired peaks: 721 WARNING @ Sun, 21 Jun 2020 20:50:46: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 21 Jun 2020 20:50:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:50:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:50:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:50:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:50:46: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 20:50:46: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 21 Jun 2020 20:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.20_model.r INFO @ Sun, 21 Jun 2020 20:50:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:50:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:50:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.10_summits.bed INFO @ Sun, 21 Jun 2020 20:51:13: Done! pass1 - making usageList (136 chroms): 1 millis pass2 - checking and writing primary data (6677 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:51:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669026/SRX4669026.20_summits.bed INFO @ Sun, 21 Jun 2020 20:51:33: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (3454 records, 4 fields): 6 millis CompletedMACS2peakCalling