Job ID = 6458556 SRX = SRX5343091 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:28:34 prefetch.2.10.7: 1) Downloading 'SRR8540868'... 2020-06-21T12:28:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:30:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:30:51 prefetch.2.10.7: 'SRR8540868' is valid 2020-06-21T12:30:51 prefetch.2.10.7: 1) 'SRR8540868' was downloaded successfully 2020-06-21T12:30:51 prefetch.2.10.7: 'SRR8540868' has 0 unresolved dependencies Read 16924773 spots for SRR8540868/SRR8540868.sra Written 16924773 spots for SRR8540868/SRR8540868.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: 00:04:18 16924773 reads; of these: 16924773 (100.00%) were unpaired; of these: 2974089 (17.57%) aligned 0 times 12406734 (73.31%) aligned exactly 1 time 1543950 (9.12%) aligned >1 times 82.43% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 3065395 / 13950684 = 0.2197 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 21:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.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 21:40:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:19: 1000000 INFO @ Sun, 21 Jun 2020 21:40:26: 2000000 INFO @ Sun, 21 Jun 2020 21:40:33: 3000000 INFO @ Sun, 21 Jun 2020 21:40:40: 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 21:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.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 21:40:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:47: 5000000 INFO @ Sun, 21 Jun 2020 21:40:49: 1000000 INFO @ Sun, 21 Jun 2020 21:40:55: 6000000 INFO @ Sun, 21 Jun 2020 21:40:57: 2000000 INFO @ Sun, 21 Jun 2020 21:41:02: 7000000 INFO @ Sun, 21 Jun 2020 21:41:04: 3000000 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 21:41:10: 8000000 INFO @ Sun, 21 Jun 2020 21:41:12: 4000000 INFO @ Sun, 21 Jun 2020 21:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.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 21:41:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:18: 9000000 INFO @ Sun, 21 Jun 2020 21:41:20: 5000000 INFO @ Sun, 21 Jun 2020 21:41:23: 1000000 INFO @ Sun, 21 Jun 2020 21:41:26: 10000000 INFO @ Sun, 21 Jun 2020 21:41:27: 6000000 INFO @ Sun, 21 Jun 2020 21:41:30: 2000000 INFO @ Sun, 21 Jun 2020 21:41:33: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:41:33: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:41:33: #1 total tags in treatment: 10885289 INFO @ Sun, 21 Jun 2020 21:41:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:33: #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 21:41:33: #1 tags after filtering in treatment: 10885276 INFO @ Sun, 21 Jun 2020 21:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:34: #2 number of paired peaks: 359 WARNING @ Sun, 21 Jun 2020 21:41:34: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 21 Jun 2020 21:41:34: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:34: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:41:34: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 21:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.05_model.r INFO @ Sun, 21 Jun 2020 21:41:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:35: 7000000 INFO @ Sun, 21 Jun 2020 21:41:37: 3000000 INFO @ Sun, 21 Jun 2020 21:41:43: 8000000 INFO @ Sun, 21 Jun 2020 21:41:44: 4000000 INFO @ Sun, 21 Jun 2020 21:41:51: 5000000 INFO @ Sun, 21 Jun 2020 21:41:51: 9000000 INFO @ Sun, 21 Jun 2020 21:41:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:58: 6000000 INFO @ Sun, 21 Jun 2020 21:41:59: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:42:04: 7000000 INFO @ Sun, 21 Jun 2020 21:42:06: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:42:06: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:42:06: #1 total tags in treatment: 10885289 INFO @ Sun, 21 Jun 2020 21:42:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:06: #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 21:42:07: #1 tags after filtering in treatment: 10885276 INFO @ Sun, 21 Jun 2020 21:42:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:07: #2 number of paired peaks: 359 WARNING @ Sun, 21 Jun 2020 21:42:07: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 21 Jun 2020 21:42:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:07: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:42:07: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 21:42:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.10_model.r INFO @ Sun, 21 Jun 2020 21:42:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.05_summits.bed INFO @ Sun, 21 Jun 2020 21:42:08: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (5495 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:42:11: 8000000 INFO @ Sun, 21 Jun 2020 21:42:17: 9000000 INFO @ Sun, 21 Jun 2020 21:42:23: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:42:29: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:42:29: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:42:29: #1 total tags in treatment: 10885289 INFO @ Sun, 21 Jun 2020 21:42:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:29: #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 21:42:29: #1 tags after filtering in treatment: 10885276 INFO @ Sun, 21 Jun 2020 21:42:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:29: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:30: #2 number of paired peaks: 359 WARNING @ Sun, 21 Jun 2020 21:42:30: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 21 Jun 2020 21:42:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:30: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 21:42:30: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 21:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.20_model.r INFO @ Sun, 21 Jun 2020 21:42:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.10_summits.bed INFO @ Sun, 21 Jun 2020 21:42:42: Done! pass1 - making usageList (105 chroms): 1 millis pass2 - checking and writing primary data (3393 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:42:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343091/SRX5343091.20_summits.bed INFO @ Sun, 21 Jun 2020 21:43:04: Done! pass1 - making usageList (85 chroms): 1 millis pass2 - checking and writing primary data (1284 records, 4 fields): 5 millis CompletedMACS2peakCalling