Job ID = 6458963 SRX = SRX5827831 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:57:19 prefetch.2.10.7: 1) Downloading 'SRR9051582'... 2020-06-21T12:57:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:01:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:01:50 prefetch.2.10.7: 1) 'SRR9051582' was downloaded successfully 2020-06-21T13:01:50 prefetch.2.10.7: 'SRR9051582' has 0 unresolved dependencies Read 42424049 spots for SRR9051582/SRR9051582.sra Written 42424049 spots for SRR9051582/SRR9051582.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: 00:09:17 42424049 reads; of these: 42424049 (100.00%) were unpaired; of these: 6492058 (15.30%) aligned 0 times 31236571 (73.63%) aligned exactly 1 time 4695420 (11.07%) aligned >1 times 84.70% overall alignment rate Time searching: 00:09:17 Overall time: 00:09:17 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 16 files... [bam_rmdupse_core] 23483232 / 35931991 = 0.6535 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 22:20:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.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 22:20:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:20:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:21:04: 1000000 INFO @ Sun, 21 Jun 2020 22:21:09: 2000000 INFO @ Sun, 21 Jun 2020 22:21:15: 3000000 INFO @ Sun, 21 Jun 2020 22:21:20: 4000000 INFO @ Sun, 21 Jun 2020 22:21:25: 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 22:21:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.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 22:21:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:21:31: 6000000 INFO @ Sun, 21 Jun 2020 22:21:35: 1000000 INFO @ Sun, 21 Jun 2020 22:21:38: 7000000 INFO @ Sun, 21 Jun 2020 22:21:43: 2000000 INFO @ Sun, 21 Jun 2020 22:21:44: 8000000 INFO @ Sun, 21 Jun 2020 22:21:50: 3000000 INFO @ Sun, 21 Jun 2020 22:21:50: 9000000 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 22:21:57: 10000000 INFO @ Sun, 21 Jun 2020 22:21:57: 4000000 INFO @ Sun, 21 Jun 2020 22:21:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.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 22:21:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:22:04: 11000000 INFO @ Sun, 21 Jun 2020 22:22:05: 5000000 INFO @ Sun, 21 Jun 2020 22:22:06: 1000000 INFO @ Sun, 21 Jun 2020 22:22:10: 12000000 INFO @ Sun, 21 Jun 2020 22:22:12: 6000000 INFO @ Sun, 21 Jun 2020 22:22:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:22:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:22:13: #1 total tags in treatment: 12448759 INFO @ Sun, 21 Jun 2020 22:22:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:13: #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 22:22:14: 2000000 INFO @ Sun, 21 Jun 2020 22:22:14: #1 tags after filtering in treatment: 12448756 INFO @ Sun, 21 Jun 2020 22:22:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:15: #2 number of paired peaks: 705 WARNING @ Sun, 21 Jun 2020 22:22:15: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sun, 21 Jun 2020 22:22:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:15: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:15: #2 predicted fragment length is 119 bps INFO @ Sun, 21 Jun 2020 22:22:15: #2 alternative fragment length(s) may be 119,598 bps INFO @ Sun, 21 Jun 2020 22:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.05_model.r INFO @ Sun, 21 Jun 2020 22:22:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:19: 7000000 INFO @ Sun, 21 Jun 2020 22:22:21: 3000000 INFO @ Sun, 21 Jun 2020 22:22:26: 8000000 INFO @ Sun, 21 Jun 2020 22:22:28: 4000000 INFO @ Sun, 21 Jun 2020 22:22:33: 9000000 INFO @ Sun, 21 Jun 2020 22:22:35: 5000000 INFO @ Sun, 21 Jun 2020 22:22:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:40: 10000000 INFO @ Sun, 21 Jun 2020 22:22:43: 6000000 INFO @ Sun, 21 Jun 2020 22:22:48: 11000000 INFO @ Sun, 21 Jun 2020 22:22:50: 7000000 INFO @ Sun, 21 Jun 2020 22:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.05_summits.bed INFO @ Sun, 21 Jun 2020 22:22:53: Done! pass1 - making usageList (542 chroms): 1 millis pass2 - checking and writing primary data (5374 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:22:55: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:22:57: 8000000 INFO @ Sun, 21 Jun 2020 22:22:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:22:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:22:58: #1 total tags in treatment: 12448759 INFO @ Sun, 21 Jun 2020 22:22:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:58: #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 22:22:59: #1 tags after filtering in treatment: 12448756 INFO @ Sun, 21 Jun 2020 22:22:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:59: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:59: #2 number of paired peaks: 705 WARNING @ Sun, 21 Jun 2020 22:22:59: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sun, 21 Jun 2020 22:22:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:00: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:00: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:00: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:00: #2 predicted fragment length is 119 bps INFO @ Sun, 21 Jun 2020 22:23:00: #2 alternative fragment length(s) may be 119,598 bps INFO @ Sun, 21 Jun 2020 22:23:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.10_model.r INFO @ Sun, 21 Jun 2020 22:23:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:03: 9000000 INFO @ Sun, 21 Jun 2020 22:23:10: 10000000 INFO @ Sun, 21 Jun 2020 22:23:17: 11000000 INFO @ Sun, 21 Jun 2020 22:23:24: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:23:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:23:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:23:27: #1 total tags in treatment: 12448759 INFO @ Sun, 21 Jun 2020 22:23:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:27: #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 22:23:27: #1 tags after filtering in treatment: 12448756 INFO @ Sun, 21 Jun 2020 22:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:27: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:28: #2 number of paired peaks: 705 WARNING @ Sun, 21 Jun 2020 22:23:28: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sun, 21 Jun 2020 22:23:28: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:28: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:28: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:28: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:28: #2 predicted fragment length is 119 bps INFO @ Sun, 21 Jun 2020 22:23:28: #2 alternative fragment length(s) may be 119,598 bps INFO @ Sun, 21 Jun 2020 22:23:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.20_model.r INFO @ Sun, 21 Jun 2020 22:23:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.10_summits.bed INFO @ Sun, 21 Jun 2020 22:23:40: Done! pass1 - making usageList (419 chroms): 2 millis pass2 - checking and writing primary data (2807 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827831/SRX5827831.20_summits.bed INFO @ Sun, 21 Jun 2020 22:24:08: Done! pass1 - making usageList (264 chroms): 1 millis pass2 - checking and writing primary data (1070 records, 4 fields): 8 millis CompletedMACS2peakCalling