Job ID = 6454532 SRX = SRX220301 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:16:39 prefetch.2.10.7: 1) Downloading 'SRR653346'... 2020-06-21T09:16:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:22:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:22:44 prefetch.2.10.7: 1) 'SRR653346' was downloaded successfully Read 24511183 spots for SRR653346/SRR653346.sra Written 24511183 spots for SRR653346/SRR653346.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: 00:06:11 24511183 reads; of these: 24511183 (100.00%) were unpaired; of these: 3311292 (13.51%) aligned 0 times 14604594 (59.58%) aligned exactly 1 time 6595297 (26.91%) aligned >1 times 86.49% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 6151256 / 21199891 = 0.2902 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 18:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.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 18:34:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:33: 1000000 INFO @ Sun, 21 Jun 2020 18:34:38: 2000000 INFO @ Sun, 21 Jun 2020 18:34:43: 3000000 INFO @ Sun, 21 Jun 2020 18:34:48: 4000000 INFO @ Sun, 21 Jun 2020 18:34:53: 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 18:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.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 18:34:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:58: 6000000 INFO @ Sun, 21 Jun 2020 18:35:03: 7000000 INFO @ Sun, 21 Jun 2020 18:35:03: 1000000 INFO @ Sun, 21 Jun 2020 18:35:09: 8000000 INFO @ Sun, 21 Jun 2020 18:35:10: 2000000 INFO @ Sun, 21 Jun 2020 18:35:14: 9000000 INFO @ Sun, 21 Jun 2020 18:35:16: 3000000 INFO @ Sun, 21 Jun 2020 18:35:20: 10000000 INFO @ Sun, 21 Jun 2020 18:35:22: 4000000 INFO @ Sun, 21 Jun 2020 18:35:25: 11000000 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 18:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.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 18:35:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:28: 5000000 INFO @ Sun, 21 Jun 2020 18:35:31: 12000000 INFO @ Sun, 21 Jun 2020 18:35:33: 1000000 INFO @ Sun, 21 Jun 2020 18:35:34: 6000000 INFO @ Sun, 21 Jun 2020 18:35:37: 13000000 INFO @ Sun, 21 Jun 2020 18:35:39: 2000000 INFO @ Sun, 21 Jun 2020 18:35:40: 7000000 INFO @ Sun, 21 Jun 2020 18:35:42: 14000000 INFO @ Sun, 21 Jun 2020 18:35:44: 3000000 INFO @ Sun, 21 Jun 2020 18:35:46: 8000000 INFO @ Sun, 21 Jun 2020 18:35:48: 15000000 INFO @ Sun, 21 Jun 2020 18:35:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:35:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:35:48: #1 total tags in treatment: 15048635 INFO @ Sun, 21 Jun 2020 18:35:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:48: #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 18:35:49: #1 tags after filtering in treatment: 15048573 INFO @ Sun, 21 Jun 2020 18:35:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:50: #2 number of paired peaks: 768 WARNING @ Sun, 21 Jun 2020 18:35:50: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sun, 21 Jun 2020 18:35:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:50: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 18:35:50: #2 alternative fragment length(s) may be 3,88 bps INFO @ Sun, 21 Jun 2020 18:35:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.05_model.r INFO @ Sun, 21 Jun 2020 18:35:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:50: 4000000 INFO @ Sun, 21 Jun 2020 18:35:52: 9000000 INFO @ Sun, 21 Jun 2020 18:35:56: 5000000 INFO @ Sun, 21 Jun 2020 18:35:58: 10000000 INFO @ Sun, 21 Jun 2020 18:36:01: 6000000 INFO @ Sun, 21 Jun 2020 18:36:04: 11000000 INFO @ Sun, 21 Jun 2020 18:36:06: 7000000 INFO @ Sun, 21 Jun 2020 18:36:10: 12000000 INFO @ Sun, 21 Jun 2020 18:36:12: 8000000 INFO @ Sun, 21 Jun 2020 18:36:16: 13000000 INFO @ Sun, 21 Jun 2020 18:36:17: 9000000 INFO @ Sun, 21 Jun 2020 18:36:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:23: 14000000 INFO @ Sun, 21 Jun 2020 18:36:23: 10000000 INFO @ Sun, 21 Jun 2020 18:36:28: 11000000 INFO @ Sun, 21 Jun 2020 18:36:29: 15000000 INFO @ Sun, 21 Jun 2020 18:36:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:36:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:36:29: #1 total tags in treatment: 15048635 INFO @ Sun, 21 Jun 2020 18:36:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:29: #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 18:36:30: #1 tags after filtering in treatment: 15048573 INFO @ Sun, 21 Jun 2020 18:36:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:31: #2 number of paired peaks: 768 WARNING @ Sun, 21 Jun 2020 18:36:31: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:31: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 18:36:31: #2 alternative fragment length(s) may be 3,88 bps INFO @ Sun, 21 Jun 2020 18:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.10_model.r INFO @ Sun, 21 Jun 2020 18:36:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:34: 12000000 INFO @ Sun, 21 Jun 2020 18:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.05_summits.bed INFO @ Sun, 21 Jun 2020 18:36:38: Done! INFO @ Sun, 21 Jun 2020 18:36:38: 13000000 pass1 - making usageList (717 chroms): 2 millis pass2 - checking and writing primary data (10380 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:36:43: 14000000 INFO @ Sun, 21 Jun 2020 18:36:48: 15000000 INFO @ Sun, 21 Jun 2020 18:36:49: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:36:49: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:36:49: #1 total tags in treatment: 15048635 INFO @ Sun, 21 Jun 2020 18:36:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:49: #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 18:36:49: #1 tags after filtering in treatment: 15048573 INFO @ Sun, 21 Jun 2020 18:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:50: #2 number of paired peaks: 768 WARNING @ Sun, 21 Jun 2020 18:36:50: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:50: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 18:36:50: #2 alternative fragment length(s) may be 3,88 bps INFO @ Sun, 21 Jun 2020 18:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.20_model.r INFO @ Sun, 21 Jun 2020 18:36:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:37:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.10_summits.bed INFO @ Sun, 21 Jun 2020 18:37:13: Done! pass1 - making usageList (537 chroms): 1 millis pass2 - checking and writing primary data (3984 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:37:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220301/SRX220301.20_summits.bed INFO @ Sun, 21 Jun 2020 18:37:38: Done! pass1 - making usageList (211 chroms): 0 millis pass2 - checking and writing primary data (795 records, 4 fields): 7 millis CompletedMACS2peakCalling