Job ID = 6498722 SRX = SRX749041 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:43:26 prefetch.2.10.7: 1) Downloading 'SRR1636769'... 2020-06-25T23:43:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:46:48 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:46:48 prefetch.2.10.7: 1) 'SRR1636769' was downloaded successfully Read 11933424 spots for SRR1636769/SRR1636769.sra Written 11933424 spots for SRR1636769/SRR1636769.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: 00:40:16 11933424 reads; of these: 11933424 (100.00%) were paired; of these: 962040 (8.06%) aligned concordantly 0 times 6682233 (56.00%) aligned concordantly exactly 1 time 4289151 (35.94%) aligned concordantly >1 times ---- 962040 pairs aligned concordantly 0 times; of these: 139243 (14.47%) aligned discordantly 1 time ---- 822797 pairs aligned 0 times concordantly or discordantly; of these: 1645594 mates make up the pairs; of these: 967123 (58.77%) aligned 0 times 351818 (21.38%) aligned exactly 1 time 326653 (19.85%) aligned >1 times 95.95% overall alignment rate Time searching: 00:40:16 Overall time: 00:40:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 713152 / 11083162 = 0.0643 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 @ Fri, 26 Jun 2020 09:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.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 @ Fri, 26 Jun 2020 09:36:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:36:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:36:47: 1000000 INFO @ Fri, 26 Jun 2020 09:36:52: 2000000 INFO @ Fri, 26 Jun 2020 09:36:57: 3000000 INFO @ Fri, 26 Jun 2020 09:37:02: 4000000 INFO @ Fri, 26 Jun 2020 09:37:06: 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 @ Fri, 26 Jun 2020 09:37:11: 6000000 INFO @ Fri, 26 Jun 2020 09:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.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 @ Fri, 26 Jun 2020 09:37:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:37:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:37:16: 7000000 INFO @ Fri, 26 Jun 2020 09:37:17: 1000000 INFO @ Fri, 26 Jun 2020 09:37:22: 8000000 INFO @ Fri, 26 Jun 2020 09:37:23: 2000000 INFO @ Fri, 26 Jun 2020 09:37:27: 9000000 INFO @ Fri, 26 Jun 2020 09:37:28: 3000000 INFO @ Fri, 26 Jun 2020 09:37:32: 10000000 INFO @ Fri, 26 Jun 2020 09:37:33: 4000000 INFO @ Fri, 26 Jun 2020 09:37:37: 11000000 INFO @ Fri, 26 Jun 2020 09:37:38: 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 @ Fri, 26 Jun 2020 09:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.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 @ Fri, 26 Jun 2020 09:37:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:37:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:37:42: 12000000 INFO @ Fri, 26 Jun 2020 09:37:44: 6000000 INFO @ Fri, 26 Jun 2020 09:37:47: 13000000 INFO @ Fri, 26 Jun 2020 09:37:47: 1000000 INFO @ Fri, 26 Jun 2020 09:37:49: 7000000 INFO @ Fri, 26 Jun 2020 09:37:53: 2000000 INFO @ Fri, 26 Jun 2020 09:37:53: 14000000 INFO @ Fri, 26 Jun 2020 09:37:54: 8000000 INFO @ Fri, 26 Jun 2020 09:37:58: 3000000 INFO @ Fri, 26 Jun 2020 09:37:58: 15000000 INFO @ Fri, 26 Jun 2020 09:37:59: 9000000 INFO @ Fri, 26 Jun 2020 09:38:03: 4000000 INFO @ Fri, 26 Jun 2020 09:38:04: 16000000 INFO @ Fri, 26 Jun 2020 09:38:05: 10000000 INFO @ Fri, 26 Jun 2020 09:38:08: 5000000 INFO @ Fri, 26 Jun 2020 09:38:09: 17000000 INFO @ Fri, 26 Jun 2020 09:38:10: 11000000 INFO @ Fri, 26 Jun 2020 09:38:13: 6000000 INFO @ Fri, 26 Jun 2020 09:38:14: 18000000 INFO @ Fri, 26 Jun 2020 09:38:15: 12000000 INFO @ Fri, 26 Jun 2020 09:38:18: 7000000 INFO @ Fri, 26 Jun 2020 09:38:20: 19000000 INFO @ Fri, 26 Jun 2020 09:38:20: 13000000 INFO @ Fri, 26 Jun 2020 09:38:23: 8000000 INFO @ Fri, 26 Jun 2020 09:38:25: 20000000 INFO @ Fri, 26 Jun 2020 09:38:26: 14000000 INFO @ Fri, 26 Jun 2020 09:38:28: 9000000 INFO @ Fri, 26 Jun 2020 09:38:31: 21000000 INFO @ Fri, 26 Jun 2020 09:38:31: 15000000 INFO @ Fri, 26 Jun 2020 09:38:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:38:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:38:33: #1 total tags in treatment: 10259367 INFO @ Fri, 26 Jun 2020 09:38:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:38:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:38:33: 10000000 INFO @ Fri, 26 Jun 2020 09:38:33: #1 tags after filtering in treatment: 9407938 INFO @ Fri, 26 Jun 2020 09:38:33: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:38:33: #1 finished! INFO @ Fri, 26 Jun 2020 09:38:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:38:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:38:34: #2 number of paired peaks: 740 WARNING @ Fri, 26 Jun 2020 09:38:34: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Fri, 26 Jun 2020 09:38:34: start model_add_line... INFO @ Fri, 26 Jun 2020 09:38:34: start X-correlation... INFO @ Fri, 26 Jun 2020 09:38:34: end of X-cor INFO @ Fri, 26 Jun 2020 09:38:34: #2 finished! INFO @ Fri, 26 Jun 2020 09:38:34: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 09:38:34: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 09:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.05_model.r INFO @ Fri, 26 Jun 2020 09:38:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:38:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:38:36: 16000000 INFO @ Fri, 26 Jun 2020 09:38:38: 11000000 INFO @ Fri, 26 Jun 2020 09:38:41: 17000000 INFO @ Fri, 26 Jun 2020 09:38:43: 12000000 INFO @ Fri, 26 Jun 2020 09:38:46: 18000000 INFO @ Fri, 26 Jun 2020 09:38:48: 13000000 INFO @ Fri, 26 Jun 2020 09:38:51: 19000000 INFO @ Fri, 26 Jun 2020 09:38:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:38:53: 14000000 INFO @ Fri, 26 Jun 2020 09:38:56: 20000000 INFO @ Fri, 26 Jun 2020 09:38:59: 15000000 INFO @ Fri, 26 Jun 2020 09:39:02: 21000000 INFO @ Fri, 26 Jun 2020 09:39:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:39:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:39:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.05_summits.bed INFO @ Fri, 26 Jun 2020 09:39:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2857 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:39:04: 16000000 INFO @ Fri, 26 Jun 2020 09:39:04: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:39:04: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:39:04: #1 total tags in treatment: 10259367 INFO @ Fri, 26 Jun 2020 09:39:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:39:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:39:04: #1 tags after filtering in treatment: 9407938 INFO @ Fri, 26 Jun 2020 09:39:04: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:39:04: #1 finished! INFO @ Fri, 26 Jun 2020 09:39:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:39:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:39:05: #2 number of paired peaks: 740 WARNING @ Fri, 26 Jun 2020 09:39:05: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Fri, 26 Jun 2020 09:39:05: start model_add_line... INFO @ Fri, 26 Jun 2020 09:39:05: start X-correlation... INFO @ Fri, 26 Jun 2020 09:39:05: end of X-cor INFO @ Fri, 26 Jun 2020 09:39:05: #2 finished! INFO @ Fri, 26 Jun 2020 09:39:05: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 09:39:05: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 09:39:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.10_model.r INFO @ Fri, 26 Jun 2020 09:39:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:39:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:39:09: 17000000 INFO @ Fri, 26 Jun 2020 09:39:14: 18000000 INFO @ Fri, 26 Jun 2020 09:39:18: 19000000 INFO @ Fri, 26 Jun 2020 09:39:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:39:23: 20000000 INFO @ Fri, 26 Jun 2020 09:39:29: 21000000 INFO @ Fri, 26 Jun 2020 09:39:31: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:39:31: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:39:31: #1 total tags in treatment: 10259367 INFO @ Fri, 26 Jun 2020 09:39:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:39:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:39:31: #1 tags after filtering in treatment: 9407938 INFO @ Fri, 26 Jun 2020 09:39:31: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:39:31: #1 finished! INFO @ Fri, 26 Jun 2020 09:39:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:39:32: #2 number of paired peaks: 740 WARNING @ Fri, 26 Jun 2020 09:39:32: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Fri, 26 Jun 2020 09:39:32: start model_add_line... INFO @ Fri, 26 Jun 2020 09:39:32: start X-correlation... INFO @ Fri, 26 Jun 2020 09:39:32: end of X-cor INFO @ Fri, 26 Jun 2020 09:39:32: #2 finished! INFO @ Fri, 26 Jun 2020 09:39:32: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 09:39:32: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 09:39:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.20_model.r INFO @ Fri, 26 Jun 2020 09:39:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:39:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:39:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:39:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.10_summits.bed INFO @ Fri, 26 Jun 2020 09:39:32: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1647 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:39:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:39:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:39:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:39:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749041/SRX749041.20_summits.bed INFO @ Fri, 26 Jun 2020 09:39:59: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1031 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。