Job ID = 6453738 SRX = SRX1433376 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:46:33 prefetch.2.10.7: 1) Downloading 'SRR2919841'... 2020-06-21T08:46:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:33 prefetch.2.10.7: 1) 'SRR2919841' was downloaded successfully Read 24060229 spots for SRR2919841/SRR2919841.sra Written 24060229 spots for SRR2919841/SRR2919841.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: 00:06:54 24060229 reads; of these: 24060229 (100.00%) were unpaired; of these: 1600972 (6.65%) aligned 0 times 17234750 (71.63%) aligned exactly 1 time 5224507 (21.71%) aligned >1 times 93.35% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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 12 files... [bam_rmdupse_core] 7820608 / 22459257 = 0.3482 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 18:05:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.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 18:05:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:20: 1000000 INFO @ Sun, 21 Jun 2020 18:05:26: 2000000 INFO @ Sun, 21 Jun 2020 18:05:33: 3000000 INFO @ Sun, 21 Jun 2020 18:05:39: 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 18:05:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.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 18:05:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:46: 5000000 INFO @ Sun, 21 Jun 2020 18:05:51: 1000000 INFO @ Sun, 21 Jun 2020 18:05:53: 6000000 INFO @ Sun, 21 Jun 2020 18:05:58: 2000000 INFO @ Sun, 21 Jun 2020 18:05:59: 7000000 INFO @ Sun, 21 Jun 2020 18:06:05: 3000000 INFO @ Sun, 21 Jun 2020 18:06:05: 8000000 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 18:06:12: 9000000 INFO @ Sun, 21 Jun 2020 18:06:12: 4000000 INFO @ Sun, 21 Jun 2020 18:06:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.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 18:06:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:18: 10000000 INFO @ Sun, 21 Jun 2020 18:06:20: 5000000 INFO @ Sun, 21 Jun 2020 18:06:21: 1000000 INFO @ Sun, 21 Jun 2020 18:06:25: 11000000 INFO @ Sun, 21 Jun 2020 18:06:27: 6000000 INFO @ Sun, 21 Jun 2020 18:06:28: 2000000 INFO @ Sun, 21 Jun 2020 18:06:33: 12000000 INFO @ Sun, 21 Jun 2020 18:06:34: 7000000 INFO @ Sun, 21 Jun 2020 18:06:35: 3000000 INFO @ Sun, 21 Jun 2020 18:06:40: 13000000 INFO @ Sun, 21 Jun 2020 18:06:41: 8000000 INFO @ Sun, 21 Jun 2020 18:06:42: 4000000 INFO @ Sun, 21 Jun 2020 18:06:46: 14000000 INFO @ Sun, 21 Jun 2020 18:06:48: 9000000 INFO @ Sun, 21 Jun 2020 18:06:49: 5000000 INFO @ Sun, 21 Jun 2020 18:06:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:06:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:06:51: #1 total tags in treatment: 14638649 INFO @ Sun, 21 Jun 2020 18:06:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:51: #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 18:06:52: #1 tags after filtering in treatment: 14638579 INFO @ Sun, 21 Jun 2020 18:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:53: #2 number of paired peaks: 943 WARNING @ Sun, 21 Jun 2020 18:06:53: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Sun, 21 Jun 2020 18:06:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:53: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:06:53: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 21 Jun 2020 18:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.05_model.r INFO @ Sun, 21 Jun 2020 18:06:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:06:55: 6000000 INFO @ Sun, 21 Jun 2020 18:06:55: 10000000 INFO @ Sun, 21 Jun 2020 18:07:02: 7000000 INFO @ Sun, 21 Jun 2020 18:07:02: 11000000 INFO @ Sun, 21 Jun 2020 18:07:08: 8000000 INFO @ Sun, 21 Jun 2020 18:07:10: 12000000 INFO @ Sun, 21 Jun 2020 18:07:15: 9000000 INFO @ Sun, 21 Jun 2020 18:07:17: 13000000 INFO @ Sun, 21 Jun 2020 18:07:22: 10000000 INFO @ Sun, 21 Jun 2020 18:07:25: 14000000 INFO @ Sun, 21 Jun 2020 18:07:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:28: 11000000 INFO @ Sun, 21 Jun 2020 18:07:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:07:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:07:30: #1 total tags in treatment: 14638649 INFO @ Sun, 21 Jun 2020 18:07:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:30: #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 18:07:30: #1 tags after filtering in treatment: 14638579 INFO @ Sun, 21 Jun 2020 18:07:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:31: #2 number of paired peaks: 943 WARNING @ Sun, 21 Jun 2020 18:07:31: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:31: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:07:31: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 21 Jun 2020 18:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.10_model.r INFO @ Sun, 21 Jun 2020 18:07:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:07:35: 12000000 INFO @ Sun, 21 Jun 2020 18:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.05_summits.bed INFO @ Sun, 21 Jun 2020 18:07:41: Done! pass1 - making usageList (528 chroms): 2 millis pass2 - checking and writing primary data (4611 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:42: 13000000 INFO @ Sun, 21 Jun 2020 18:07:48: 14000000 INFO @ Sun, 21 Jun 2020 18:07:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:07:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:07:53: #1 total tags in treatment: 14638649 INFO @ Sun, 21 Jun 2020 18:07:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:53: #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 18:07:54: #1 tags after filtering in treatment: 14638579 INFO @ Sun, 21 Jun 2020 18:07:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:55: #2 number of paired peaks: 943 WARNING @ Sun, 21 Jun 2020 18:07:55: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:55: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:07:55: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 21 Jun 2020 18:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.20_model.r INFO @ Sun, 21 Jun 2020 18:07:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.10_summits.bed INFO @ Sun, 21 Jun 2020 18:08:19: Done! pass1 - making usageList (478 chroms): 2 millis pass2 - checking and writing primary data (2952 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433376/SRX1433376.20_summits.bed INFO @ Sun, 21 Jun 2020 18:08:42: Done! pass1 - making usageList (376 chroms): 2 millis pass2 - checking and writing primary data (1604 records, 4 fields): 23 millis CompletedMACS2peakCalling