Job ID = 6453837 SRX = SRX152092 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:43:17 prefetch.2.10.7: 1) Downloading 'SRR504948'... 2020-06-21T08:43:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:50:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:50:32 prefetch.2.10.7: 1) 'SRR504948' was downloaded successfully Read 45299559 spots for SRR504948/SRR504948.sra Written 45299559 spots for SRR504948/SRR504948.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:49 45299559 reads; of these: 45299559 (100.00%) were unpaired; of these: 1943700 (4.29%) aligned 0 times 28991423 (64.00%) aligned exactly 1 time 14364436 (31.71%) aligned >1 times 95.71% overall alignment rate Time searching: 00:18:50 Overall time: 00:18:50 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 20 files... [bam_rmdupse_core] 23201700 / 43355859 = 0.5351 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 18:21:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.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 18:21:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:17: 1000000 INFO @ Sun, 21 Jun 2020 18:21:22: 2000000 INFO @ Sun, 21 Jun 2020 18:21:28: 3000000 INFO @ Sun, 21 Jun 2020 18:21:33: 4000000 INFO @ Sun, 21 Jun 2020 18:21:39: 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 18:21:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.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 18:21:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:44: 6000000 INFO @ Sun, 21 Jun 2020 18:21:47: 1000000 INFO @ Sun, 21 Jun 2020 18:21:50: 7000000 INFO @ Sun, 21 Jun 2020 18:21:53: 2000000 INFO @ Sun, 21 Jun 2020 18:21:55: 8000000 INFO @ Sun, 21 Jun 2020 18:21:59: 3000000 INFO @ Sun, 21 Jun 2020 18:22:01: 9000000 INFO @ Sun, 21 Jun 2020 18:22:06: 4000000 INFO @ Sun, 21 Jun 2020 18:22:07: 10000000 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 18:22:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.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 18:22:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:12: 5000000 INFO @ Sun, 21 Jun 2020 18:22:12: 11000000 INFO @ Sun, 21 Jun 2020 18:22:17: 1000000 INFO @ Sun, 21 Jun 2020 18:22:18: 6000000 INFO @ Sun, 21 Jun 2020 18:22:18: 12000000 INFO @ Sun, 21 Jun 2020 18:22:23: 2000000 INFO @ Sun, 21 Jun 2020 18:22:24: 13000000 INFO @ Sun, 21 Jun 2020 18:22:24: 7000000 INFO @ Sun, 21 Jun 2020 18:22:29: 3000000 INFO @ Sun, 21 Jun 2020 18:22:29: 14000000 INFO @ Sun, 21 Jun 2020 18:22:30: 8000000 INFO @ Sun, 21 Jun 2020 18:22:35: 4000000 INFO @ Sun, 21 Jun 2020 18:22:35: 15000000 INFO @ Sun, 21 Jun 2020 18:22:36: 9000000 INFO @ Sun, 21 Jun 2020 18:22:40: 5000000 INFO @ Sun, 21 Jun 2020 18:22:41: 16000000 INFO @ Sun, 21 Jun 2020 18:22:42: 10000000 INFO @ Sun, 21 Jun 2020 18:22:46: 6000000 INFO @ Sun, 21 Jun 2020 18:22:47: 17000000 INFO @ Sun, 21 Jun 2020 18:22:48: 11000000 INFO @ Sun, 21 Jun 2020 18:22:51: 7000000 INFO @ Sun, 21 Jun 2020 18:22:52: 18000000 INFO @ Sun, 21 Jun 2020 18:22:54: 12000000 INFO @ Sun, 21 Jun 2020 18:22:57: 8000000 INFO @ Sun, 21 Jun 2020 18:22:58: 19000000 INFO @ Sun, 21 Jun 2020 18:23:01: 13000000 INFO @ Sun, 21 Jun 2020 18:23:02: 9000000 INFO @ Sun, 21 Jun 2020 18:23:04: 20000000 INFO @ Sun, 21 Jun 2020 18:23:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:23:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:23:05: #1 total tags in treatment: 20154159 INFO @ Sun, 21 Jun 2020 18:23:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:05: #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 18:23:06: #1 tags after filtering in treatment: 20154156 INFO @ Sun, 21 Jun 2020 18:23:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:07: 14000000 INFO @ Sun, 21 Jun 2020 18:23:07: #2 number of paired peaks: 935 WARNING @ Sun, 21 Jun 2020 18:23:07: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:07: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 18:23:07: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 18:23:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.05_model.r WARNING @ Sun, 21 Jun 2020 18:23:07: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:07: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 18:23:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:23:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:08: 10000000 INFO @ Sun, 21 Jun 2020 18:23:13: 15000000 INFO @ Sun, 21 Jun 2020 18:23:13: 11000000 INFO @ Sun, 21 Jun 2020 18:23:19: 12000000 INFO @ Sun, 21 Jun 2020 18:23:19: 16000000 INFO @ Sun, 21 Jun 2020 18:23:24: 13000000 INFO @ Sun, 21 Jun 2020 18:23:25: 17000000 INFO @ Sun, 21 Jun 2020 18:23:30: 14000000 INFO @ Sun, 21 Jun 2020 18:23:31: 18000000 INFO @ Sun, 21 Jun 2020 18:23:36: 15000000 INFO @ Sun, 21 Jun 2020 18:23:38: 19000000 INFO @ Sun, 21 Jun 2020 18:23:41: 16000000 INFO @ Sun, 21 Jun 2020 18:23:44: 20000000 INFO @ Sun, 21 Jun 2020 18:23:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:23:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:23:45: #1 total tags in treatment: 20154159 INFO @ Sun, 21 Jun 2020 18:23:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:45: #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 18:23:46: #1 tags after filtering in treatment: 20154156 INFO @ Sun, 21 Jun 2020 18:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:46: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:23:47: 17000000 INFO @ Sun, 21 Jun 2020 18:23:47: #2 number of paired peaks: 935 WARNING @ Sun, 21 Jun 2020 18:23:47: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:48: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 18:23:48: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 18:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.10_model.r WARNING @ Sun, 21 Jun 2020 18:23:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:23:48: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 18:23:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:23:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:53: 18000000 INFO @ Sun, 21 Jun 2020 18:23:58: 19000000 INFO @ Sun, 21 Jun 2020 18:24:04: 20000000 INFO @ Sun, 21 Jun 2020 18:24:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:24:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:24:05: #1 total tags in treatment: 20154159 INFO @ Sun, 21 Jun 2020 18:24:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:05: #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 18:24:05: #1 tags after filtering in treatment: 20154156 INFO @ Sun, 21 Jun 2020 18:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:07: #2 number of paired peaks: 935 WARNING @ Sun, 21 Jun 2020 18:24:07: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Sun, 21 Jun 2020 18:24:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:07: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 18:24:07: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 18:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.20_model.r WARNING @ Sun, 21 Jun 2020 18:24:07: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:24:07: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 18:24:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:24:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.05_summits.bed INFO @ Sun, 21 Jun 2020 18:24:07: Done! pass1 - making usageList (649 chroms): 2 millis pass2 - checking and writing primary data (7458 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:24:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.10_summits.bed INFO @ Sun, 21 Jun 2020 18:24:49: Done! pass1 - making usageList (475 chroms): 2 millis pass2 - checking and writing primary data (5096 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:25:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152092/SRX152092.20_summits.bed INFO @ Sun, 21 Jun 2020 18:25:06: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (1262 records, 4 fields): 8 millis CompletedMACS2peakCalling