Job ID = 6455617 SRX = SRX287930 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:10:21 prefetch.2.10.7: 1) Downloading 'SRR870119'... 2020-06-21T10:10:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:12:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:12:59 prefetch.2.10.7: 'SRR870119' is valid 2020-06-21T10:12:59 prefetch.2.10.7: 1) 'SRR870119' was downloaded successfully Read 12148753 spots for SRR870119/SRR870119.sra Written 12148753 spots for SRR870119/SRR870119.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: 00:03:54 12148753 reads; of these: 12148753 (100.00%) were unpaired; of these: 741202 (6.10%) aligned 0 times 7741912 (63.73%) aligned exactly 1 time 3665639 (30.17%) aligned >1 times 93.90% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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 8 files... [bam_rmdupse_core] 2231321 / 11407551 = 0.1956 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 19:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.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 19:20:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:20:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:20:51: 1000000 INFO @ Sun, 21 Jun 2020 19:20:59: 2000000 INFO @ Sun, 21 Jun 2020 19:21:07: 3000000 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 19:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.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 19:21:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:14: 4000000 INFO @ Sun, 21 Jun 2020 19:21:21: 1000000 INFO @ Sun, 21 Jun 2020 19:21:23: 5000000 INFO @ Sun, 21 Jun 2020 19:21:29: 2000000 INFO @ Sun, 21 Jun 2020 19:21:31: 6000000 INFO @ Sun, 21 Jun 2020 19:21:36: 3000000 INFO @ Sun, 21 Jun 2020 19:21:39: 7000000 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 19:21:43: 4000000 INFO @ Sun, 21 Jun 2020 19:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.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 19:21:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:48: 8000000 INFO @ Sun, 21 Jun 2020 19:21:51: 5000000 INFO @ Sun, 21 Jun 2020 19:21:52: 1000000 INFO @ Sun, 21 Jun 2020 19:21:56: 9000000 INFO @ Sun, 21 Jun 2020 19:21:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:21:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:21:58: #1 total tags in treatment: 9176230 INFO @ Sun, 21 Jun 2020 19:21:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:21:58: #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 19:21:58: 6000000 INFO @ Sun, 21 Jun 2020 19:21:58: #1 tags after filtering in treatment: 9176230 INFO @ Sun, 21 Jun 2020 19:21:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:21:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:21:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:21:59: #2 number of paired peaks: 912 WARNING @ Sun, 21 Jun 2020 19:21:59: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Sun, 21 Jun 2020 19:21:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:21:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:21:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:21:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:21:59: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:21:59: #2 alternative fragment length(s) may be 4,42,564 bps INFO @ Sun, 21 Jun 2020 19:21:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.05_model.r WARNING @ Sun, 21 Jun 2020 19:21:59: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:21:59: #2 You may need to consider one of the other alternative d(s): 4,42,564 WARNING @ Sun, 21 Jun 2020 19:21:59: #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 19:21:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:21:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:59: 2000000 INFO @ Sun, 21 Jun 2020 19:22:05: 7000000 INFO @ Sun, 21 Jun 2020 19:22:07: 3000000 INFO @ Sun, 21 Jun 2020 19:22:13: 8000000 INFO @ Sun, 21 Jun 2020 19:22:15: 4000000 INFO @ Sun, 21 Jun 2020 19:22:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:20: 9000000 INFO @ Sun, 21 Jun 2020 19:22:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:22: #1 total tags in treatment: 9176230 INFO @ Sun, 21 Jun 2020 19:22:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:22: #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 19:22:22: #1 tags after filtering in treatment: 9176230 INFO @ Sun, 21 Jun 2020 19:22:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:22: 5000000 INFO @ Sun, 21 Jun 2020 19:22:23: #2 number of paired peaks: 912 WARNING @ Sun, 21 Jun 2020 19:22:23: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:23: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:22:23: #2 alternative fragment length(s) may be 4,42,564 bps INFO @ Sun, 21 Jun 2020 19:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.10_model.r WARNING @ Sun, 21 Jun 2020 19:22:23: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:22:23: #2 You may need to consider one of the other alternative d(s): 4,42,564 WARNING @ Sun, 21 Jun 2020 19:22:23: #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 19:22:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.05_summits.bed INFO @ Sun, 21 Jun 2020 19:22:27: Done! pass1 - making usageList (610 chroms): 1 millis pass2 - checking and writing primary data (2272 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:22:30: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:22:37: 7000000 INFO @ Sun, 21 Jun 2020 19:22:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:44: 8000000 INFO @ Sun, 21 Jun 2020 19:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:22:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:22:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.10_summits.bed INFO @ Sun, 21 Jun 2020 19:22:51: Done! pass1 - making usageList (499 chroms): 2 millis pass2 - checking and writing primary data (1801 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:22:52: 9000000 INFO @ Sun, 21 Jun 2020 19:22:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:53: #1 total tags in treatment: 9176230 INFO @ Sun, 21 Jun 2020 19:22:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:53: #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 19:22:53: #1 tags after filtering in treatment: 9176230 INFO @ Sun, 21 Jun 2020 19:22:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:54: #2 number of paired peaks: 912 WARNING @ Sun, 21 Jun 2020 19:22:54: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:54: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:22:54: #2 alternative fragment length(s) may be 4,42,564 bps INFO @ Sun, 21 Jun 2020 19:22:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.20_model.r WARNING @ Sun, 21 Jun 2020 19:22:54: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:22:54: #2 You may need to consider one of the other alternative d(s): 4,42,564 WARNING @ Sun, 21 Jun 2020 19:22:54: #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 19:22:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:23:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287930/SRX287930.20_summits.bed INFO @ Sun, 21 Jun 2020 19:23:22: Done! pass1 - making usageList (333 chroms): 1 millis pass2 - checking and writing primary data (740 records, 4 fields): 10 millis CompletedMACS2peakCalling