Job ID = 6454156 SRX = SRX1840075 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:00:04 prefetch.2.10.7: 1) Downloading 'SRR3661301'... 2020-06-21T09:00:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:03:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:47 prefetch.2.10.7: 1) 'SRR3661301' was downloaded successfully Read 16974732 spots for SRR3661301/SRR3661301.sra Written 16974732 spots for SRR3661301/SRR3661301.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: 00:10:52 16974732 reads; of these: 16974732 (100.00%) were unpaired; of these: 828678 (4.88%) aligned 0 times 11650822 (68.64%) aligned exactly 1 time 4495232 (26.48%) aligned >1 times 95.12% overall alignment rate Time searching: 00:10:52 Overall time: 00:10:52 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] 4555535 / 16146054 = 0.2821 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 18:24:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.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 18:24:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:21: 1000000 INFO @ Sun, 21 Jun 2020 18:24:30: 2000000 INFO @ Sun, 21 Jun 2020 18:24:39: 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 18:24:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.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 18:24:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:49: 4000000 INFO @ Sun, 21 Jun 2020 18:24:52: 1000000 INFO @ Sun, 21 Jun 2020 18:24:58: 5000000 INFO @ Sun, 21 Jun 2020 18:25:02: 2000000 INFO @ Sun, 21 Jun 2020 18:25:08: 6000000 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 18:25:12: 3000000 INFO @ Sun, 21 Jun 2020 18:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.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 18:25:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:18: 7000000 INFO @ Sun, 21 Jun 2020 18:25:22: 4000000 INFO @ Sun, 21 Jun 2020 18:25:22: 1000000 INFO @ Sun, 21 Jun 2020 18:25:28: 8000000 INFO @ Sun, 21 Jun 2020 18:25:32: 5000000 INFO @ Sun, 21 Jun 2020 18:25:32: 2000000 INFO @ Sun, 21 Jun 2020 18:25:38: 9000000 INFO @ Sun, 21 Jun 2020 18:25:42: 6000000 INFO @ Sun, 21 Jun 2020 18:25:42: 3000000 INFO @ Sun, 21 Jun 2020 18:25:49: 10000000 INFO @ Sun, 21 Jun 2020 18:25:52: 7000000 INFO @ Sun, 21 Jun 2020 18:25:52: 4000000 INFO @ Sun, 21 Jun 2020 18:26:00: 11000000 INFO @ Sun, 21 Jun 2020 18:26:02: 8000000 INFO @ Sun, 21 Jun 2020 18:26:02: 5000000 INFO @ Sun, 21 Jun 2020 18:26:06: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:26:06: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:26:06: #1 total tags in treatment: 11590519 INFO @ Sun, 21 Jun 2020 18:26:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:06: #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 18:26:07: #1 tags after filtering in treatment: 11590517 INFO @ Sun, 21 Jun 2020 18:26:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:08: #2 number of paired peaks: 673 WARNING @ Sun, 21 Jun 2020 18:26:08: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sun, 21 Jun 2020 18:26:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:08: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 18:26:08: #2 alternative fragment length(s) may be 95,589 bps INFO @ Sun, 21 Jun 2020 18:26:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.05_model.r WARNING @ Sun, 21 Jun 2020 18:26:08: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:26:08: #2 You may need to consider one of the other alternative d(s): 95,589 WARNING @ Sun, 21 Jun 2020 18:26:08: #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 18:26:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:26:12: 9000000 INFO @ Sun, 21 Jun 2020 18:26:13: 6000000 INFO @ Sun, 21 Jun 2020 18:26:23: 10000000 INFO @ Sun, 21 Jun 2020 18:26:23: 7000000 INFO @ Sun, 21 Jun 2020 18:26:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:26:33: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:26:34: 8000000 INFO @ Sun, 21 Jun 2020 18:26:40: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:26:40: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:26:40: #1 total tags in treatment: 11590519 INFO @ Sun, 21 Jun 2020 18:26:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:40: #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 18:26:41: #1 tags after filtering in treatment: 11590517 INFO @ Sun, 21 Jun 2020 18:26:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:41: #2 number of paired peaks: 673 WARNING @ Sun, 21 Jun 2020 18:26:41: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sun, 21 Jun 2020 18:26:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:42: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 18:26:42: #2 alternative fragment length(s) may be 95,589 bps INFO @ Sun, 21 Jun 2020 18:26:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.10_model.r WARNING @ Sun, 21 Jun 2020 18:26:42: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:26:42: #2 You may need to consider one of the other alternative d(s): 95,589 WARNING @ Sun, 21 Jun 2020 18:26:42: #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 18:26:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.05_summits.bed INFO @ Sun, 21 Jun 2020 18:26:42: Done! pass1 - making usageList (781 chroms): 3 millis pass2 - checking and writing primary data (2310 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:26:45: 9000000 INFO @ Sun, 21 Jun 2020 18:26:57: 10000000 INFO @ Sun, 21 Jun 2020 18:27:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:07: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:27:14: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:27:14: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:27:14: #1 total tags in treatment: 11590519 INFO @ Sun, 21 Jun 2020 18:27:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:14: #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 18:27:15: #1 tags after filtering in treatment: 11590517 INFO @ Sun, 21 Jun 2020 18:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.10_summits.bed INFO @ Sun, 21 Jun 2020 18:27:15: Done! pass1 - making usageList (676 chroms): 2 millis pass2 - checking and writing primary data (1611 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:27:16: #2 number of paired peaks: 673 WARNING @ Sun, 21 Jun 2020 18:27:16: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:16: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 18:27:16: #2 alternative fragment length(s) may be 95,589 bps INFO @ Sun, 21 Jun 2020 18:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.20_model.r WARNING @ Sun, 21 Jun 2020 18:27:16: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:16: #2 You may need to consider one of the other alternative d(s): 95,589 WARNING @ Sun, 21 Jun 2020 18:27:16: #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 18:27:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840075/SRX1840075.20_summits.bed INFO @ Sun, 21 Jun 2020 18:27:50: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (1033 records, 4 fields): 31 millis CompletedMACS2peakCalling