Job ID = 6459052 SRX = SRX6386733 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:49:37 prefetch.2.10.7: 1) Downloading 'SRR9624465'... 2020-06-21T12:49:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:51:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:51:28 prefetch.2.10.7: 'SRR9624465' is valid 2020-06-21T12:51:28 prefetch.2.10.7: 1) 'SRR9624465' was downloaded successfully Read 10923595 spots for SRR9624465/SRR9624465.sra Written 10923595 spots for SRR9624465/SRR9624465.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: 00:02:51 10923595 reads; of these: 10923595 (100.00%) were unpaired; of these: 821222 (7.52%) aligned 0 times 7323532 (67.04%) aligned exactly 1 time 2778841 (25.44%) aligned >1 times 92.48% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 2807978 / 10102373 = 0.2780 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 21:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.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 21:57:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:51: 1000000 INFO @ Sun, 21 Jun 2020 21:57:57: 2000000 INFO @ Sun, 21 Jun 2020 21:58:03: 3000000 INFO @ Sun, 21 Jun 2020 21:58:10: 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 21:58:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.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 21:58:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:16: 5000000 INFO @ Sun, 21 Jun 2020 21:58:20: 1000000 INFO @ Sun, 21 Jun 2020 21:58:23: 6000000 INFO @ Sun, 21 Jun 2020 21:58:26: 2000000 INFO @ Sun, 21 Jun 2020 21:58:29: 7000000 INFO @ Sun, 21 Jun 2020 21:58:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:58:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:58:31: #1 total tags in treatment: 7294395 INFO @ Sun, 21 Jun 2020 21:58:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:31: #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 21:58:32: 3000000 INFO @ Sun, 21 Jun 2020 21:58:32: #1 tags after filtering in treatment: 7294377 INFO @ Sun, 21 Jun 2020 21:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:32: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:32: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 21:58:32: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:32: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:58:32: #2 alternative fragment length(s) may be 4,43,576 bps INFO @ Sun, 21 Jun 2020 21:58:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.05_model.r WARNING @ Sun, 21 Jun 2020 21:58:32: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:32: #2 You may need to consider one of the other alternative d(s): 4,43,576 WARNING @ Sun, 21 Jun 2020 21:58:32: #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 21:58:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:37: 4000000 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 21:58:42: 5000000 INFO @ Sun, 21 Jun 2020 21:58:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.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 21:58:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:48: 6000000 INFO @ Sun, 21 Jun 2020 21:58:50: 1000000 INFO @ Sun, 21 Jun 2020 21:58:54: 7000000 INFO @ Sun, 21 Jun 2020 21:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.05_summits.bed INFO @ Sun, 21 Jun 2020 21:58:55: Done! INFO @ Sun, 21 Jun 2020 21:58:55: 2000000 pass1 - making usageList (603 chroms): 1 millis pass2 - checking and writing primary data (2298 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:58:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:58:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:58:56: #1 total tags in treatment: 7294395 INFO @ Sun, 21 Jun 2020 21:58:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:56: #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 21:58:56: #1 tags after filtering in treatment: 7294377 INFO @ Sun, 21 Jun 2020 21:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:57: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 21:58:57: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:57: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:58:57: #2 alternative fragment length(s) may be 4,43,576 bps INFO @ Sun, 21 Jun 2020 21:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.10_model.r WARNING @ Sun, 21 Jun 2020 21:58:57: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:57: #2 You may need to consider one of the other alternative d(s): 4,43,576 WARNING @ Sun, 21 Jun 2020 21:58:57: #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 21:58:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:01: 3000000 INFO @ Sun, 21 Jun 2020 21:59:06: 4000000 INFO @ Sun, 21 Jun 2020 21:59:12: 5000000 INFO @ Sun, 21 Jun 2020 21:59:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:17: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:59:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.10_summits.bed INFO @ Sun, 21 Jun 2020 21:59:20: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (1842 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:23: 7000000 INFO @ Sun, 21 Jun 2020 21:59:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:59:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:59:24: #1 total tags in treatment: 7294395 INFO @ Sun, 21 Jun 2020 21:59:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:24: #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 21:59:25: #1 tags after filtering in treatment: 7294377 INFO @ Sun, 21 Jun 2020 21:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:25: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 21:59:25: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:25: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:59:25: #2 alternative fragment length(s) may be 4,43,576 bps INFO @ Sun, 21 Jun 2020 21:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.20_model.r WARNING @ Sun, 21 Jun 2020 21:59:25: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:25: #2 You may need to consider one of the other alternative d(s): 4,43,576 WARNING @ Sun, 21 Jun 2020 21:59:25: #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 21:59:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:59:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386733/SRX6386733.20_summits.bed INFO @ Sun, 21 Jun 2020 21:59:49: Done! pass1 - making usageList (365 chroms): 1 millis pass2 - checking and writing primary data (962 records, 4 fields): 11 millis CompletedMACS2peakCalling