Job ID = 6458976 SRX = SRX5827841 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:58:34 prefetch.2.10.7: 1) Downloading 'SRR9051592'... 2020-06-21T12:58:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:03:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:03:56 prefetch.2.10.7: 1) 'SRR9051592' was downloaded successfully 2020-06-21T13:03:56 prefetch.2.10.7: 'SRR9051592' has 0 unresolved dependencies Read 30626481 spots for SRR9051592/SRR9051592.sra Written 30626481 spots for SRR9051592/SRR9051592.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: 00:07:38 30626481 reads; of these: 30626481 (100.00%) were unpaired; of these: 4495777 (14.68%) aligned 0 times 20076921 (65.55%) aligned exactly 1 time 6053783 (19.77%) aligned >1 times 85.32% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 13930307 / 26130704 = 0.5331 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 22:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.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 22:21:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:21:36: 1000000 INFO @ Sun, 21 Jun 2020 22:21:43: 2000000 INFO @ Sun, 21 Jun 2020 22:21:51: 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 22:21:59: 4000000 INFO @ Sun, 21 Jun 2020 22:21:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.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 22:21:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:22:05: 1000000 INFO @ Sun, 21 Jun 2020 22:22:07: 5000000 INFO @ Sun, 21 Jun 2020 22:22:11: 2000000 INFO @ Sun, 21 Jun 2020 22:22:16: 6000000 INFO @ Sun, 21 Jun 2020 22:22:18: 3000000 INFO @ Sun, 21 Jun 2020 22:22:25: 4000000 INFO @ Sun, 21 Jun 2020 22:22:25: 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 22:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.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 22:22:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:22:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:22:31: 5000000 INFO @ Sun, 21 Jun 2020 22:22:34: 8000000 INFO @ Sun, 21 Jun 2020 22:22:37: 6000000 INFO @ Sun, 21 Jun 2020 22:22:38: 1000000 INFO @ Sun, 21 Jun 2020 22:22:43: 9000000 INFO @ Sun, 21 Jun 2020 22:22:43: 7000000 INFO @ Sun, 21 Jun 2020 22:22:48: 2000000 INFO @ Sun, 21 Jun 2020 22:22:50: 8000000 INFO @ Sun, 21 Jun 2020 22:22:53: 10000000 INFO @ Sun, 21 Jun 2020 22:22:56: 9000000 INFO @ Sun, 21 Jun 2020 22:22:57: 3000000 INFO @ Sun, 21 Jun 2020 22:23:03: 11000000 INFO @ Sun, 21 Jun 2020 22:23:03: 10000000 INFO @ Sun, 21 Jun 2020 22:23:07: 4000000 INFO @ Sun, 21 Jun 2020 22:23:09: 11000000 INFO @ Sun, 21 Jun 2020 22:23:12: 12000000 INFO @ Sun, 21 Jun 2020 22:23:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:23:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:23:14: #1 total tags in treatment: 12200397 INFO @ Sun, 21 Jun 2020 22:23:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:14: #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 22:23:15: #1 tags after filtering in treatment: 12200397 INFO @ Sun, 21 Jun 2020 22:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:15: #2 number of paired peaks: 829 WARNING @ Sun, 21 Jun 2020 22:23:15: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Sun, 21 Jun 2020 22:23:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:16: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:16: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:16: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:16: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:23:16: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 22:23:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.05_model.r WARNING @ Sun, 21 Jun 2020 22:23:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:16: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 22:23:16: #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 22:23:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:16: 12000000 INFO @ Sun, 21 Jun 2020 22:23:16: 5000000 INFO @ Sun, 21 Jun 2020 22:23:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:23:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:23:17: #1 total tags in treatment: 12200397 INFO @ Sun, 21 Jun 2020 22:23:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:17: #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 22:23:18: #1 tags after filtering in treatment: 12200397 INFO @ Sun, 21 Jun 2020 22:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:19: #2 number of paired peaks: 829 WARNING @ Sun, 21 Jun 2020 22:23:19: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Sun, 21 Jun 2020 22:23:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:19: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:23:19: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 22:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.10_model.r WARNING @ Sun, 21 Jun 2020 22:23:19: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:19: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 22:23:19: #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 22:23:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:25: 6000000 INFO @ Sun, 21 Jun 2020 22:23:34: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:23:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:42: 8000000 INFO @ Sun, 21 Jun 2020 22:23:50: 9000000 INFO @ Sun, 21 Jun 2020 22:23:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.05_summits.bed INFO @ Sun, 21 Jun 2020 22:23:51: Done! pass1 - making usageList (697 chroms): 2 millis pass2 - checking and writing primary data (2716 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.10_summits.bed INFO @ Sun, 21 Jun 2020 22:23:52: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (1926 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:58: 10000000 INFO @ Sun, 21 Jun 2020 22:24:05: 11000000 INFO @ Sun, 21 Jun 2020 22:24:12: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:24:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:24:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:24:13: #1 total tags in treatment: 12200397 INFO @ Sun, 21 Jun 2020 22:24:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:24:13: #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 22:24:14: #1 tags after filtering in treatment: 12200397 INFO @ Sun, 21 Jun 2020 22:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:24:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:24:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:24:15: #2 number of paired peaks: 829 WARNING @ Sun, 21 Jun 2020 22:24:15: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Sun, 21 Jun 2020 22:24:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:24:15: start X-correlation... INFO @ Sun, 21 Jun 2020 22:24:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:24:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:24:15: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:24:15: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 22:24:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.20_model.r WARNING @ Sun, 21 Jun 2020 22:24:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:24:15: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 22:24:15: #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 22:24:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:24:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:24:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827841/SRX5827841.20_summits.bed INFO @ Sun, 21 Jun 2020 22:24:50: Done! pass1 - making usageList (389 chroms): 1 millis pass2 - checking and writing primary data (1100 records, 4 fields): 24 millis CompletedMACS2peakCalling