Job ID = 6508748 SRX = SRX467104 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:51:24 prefetch.2.10.7: 1) Downloading 'SRR1164528'... 2020-06-26T14:51:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:53:05 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:53:05 prefetch.2.10.7: 1) 'SRR1164528' was downloaded successfully Read 16856264 spots for SRR1164528/SRR1164528.sra Written 16856264 spots for SRR1164528/SRR1164528.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: 00:05:11 16856264 reads; of these: 16856264 (100.00%) were unpaired; of these: 1018511 (6.04%) aligned 0 times 11929928 (70.77%) aligned exactly 1 time 3907825 (23.18%) aligned >1 times 93.96% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 1909755 / 15837753 = 0.1206 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 @ Sat, 27 Jun 2020 00:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.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 @ Sat, 27 Jun 2020 00:03:46: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:03:46: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:03:51: 1000000 INFO @ Sat, 27 Jun 2020 00:03:57: 2000000 INFO @ Sat, 27 Jun 2020 00:04:02: 3000000 INFO @ Sat, 27 Jun 2020 00:04:08: 4000000 INFO @ Sat, 27 Jun 2020 00:04:13: 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 @ Sat, 27 Jun 2020 00:04:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.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 @ Sat, 27 Jun 2020 00:04:16: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:04:16: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:04:19: 6000000 INFO @ Sat, 27 Jun 2020 00:04:21: 1000000 INFO @ Sat, 27 Jun 2020 00:04:25: 7000000 INFO @ Sat, 27 Jun 2020 00:04:27: 2000000 INFO @ Sat, 27 Jun 2020 00:04:31: 8000000 INFO @ Sat, 27 Jun 2020 00:04:33: 3000000 INFO @ Sat, 27 Jun 2020 00:04:36: 9000000 INFO @ Sat, 27 Jun 2020 00:04:38: 4000000 INFO @ Sat, 27 Jun 2020 00:04:42: 10000000 INFO @ Sat, 27 Jun 2020 00:04:44: 5000000 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 @ Sat, 27 Jun 2020 00:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.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 @ Sat, 27 Jun 2020 00:04:46: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:04:46: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:04:48: 11000000 INFO @ Sat, 27 Jun 2020 00:04:49: 6000000 INFO @ Sat, 27 Jun 2020 00:04:53: 1000000 INFO @ Sat, 27 Jun 2020 00:04:54: 12000000 INFO @ Sat, 27 Jun 2020 00:04:55: 7000000 INFO @ Sat, 27 Jun 2020 00:04:59: 2000000 INFO @ Sat, 27 Jun 2020 00:05:00: 13000000 INFO @ Sat, 27 Jun 2020 00:05:01: 8000000 INFO @ Sat, 27 Jun 2020 00:05:06: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:05:06: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:05:06: #1 total tags in treatment: 13927998 INFO @ Sat, 27 Jun 2020 00:05:06: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:05:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:05:06: 9000000 INFO @ Sat, 27 Jun 2020 00:05:06: 3000000 INFO @ Sat, 27 Jun 2020 00:05:06: #1 tags after filtering in treatment: 13927998 INFO @ Sat, 27 Jun 2020 00:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:05:06: #1 finished! INFO @ Sat, 27 Jun 2020 00:05:06: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:05:07: #2 number of paired peaks: 386 WARNING @ Sat, 27 Jun 2020 00:05:07: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sat, 27 Jun 2020 00:05:07: start model_add_line... INFO @ Sat, 27 Jun 2020 00:05:07: start X-correlation... INFO @ Sat, 27 Jun 2020 00:05:07: end of X-cor INFO @ Sat, 27 Jun 2020 00:05:07: #2 finished! INFO @ Sat, 27 Jun 2020 00:05:07: #2 predicted fragment length is 40 bps INFO @ Sat, 27 Jun 2020 00:05:07: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sat, 27 Jun 2020 00:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.05_model.r WARNING @ Sat, 27 Jun 2020 00:05:07: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:05:07: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sat, 27 Jun 2020 00:05:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:05:07: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:05:12: 10000000 INFO @ Sat, 27 Jun 2020 00:05:13: 4000000 INFO @ Sat, 27 Jun 2020 00:05:17: 11000000 INFO @ Sat, 27 Jun 2020 00:05:20: 5000000 INFO @ Sat, 27 Jun 2020 00:05:24: 12000000 INFO @ Sat, 27 Jun 2020 00:05:26: 6000000 INFO @ Sat, 27 Jun 2020 00:05:29: 13000000 INFO @ Sat, 27 Jun 2020 00:05:33: 7000000 INFO @ Sat, 27 Jun 2020 00:05:35: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:05:35: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:05:35: #1 total tags in treatment: 13927998 INFO @ Sat, 27 Jun 2020 00:05:35: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:05:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:05:36: #1 tags after filtering in treatment: 13927998 INFO @ Sat, 27 Jun 2020 00:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:05:36: #1 finished! INFO @ Sat, 27 Jun 2020 00:05:36: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:05:37: #2 number of paired peaks: 386 WARNING @ Sat, 27 Jun 2020 00:05:37: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sat, 27 Jun 2020 00:05:37: start model_add_line... INFO @ Sat, 27 Jun 2020 00:05:37: start X-correlation... INFO @ Sat, 27 Jun 2020 00:05:37: end of X-cor INFO @ Sat, 27 Jun 2020 00:05:37: #2 finished! INFO @ Sat, 27 Jun 2020 00:05:37: #2 predicted fragment length is 40 bps INFO @ Sat, 27 Jun 2020 00:05:37: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sat, 27 Jun 2020 00:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.10_model.r WARNING @ Sat, 27 Jun 2020 00:05:37: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:05:37: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sat, 27 Jun 2020 00:05:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:05:37: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:05:37: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:05:40: 8000000 INFO @ Sat, 27 Jun 2020 00:05:47: 9000000 INFO @ Sat, 27 Jun 2020 00:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.05_summits.bed INFO @ Sat, 27 Jun 2020 00:05:52: Done! pass1 - making usageList (528 chroms): 1 millis pass2 - checking and writing primary data (2198 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:05:53: 10000000 INFO @ Sat, 27 Jun 2020 00:06:00: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:06:06: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:06:07: 12000000 INFO @ Sat, 27 Jun 2020 00:06:14: 13000000 INFO @ Sat, 27 Jun 2020 00:06:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:06:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:06:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.10_summits.bed INFO @ Sat, 27 Jun 2020 00:06:20: Done! INFO @ Sat, 27 Jun 2020 00:06:20: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:06:20: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:06:20: #1 total tags in treatment: 13927998 INFO @ Sat, 27 Jun 2020 00:06:20: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:06:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (446 chroms): 2 millis pass2 - checking and writing primary data (1566 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:06:21: #1 tags after filtering in treatment: 13927998 INFO @ Sat, 27 Jun 2020 00:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:06:21: #1 finished! INFO @ Sat, 27 Jun 2020 00:06:21: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:06:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:06:22: #2 number of paired peaks: 386 WARNING @ Sat, 27 Jun 2020 00:06:22: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sat, 27 Jun 2020 00:06:22: start model_add_line... INFO @ Sat, 27 Jun 2020 00:06:22: start X-correlation... INFO @ Sat, 27 Jun 2020 00:06:22: end of X-cor INFO @ Sat, 27 Jun 2020 00:06:22: #2 finished! INFO @ Sat, 27 Jun 2020 00:06:22: #2 predicted fragment length is 40 bps INFO @ Sat, 27 Jun 2020 00:06:22: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sat, 27 Jun 2020 00:06:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.20_model.r WARNING @ Sat, 27 Jun 2020 00:06:22: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:06:22: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sat, 27 Jun 2020 00:06:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:06:22: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:06:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:06:52: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467104/SRX467104.20_summits.bed INFO @ Sat, 27 Jun 2020 00:07:06: Done! pass1 - making usageList (232 chroms): 0 millis pass2 - checking and writing primary data (480 records, 4 fields): 11 millis CompletedMACS2peakCalling