Job ID = 6454612 SRX = SRX2399657 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:29 prefetch.2.10.7: 1) Downloading 'SRR5081491'... 2020-06-21T09:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:31:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:31:12 prefetch.2.10.7: 1) 'SRR5081491' was downloaded successfully 2020-06-21T09:31:12 prefetch.2.10.7: 'SRR5081491' has 0 unresolved dependencies Read 32523795 spots for SRR5081491/SRR5081491.sra Written 32523795 spots for SRR5081491/SRR5081491.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:07 32523795 reads; of these: 32523795 (100.00%) were unpaired; of these: 15580213 (47.90%) aligned 0 times 10288018 (31.63%) aligned exactly 1 time 6655564 (20.46%) aligned >1 times 52.10% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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] 4574147 / 16943582 = 0.2700 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 18:45:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.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 18:45:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:41: 1000000 INFO @ Sun, 21 Jun 2020 18:45:46: 2000000 INFO @ Sun, 21 Jun 2020 18:45:52: 3000000 INFO @ Sun, 21 Jun 2020 18:45:58: 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 18:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.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 18:46:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:03: 5000000 INFO @ Sun, 21 Jun 2020 18:46:09: 1000000 INFO @ Sun, 21 Jun 2020 18:46:09: 6000000 INFO @ Sun, 21 Jun 2020 18:46:14: 2000000 INFO @ Sun, 21 Jun 2020 18:46:14: 7000000 INFO @ Sun, 21 Jun 2020 18:46:20: 3000000 INFO @ Sun, 21 Jun 2020 18:46:20: 8000000 INFO @ Sun, 21 Jun 2020 18:46:26: 9000000 INFO @ Sun, 21 Jun 2020 18:46:26: 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 18:46:32: 5000000 INFO @ Sun, 21 Jun 2020 18:46:32: 10000000 INFO @ Sun, 21 Jun 2020 18:46:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.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 18:46:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:38: 6000000 INFO @ Sun, 21 Jun 2020 18:46:38: 11000000 INFO @ Sun, 21 Jun 2020 18:46:39: 1000000 INFO @ Sun, 21 Jun 2020 18:46:44: 7000000 INFO @ Sun, 21 Jun 2020 18:46:44: 12000000 INFO @ Sun, 21 Jun 2020 18:46:45: 2000000 INFO @ Sun, 21 Jun 2020 18:46:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:46:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:46:46: #1 total tags in treatment: 12369435 INFO @ Sun, 21 Jun 2020 18:46:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:46: #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 18:46:47: #1 tags after filtering in treatment: 12369435 INFO @ Sun, 21 Jun 2020 18:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:48: #2 number of paired peaks: 524 WARNING @ Sun, 21 Jun 2020 18:46:48: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:48: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 18:46:48: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 18:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.05_model.r WARNING @ Sun, 21 Jun 2020 18:46:48: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:48: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 18:46:48: #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 18:46:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:50: 8000000 INFO @ Sun, 21 Jun 2020 18:46:51: 3000000 INFO @ Sun, 21 Jun 2020 18:46:56: 9000000 INFO @ Sun, 21 Jun 2020 18:46:57: 4000000 INFO @ Sun, 21 Jun 2020 18:47:02: 10000000 INFO @ Sun, 21 Jun 2020 18:47:03: 5000000 INFO @ Sun, 21 Jun 2020 18:47:07: 11000000 INFO @ Sun, 21 Jun 2020 18:47:09: 6000000 INFO @ Sun, 21 Jun 2020 18:47:13: 12000000 INFO @ Sun, 21 Jun 2020 18:47:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:14: 7000000 INFO @ Sun, 21 Jun 2020 18:47:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:16: #1 total tags in treatment: 12369435 INFO @ Sun, 21 Jun 2020 18:47:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:16: #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 18:47:16: #1 tags after filtering in treatment: 12369435 INFO @ Sun, 21 Jun 2020 18:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:17: #2 number of paired peaks: 524 WARNING @ Sun, 21 Jun 2020 18:47:17: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:17: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 18:47:17: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 18:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.10_model.r WARNING @ Sun, 21 Jun 2020 18:47:17: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:47:17: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 18:47:17: #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 18:47:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:20: 8000000 INFO @ Sun, 21 Jun 2020 18:47:26: 9000000 INFO @ Sun, 21 Jun 2020 18:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.05_summits.bed INFO @ Sun, 21 Jun 2020 18:47:28: Done! pass1 - making usageList (697 chroms): 2 millis pass2 - checking and writing primary data (3072 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:47:32: 10000000 INFO @ Sun, 21 Jun 2020 18:47:37: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:47:43: 12000000 INFO @ Sun, 21 Jun 2020 18:47:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:45: #1 total tags in treatment: 12369435 INFO @ Sun, 21 Jun 2020 18:47:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:45: #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 18:47:46: #1 tags after filtering in treatment: 12369435 INFO @ Sun, 21 Jun 2020 18:47:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:47: #2 number of paired peaks: 524 WARNING @ Sun, 21 Jun 2020 18:47:47: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:47: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 18:47:47: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 18:47:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.20_model.r WARNING @ Sun, 21 Jun 2020 18:47:47: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:47:47: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 18:47:47: #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 18:47:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.10_summits.bed INFO @ Sun, 21 Jun 2020 18:47:58: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (1736 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:48:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399657/SRX2399657.20_summits.bed INFO @ Sun, 21 Jun 2020 18:48:28: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 9 millis CompletedMACS2peakCalling