Job ID = 6498036 SRX = SRX287909 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:02:05 prefetch.2.10.7: 1) Downloading 'SRR870098'... 2020-06-25T23:02:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:05:02 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:05:02 prefetch.2.10.7: 1) 'SRR870098' was downloaded successfully Read 19930693 spots for SRR870098/SRR870098.sra Written 19930693 spots for SRR870098/SRR870098.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: 00:09:27 19930693 reads; of these: 19930693 (100.00%) were unpaired; of these: 1257623 (6.31%) aligned 0 times 12952922 (64.99%) aligned exactly 1 time 5720148 (28.70%) aligned >1 times 93.69% overall alignment rate Time searching: 00:09:27 Overall time: 00:09:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2339672 / 18673070 = 0.1253 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 @ Fri, 26 Jun 2020 08:20:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.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 @ Fri, 26 Jun 2020 08:20:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:20:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:20:53: 1000000 INFO @ Fri, 26 Jun 2020 08:21:00: 2000000 INFO @ Fri, 26 Jun 2020 08:21:07: 3000000 INFO @ Fri, 26 Jun 2020 08:21:14: 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 @ Fri, 26 Jun 2020 08:21:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.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 @ Fri, 26 Jun 2020 08:21:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:21:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:21:21: 5000000 INFO @ Fri, 26 Jun 2020 08:21:23: 1000000 INFO @ Fri, 26 Jun 2020 08:21:28: 6000000 INFO @ Fri, 26 Jun 2020 08:21:30: 2000000 INFO @ Fri, 26 Jun 2020 08:21:35: 7000000 INFO @ Fri, 26 Jun 2020 08:21:37: 3000000 INFO @ Fri, 26 Jun 2020 08:21:42: 8000000 INFO @ Fri, 26 Jun 2020 08:21:44: 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 @ Fri, 26 Jun 2020 08:21:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.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 @ Fri, 26 Jun 2020 08:21:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:21:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:21:49: 9000000 INFO @ Fri, 26 Jun 2020 08:21:51: 5000000 INFO @ Fri, 26 Jun 2020 08:21:53: 1000000 INFO @ Fri, 26 Jun 2020 08:21:57: 10000000 INFO @ Fri, 26 Jun 2020 08:21:58: 6000000 INFO @ Fri, 26 Jun 2020 08:21:59: 2000000 INFO @ Fri, 26 Jun 2020 08:22:04: 11000000 INFO @ Fri, 26 Jun 2020 08:22:05: 7000000 INFO @ Fri, 26 Jun 2020 08:22:06: 3000000 INFO @ Fri, 26 Jun 2020 08:22:11: 12000000 INFO @ Fri, 26 Jun 2020 08:22:12: 4000000 INFO @ Fri, 26 Jun 2020 08:22:12: 8000000 INFO @ Fri, 26 Jun 2020 08:22:18: 5000000 INFO @ Fri, 26 Jun 2020 08:22:19: 13000000 INFO @ Fri, 26 Jun 2020 08:22:19: 9000000 INFO @ Fri, 26 Jun 2020 08:22:25: 6000000 INFO @ Fri, 26 Jun 2020 08:22:26: 14000000 INFO @ Fri, 26 Jun 2020 08:22:26: 10000000 INFO @ Fri, 26 Jun 2020 08:22:31: 7000000 INFO @ Fri, 26 Jun 2020 08:22:33: 15000000 INFO @ Fri, 26 Jun 2020 08:22:34: 11000000 INFO @ Fri, 26 Jun 2020 08:22:38: 8000000 INFO @ Fri, 26 Jun 2020 08:22:40: 16000000 INFO @ Fri, 26 Jun 2020 08:22:41: 12000000 INFO @ Fri, 26 Jun 2020 08:22:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:22:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:22:43: #1 total tags in treatment: 16333398 INFO @ Fri, 26 Jun 2020 08:22:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:22:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:22:43: #1 tags after filtering in treatment: 16333398 INFO @ Fri, 26 Jun 2020 08:22:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:22:43: #1 finished! INFO @ Fri, 26 Jun 2020 08:22:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:22:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:22:44: #2 number of paired peaks: 202 WARNING @ Fri, 26 Jun 2020 08:22:44: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 26 Jun 2020 08:22:44: start model_add_line... INFO @ Fri, 26 Jun 2020 08:22:44: start X-correlation... INFO @ Fri, 26 Jun 2020 08:22:44: 9000000 INFO @ Fri, 26 Jun 2020 08:22:44: end of X-cor INFO @ Fri, 26 Jun 2020 08:22:44: #2 finished! INFO @ Fri, 26 Jun 2020 08:22:44: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 08:22:44: #2 alternative fragment length(s) may be 42 bps INFO @ Fri, 26 Jun 2020 08:22:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.05_model.r WARNING @ Fri, 26 Jun 2020 08:22:44: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:22:44: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Fri, 26 Jun 2020 08:22:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:22:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:22:48: 13000000 INFO @ Fri, 26 Jun 2020 08:22:51: 10000000 INFO @ Fri, 26 Jun 2020 08:22:55: 14000000 INFO @ Fri, 26 Jun 2020 08:22:57: 11000000 INFO @ Fri, 26 Jun 2020 08:23:02: 15000000 INFO @ Fri, 26 Jun 2020 08:23:04: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:23:09: 16000000 INFO @ Fri, 26 Jun 2020 08:23:11: 13000000 INFO @ Fri, 26 Jun 2020 08:23:11: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:23:11: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:23:11: #1 total tags in treatment: 16333398 INFO @ Fri, 26 Jun 2020 08:23:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:23:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:23:12: #1 tags after filtering in treatment: 16333398 INFO @ Fri, 26 Jun 2020 08:23:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:23:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:23:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:23:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:23:13: #2 number of paired peaks: 202 WARNING @ Fri, 26 Jun 2020 08:23:13: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 26 Jun 2020 08:23:13: start model_add_line... INFO @ Fri, 26 Jun 2020 08:23:13: start X-correlation... INFO @ Fri, 26 Jun 2020 08:23:13: end of X-cor INFO @ Fri, 26 Jun 2020 08:23:13: #2 finished! INFO @ Fri, 26 Jun 2020 08:23:13: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 08:23:13: #2 alternative fragment length(s) may be 42 bps INFO @ Fri, 26 Jun 2020 08:23:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.10_model.r WARNING @ Fri, 26 Jun 2020 08:23:13: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:23:13: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Fri, 26 Jun 2020 08:23:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:23:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:17: 14000000 INFO @ Fri, 26 Jun 2020 08:23:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:23:22: 15000000 INFO @ Fri, 26 Jun 2020 08:23:28: 16000000 INFO @ Fri, 26 Jun 2020 08:23:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:23:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:23:30: #1 total tags in treatment: 16333398 INFO @ Fri, 26 Jun 2020 08:23:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:23:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:23:30: #1 tags after filtering in treatment: 16333398 INFO @ Fri, 26 Jun 2020 08:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:23:30: #1 finished! INFO @ Fri, 26 Jun 2020 08:23:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:23:31: #2 number of paired peaks: 202 WARNING @ Fri, 26 Jun 2020 08:23:31: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 26 Jun 2020 08:23:31: start model_add_line... INFO @ Fri, 26 Jun 2020 08:23:31: start X-correlation... INFO @ Fri, 26 Jun 2020 08:23:31: end of X-cor INFO @ Fri, 26 Jun 2020 08:23:31: #2 finished! INFO @ Fri, 26 Jun 2020 08:23:31: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 08:23:31: #2 alternative fragment length(s) may be 42 bps INFO @ Fri, 26 Jun 2020 08:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.20_model.r WARNING @ Fri, 26 Jun 2020 08:23:31: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:23:31: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Fri, 26 Jun 2020 08:23:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:23:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.05_summits.bed INFO @ Fri, 26 Jun 2020 08:23:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2156 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:23:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.10_summits.bed INFO @ Fri, 26 Jun 2020 08:24:02: Done! INFO @ Fri, 26 Jun 2020 08:24:02: #3 Call peaks for each chromosome... pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1857 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:24:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287909/SRX287909.20_summits.bed INFO @ Fri, 26 Jun 2020 08:24:18: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1367 records, 4 fields): 3 millis CompletedMACS2peakCalling