Job ID = 6452431 SRX = SRX013054 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:36:27 prefetch.2.10.7: 1) Downloading 'SRR030320'... 2020-06-21T07:36:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:37:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:37:57 prefetch.2.10.7: 'SRR030320' is valid 2020-06-21T07:37:57 prefetch.2.10.7: 1) 'SRR030320' was downloaded successfully Read 7632922 spots for SRR030320/SRR030320.sra Written 7632922 spots for SRR030320/SRR030320.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: 00:01:27 7632922 reads; of these: 7632922 (100.00%) were unpaired; of these: 610661 (8.00%) aligned 0 times 5893379 (77.21%) aligned exactly 1 time 1128882 (14.79%) aligned >1 times 92.00% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 550796 / 7022261 = 0.0784 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 16:41:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.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 16:41:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:40: 1000000 INFO @ Sun, 21 Jun 2020 16:41:46: 2000000 INFO @ Sun, 21 Jun 2020 16:41:51: 3000000 INFO @ Sun, 21 Jun 2020 16:41:57: 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 16:42:03: 5000000 INFO @ Sun, 21 Jun 2020 16:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.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 16:42:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:42:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:42:09: 6000000 INFO @ Sun, 21 Jun 2020 16:42:10: 1000000 INFO @ Sun, 21 Jun 2020 16:42:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:42:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:42:12: #1 total tags in treatment: 6471465 INFO @ Sun, 21 Jun 2020 16:42:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:42:12: #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 16:42:13: #1 tags after filtering in treatment: 6471398 INFO @ Sun, 21 Jun 2020 16:42:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:42:13: #1 finished! INFO @ Sun, 21 Jun 2020 16:42:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:42:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:42:13: #2 number of paired peaks: 271 WARNING @ Sun, 21 Jun 2020 16:42:13: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 21 Jun 2020 16:42:13: start model_add_line... INFO @ Sun, 21 Jun 2020 16:42:13: start X-correlation... INFO @ Sun, 21 Jun 2020 16:42:13: end of X-cor INFO @ Sun, 21 Jun 2020 16:42:13: #2 finished! INFO @ Sun, 21 Jun 2020 16:42:13: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 16:42:13: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 16:42:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.05_model.r WARNING @ Sun, 21 Jun 2020 16:42:13: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:42:13: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 16:42:13: #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 16:42:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:42:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:42:15: 2000000 INFO @ Sun, 21 Jun 2020 16:42:20: 3000000 INFO @ Sun, 21 Jun 2020 16:42:25: 4000000 INFO @ Sun, 21 Jun 2020 16:42:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:42:30: 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 @ Sun, 21 Jun 2020 16:42:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:42:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:42:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.05_summits.bed INFO @ Sun, 21 Jun 2020 16:42:34: Done! INFO @ Sun, 21 Jun 2020 16:42:36: 6000000 pass1 - making usageList (138 chroms): 1 millis pass2 - checking and writing primary data (740 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:42:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:42:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:42:38: #1 total tags in treatment: 6471465 INFO @ Sun, 21 Jun 2020 16:42:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:42:38: #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 16:42:39: #1 tags after filtering in treatment: 6471398 INFO @ Sun, 21 Jun 2020 16:42:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:42:39: #1 finished! INFO @ Sun, 21 Jun 2020 16:42:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.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 16:42:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:42:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:42:39: #2 number of paired peaks: 271 WARNING @ Sun, 21 Jun 2020 16:42:39: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 21 Jun 2020 16:42:39: start model_add_line... INFO @ Sun, 21 Jun 2020 16:42:39: start X-correlation... INFO @ Sun, 21 Jun 2020 16:42:39: end of X-cor INFO @ Sun, 21 Jun 2020 16:42:39: #2 finished! INFO @ Sun, 21 Jun 2020 16:42:39: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 16:42:39: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 16:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.10_model.r WARNING @ Sun, 21 Jun 2020 16:42:39: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:42:39: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 16:42:39: #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 16:42:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:42:45: 1000000 INFO @ Sun, 21 Jun 2020 16:42:51: 2000000 INFO @ Sun, 21 Jun 2020 16:42:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:42:56: 3000000 INFO @ Sun, 21 Jun 2020 16:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.10_summits.bed INFO @ Sun, 21 Jun 2020 16:43:00: Done! INFO @ Sun, 21 Jun 2020 16:43:02: 4000000 pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (238 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:43:08: 5000000 INFO @ Sun, 21 Jun 2020 16:43:14: 6000000 INFO @ Sun, 21 Jun 2020 16:43:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:43:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:43:17: #1 total tags in treatment: 6471465 INFO @ Sun, 21 Jun 2020 16:43:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:43:17: #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 16:43:17: #1 tags after filtering in treatment: 6471398 INFO @ Sun, 21 Jun 2020 16:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:43:17: #1 finished! INFO @ Sun, 21 Jun 2020 16:43:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:43:18: #2 number of paired peaks: 271 WARNING @ Sun, 21 Jun 2020 16:43:18: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 21 Jun 2020 16:43:18: start model_add_line... INFO @ Sun, 21 Jun 2020 16:43:18: start X-correlation... INFO @ Sun, 21 Jun 2020 16:43:18: end of X-cor INFO @ Sun, 21 Jun 2020 16:43:18: #2 finished! INFO @ Sun, 21 Jun 2020 16:43:18: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 16:43:18: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 16:43:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.20_model.r WARNING @ Sun, 21 Jun 2020 16:43:18: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:43:18: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 16:43:18: #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 16:43:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:43:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:43:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:43:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:43:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:43:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013054/SRX013054.20_summits.bed INFO @ Sun, 21 Jun 2020 16:43:39: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 24 millis CompletedMACS2peakCalling