Job ID = 6456475 SRX = SRX348460 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:49:20 prefetch.2.10.7: 1) Downloading 'SRR976144'... 2020-06-21T10:49:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:10:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:10:23 prefetch.2.10.7: 1) 'SRR976144' was downloaded successfully Read 47987333 spots for SRR976144/SRR976144.sra Written 47987333 spots for SRR976144/SRR976144.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: 00:14:18 47987333 reads; of these: 47987333 (100.00%) were unpaired; of these: 37438086 (78.02%) aligned 0 times 7407601 (15.44%) aligned exactly 1 time 3141646 (6.55%) aligned >1 times 21.98% overall alignment rate Time searching: 00:14:18 Overall time: 00:14:18 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] 2619964 / 10549247 = 0.2484 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 20:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.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 20:32:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:32:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:32:55: 1000000 INFO @ Sun, 21 Jun 2020 20:33:03: 2000000 INFO @ Sun, 21 Jun 2020 20:33:11: 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 20:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.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 20:33:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:33:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:33:18: 4000000 INFO @ Sun, 21 Jun 2020 20:33:24: 1000000 INFO @ Sun, 21 Jun 2020 20:33:26: 5000000 INFO @ Sun, 21 Jun 2020 20:33:32: 2000000 INFO @ Sun, 21 Jun 2020 20:33:35: 6000000 INFO @ Sun, 21 Jun 2020 20:33:40: 3000000 INFO @ Sun, 21 Jun 2020 20:33:43: 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 20:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.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 20:33:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:33:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:33:48: 4000000 INFO @ Sun, 21 Jun 2020 20:33:51: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:33:51: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:33:51: #1 total tags in treatment: 7929283 INFO @ Sun, 21 Jun 2020 20:33:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:51: #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 20:33:51: #1 tags after filtering in treatment: 7929274 INFO @ Sun, 21 Jun 2020 20:33:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:51: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:52: #2 number of paired peaks: 788 WARNING @ Sun, 21 Jun 2020 20:33:52: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sun, 21 Jun 2020 20:33:52: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:52: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 20:33:52: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 20:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.05_model.r WARNING @ Sun, 21 Jun 2020 20:33:52: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:33:52: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 21 Jun 2020 20:33:52: #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 20:33:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:33:54: 1000000 INFO @ Sun, 21 Jun 2020 20:33:56: 5000000 INFO @ Sun, 21 Jun 2020 20:34:01: 2000000 INFO @ Sun, 21 Jun 2020 20:34:04: 6000000 INFO @ Sun, 21 Jun 2020 20:34:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:08: 3000000 INFO @ Sun, 21 Jun 2020 20:34:12: 7000000 INFO @ Sun, 21 Jun 2020 20:34:15: 4000000 INFO @ Sun, 21 Jun 2020 20:34:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.05_summits.bed INFO @ Sun, 21 Jun 2020 20:34:16: Done! pass1 - making usageList (697 chroms): 2 millis pass2 - checking and writing primary data (1988 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:34:20: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:34:20: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:34:20: #1 total tags in treatment: 7929283 INFO @ Sun, 21 Jun 2020 20:34:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:20: #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 20:34:20: #1 tags after filtering in treatment: 7929274 INFO @ Sun, 21 Jun 2020 20:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:21: #2 number of paired peaks: 788 WARNING @ Sun, 21 Jun 2020 20:34:21: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:21: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 20:34:21: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 20:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.10_model.r WARNING @ Sun, 21 Jun 2020 20:34:21: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:34:21: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 21 Jun 2020 20:34:21: #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 20:34:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:22: 5000000 INFO @ Sun, 21 Jun 2020 20:34:29: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:34:36: 7000000 INFO @ Sun, 21 Jun 2020 20:34:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:42: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:34:42: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:34:42: #1 total tags in treatment: 7929283 INFO @ Sun, 21 Jun 2020 20:34:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:42: #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 20:34:43: #1 tags after filtering in treatment: 7929274 INFO @ Sun, 21 Jun 2020 20:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:44: #2 number of paired peaks: 788 WARNING @ Sun, 21 Jun 2020 20:34:44: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:44: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:44: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:44: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:44: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 20:34:44: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 20:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.20_model.r WARNING @ Sun, 21 Jun 2020 20:34:44: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:34:44: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 21 Jun 2020 20:34:44: #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 20:34:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.10_summits.bed INFO @ Sun, 21 Jun 2020 20:34:46: Done! pass1 - making usageList (578 chroms): 1 millis pass2 - checking and writing primary data (1430 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:35:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348460/SRX348460.20_summits.bed INFO @ Sun, 21 Jun 2020 20:35:09: Done! pass1 - making usageList (407 chroms): 1 millis pass2 - checking and writing primary data (760 records, 4 fields): 12 millis CompletedMACS2peakCalling