Job ID = 6456217 SRX = SRX331374 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:40:23 prefetch.2.10.7: 1) Downloading 'SRR947611'... 2020-06-21T10:40:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:45:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:45:29 prefetch.2.10.7: 1) 'SRR947611' was downloaded successfully Read 21559305 spots for SRR947611/SRR947611.sra Written 21559305 spots for SRR947611/SRR947611.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: 00:05:53 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1516194 (7.03%) aligned 0 times 15525166 (72.01%) aligned exactly 1 time 4517945 (20.96%) aligned >1 times 92.97% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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 12 files... [bam_rmdupse_core] 2295255 / 20043111 = 0.1145 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 19:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.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 19:57:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:42: 1000000 INFO @ Sun, 21 Jun 2020 19:57:47: 2000000 INFO @ Sun, 21 Jun 2020 19:57:52: 3000000 INFO @ Sun, 21 Jun 2020 19:57:56: 4000000 INFO @ Sun, 21 Jun 2020 19:58:01: 5000000 INFO @ Sun, 21 Jun 2020 19:58:06: 6000000 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 19:58:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.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 19:58:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:10: 7000000 INFO @ Sun, 21 Jun 2020 19:58:12: 1000000 INFO @ Sun, 21 Jun 2020 19:58:15: 8000000 INFO @ Sun, 21 Jun 2020 19:58:17: 2000000 INFO @ Sun, 21 Jun 2020 19:58:19: 9000000 INFO @ Sun, 21 Jun 2020 19:58:22: 3000000 INFO @ Sun, 21 Jun 2020 19:58:24: 10000000 INFO @ Sun, 21 Jun 2020 19:58:26: 4000000 INFO @ Sun, 21 Jun 2020 19:58:29: 11000000 INFO @ Sun, 21 Jun 2020 19:58:31: 5000000 INFO @ Sun, 21 Jun 2020 19:58:33: 12000000 INFO @ Sun, 21 Jun 2020 19:58:36: 6000000 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 19:58:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.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 19:58:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:38: 13000000 INFO @ Sun, 21 Jun 2020 19:58:40: 7000000 INFO @ Sun, 21 Jun 2020 19:58:42: 1000000 INFO @ Sun, 21 Jun 2020 19:58:43: 14000000 INFO @ Sun, 21 Jun 2020 19:58:45: 8000000 INFO @ Sun, 21 Jun 2020 19:58:47: 2000000 INFO @ Sun, 21 Jun 2020 19:58:48: 15000000 INFO @ Sun, 21 Jun 2020 19:58:50: 9000000 INFO @ Sun, 21 Jun 2020 19:58:52: 3000000 INFO @ Sun, 21 Jun 2020 19:58:53: 16000000 INFO @ Sun, 21 Jun 2020 19:58:54: 10000000 INFO @ Sun, 21 Jun 2020 19:58:56: 4000000 INFO @ Sun, 21 Jun 2020 19:58:57: 17000000 INFO @ Sun, 21 Jun 2020 19:58:59: 11000000 INFO @ Sun, 21 Jun 2020 19:59:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:59:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:59:01: #1 total tags in treatment: 17747856 INFO @ Sun, 21 Jun 2020 19:59:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:01: #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 19:59:01: 5000000 INFO @ Sun, 21 Jun 2020 19:59:02: #1 tags after filtering in treatment: 17747856 INFO @ Sun, 21 Jun 2020 19:59:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:03: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 19:59:03: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 19:59:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:03: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:59:03: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.05_model.r WARNING @ Sun, 21 Jun 2020 19:59:03: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:59:03: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:59:03: #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 19:59:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:04: 12000000 INFO @ Sun, 21 Jun 2020 19:59:06: 6000000 INFO @ Sun, 21 Jun 2020 19:59:08: 13000000 INFO @ Sun, 21 Jun 2020 19:59:10: 7000000 INFO @ Sun, 21 Jun 2020 19:59:13: 14000000 INFO @ Sun, 21 Jun 2020 19:59:15: 8000000 INFO @ Sun, 21 Jun 2020 19:59:18: 15000000 INFO @ Sun, 21 Jun 2020 19:59:20: 9000000 INFO @ Sun, 21 Jun 2020 19:59:23: 16000000 INFO @ Sun, 21 Jun 2020 19:59:24: 10000000 INFO @ Sun, 21 Jun 2020 19:59:27: 17000000 INFO @ Sun, 21 Jun 2020 19:59:29: 11000000 INFO @ Sun, 21 Jun 2020 19:59:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:59:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:59:31: #1 total tags in treatment: 17747856 INFO @ Sun, 21 Jun 2020 19:59:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:31: #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 19:59:32: #1 tags after filtering in treatment: 17747856 INFO @ Sun, 21 Jun 2020 19:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:33: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 19:59:33: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 19:59:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:33: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:59:33: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.10_model.r WARNING @ Sun, 21 Jun 2020 19:59:33: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:59:33: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:59:33: #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 19:59:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:34: 12000000 INFO @ Sun, 21 Jun 2020 19:59:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:38: 13000000 INFO @ Sun, 21 Jun 2020 19:59:43: 14000000 INFO @ Sun, 21 Jun 2020 19:59:48: 15000000 INFO @ Sun, 21 Jun 2020 19:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.05_summits.bed INFO @ Sun, 21 Jun 2020 19:59:51: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (2117 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:59:53: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:59:57: 17000000 INFO @ Sun, 21 Jun 2020 20:00:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:00:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:00:01: #1 total tags in treatment: 17747856 INFO @ Sun, 21 Jun 2020 20:00:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:01: #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 20:00:02: #1 tags after filtering in treatment: 17747856 INFO @ Sun, 21 Jun 2020 20:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:03: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 20:00:03: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:03: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 20:00:03: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 20:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.20_model.r WARNING @ Sun, 21 Jun 2020 20:00:03: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:00:03: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 20:00:03: #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 20:00:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.10_summits.bed INFO @ Sun, 21 Jun 2020 20:00:21: Done! pass1 - making usageList (423 chroms): 1 millis pass2 - checking and writing primary data (1345 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:00:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331374/SRX331374.20_summits.bed INFO @ Sun, 21 Jun 2020 20:00:50: Done! pass1 - making usageList (216 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 8 millis CompletedMACS2peakCalling