Job ID = 6456102 SRX = SRX318778 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:35:44 prefetch.2.10.7: 1) Downloading 'SRR927094'... 2020-06-21T10:35:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:35 prefetch.2.10.7: 1) 'SRR927094' was downloaded successfully Read 18493128 spots for SRR927094/SRR927094.sra Written 18493128 spots for SRR927094/SRR927094.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: 00:05:14 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1283946 (6.94%) aligned 0 times 13227000 (71.52%) aligned exactly 1 time 3982182 (21.53%) aligned >1 times 93.06% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 1868601 / 17209182 = 0.1086 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 19:49:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.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 19:49:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:25: 1000000 INFO @ Sun, 21 Jun 2020 19:49:30: 2000000 INFO @ Sun, 21 Jun 2020 19:49:35: 3000000 INFO @ Sun, 21 Jun 2020 19:49:40: 4000000 INFO @ Sun, 21 Jun 2020 19:49:45: 5000000 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 19:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.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 19:49:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:51: 6000000 INFO @ Sun, 21 Jun 2020 19:49:55: 1000000 INFO @ Sun, 21 Jun 2020 19:49:56: 7000000 INFO @ Sun, 21 Jun 2020 19:50:01: 2000000 INFO @ Sun, 21 Jun 2020 19:50:02: 8000000 INFO @ Sun, 21 Jun 2020 19:50:06: 3000000 INFO @ Sun, 21 Jun 2020 19:50:07: 9000000 INFO @ Sun, 21 Jun 2020 19:50:12: 4000000 INFO @ Sun, 21 Jun 2020 19:50:13: 10000000 INFO @ Sun, 21 Jun 2020 19:50:17: 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 19:50:18: 11000000 INFO @ Sun, 21 Jun 2020 19:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.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 19:50:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:23: 6000000 INFO @ Sun, 21 Jun 2020 19:50:24: 12000000 INFO @ Sun, 21 Jun 2020 19:50:25: 1000000 INFO @ Sun, 21 Jun 2020 19:50:29: 7000000 INFO @ Sun, 21 Jun 2020 19:50:29: 13000000 INFO @ Sun, 21 Jun 2020 19:50:31: 2000000 INFO @ Sun, 21 Jun 2020 19:50:34: 8000000 INFO @ Sun, 21 Jun 2020 19:50:35: 14000000 INFO @ Sun, 21 Jun 2020 19:50:36: 3000000 INFO @ Sun, 21 Jun 2020 19:50:40: 9000000 INFO @ Sun, 21 Jun 2020 19:50:41: 15000000 INFO @ Sun, 21 Jun 2020 19:50:42: 4000000 INFO @ Sun, 21 Jun 2020 19:50:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:43: #1 total tags in treatment: 15340581 INFO @ Sun, 21 Jun 2020 19:50:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:43: #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 19:50:43: #1 tags after filtering in treatment: 15340579 INFO @ Sun, 21 Jun 2020 19:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:44: #2 number of paired peaks: 309 WARNING @ Sun, 21 Jun 2020 19:50:44: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:44: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:50:44: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.05_model.r WARNING @ Sun, 21 Jun 2020 19:50:44: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:44: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:50:44: #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 19:50:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:45: 10000000 INFO @ Sun, 21 Jun 2020 19:50:47: 5000000 INFO @ Sun, 21 Jun 2020 19:50:51: 11000000 INFO @ Sun, 21 Jun 2020 19:50:53: 6000000 INFO @ Sun, 21 Jun 2020 19:50:56: 12000000 INFO @ Sun, 21 Jun 2020 19:50:58: 7000000 INFO @ Sun, 21 Jun 2020 19:51:02: 13000000 INFO @ Sun, 21 Jun 2020 19:51:04: 8000000 INFO @ Sun, 21 Jun 2020 19:51:07: 14000000 INFO @ Sun, 21 Jun 2020 19:51:09: 9000000 INFO @ Sun, 21 Jun 2020 19:51:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:13: 15000000 INFO @ Sun, 21 Jun 2020 19:51:15: 10000000 INFO @ Sun, 21 Jun 2020 19:51:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:15: #1 total tags in treatment: 15340581 INFO @ Sun, 21 Jun 2020 19:51:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:15: #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 19:51:16: #1 tags after filtering in treatment: 15340579 INFO @ Sun, 21 Jun 2020 19:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:17: #2 number of paired peaks: 309 WARNING @ Sun, 21 Jun 2020 19:51:17: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 21 Jun 2020 19:51:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:17: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:51:17: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.10_model.r WARNING @ Sun, 21 Jun 2020 19:51:17: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:51:17: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:51:17: #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 19:51:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:20: 11000000 INFO @ Sun, 21 Jun 2020 19:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.05_summits.bed INFO @ Sun, 21 Jun 2020 19:51:25: Done! pass1 - making usageList (511 chroms): 1 millis pass2 - checking and writing primary data (2168 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:26: 12000000 INFO @ Sun, 21 Jun 2020 19:51:31: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:51:36: 14000000 INFO @ Sun, 21 Jun 2020 19:51:42: 15000000 INFO @ Sun, 21 Jun 2020 19:51:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:44: #1 total tags in treatment: 15340581 INFO @ Sun, 21 Jun 2020 19:51:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:44: #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 19:51:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:44: #1 tags after filtering in treatment: 15340579 INFO @ Sun, 21 Jun 2020 19:51:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:45: #2 number of paired peaks: 309 WARNING @ Sun, 21 Jun 2020 19:51:45: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 21 Jun 2020 19:51:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:45: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:51:45: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.20_model.r WARNING @ Sun, 21 Jun 2020 19:51:45: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:51:45: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:51:45: #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 19:51:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.10_summits.bed INFO @ Sun, 21 Jun 2020 19:51:58: Done! pass1 - making usageList (401 chroms): 1 millis pass2 - checking and writing primary data (1202 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:52:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318778/SRX318778.20_summits.bed INFO @ Sun, 21 Jun 2020 19:52:27: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 8 millis CompletedMACS2peakCalling