Job ID = 6455309 SRX = SRX287683 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:57:10 prefetch.2.10.7: 1) Downloading 'SRR869871'... 2020-06-21T09:57:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:42 prefetch.2.10.7: 1) 'SRR869871' was downloaded successfully Read 18630340 spots for SRR869871/SRR869871.sra Written 18630340 spots for SRR869871/SRR869871.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: 00:04:30 18630340 reads; of these: 18630340 (100.00%) were unpaired; of these: 1186387 (6.37%) aligned 0 times 15443093 (82.89%) aligned exactly 1 time 2000860 (10.74%) aligned >1 times 93.63% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 1375035 / 17443953 = 0.0788 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 19:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.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 19:09:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:02: 1000000 INFO @ Sun, 21 Jun 2020 19:10:08: 2000000 INFO @ Sun, 21 Jun 2020 19:10:14: 3000000 INFO @ Sun, 21 Jun 2020 19:10:20: 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 19:10:25: 5000000 INFO @ Sun, 21 Jun 2020 19:10:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.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 19:10:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:31: 6000000 INFO @ Sun, 21 Jun 2020 19:10:32: 1000000 INFO @ Sun, 21 Jun 2020 19:10:36: 7000000 INFO @ Sun, 21 Jun 2020 19:10:38: 2000000 INFO @ Sun, 21 Jun 2020 19:10:42: 8000000 INFO @ Sun, 21 Jun 2020 19:10:44: 3000000 INFO @ Sun, 21 Jun 2020 19:10:48: 9000000 INFO @ Sun, 21 Jun 2020 19:10:49: 4000000 INFO @ Sun, 21 Jun 2020 19:10:54: 10000000 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 19:10:55: 5000000 INFO @ Sun, 21 Jun 2020 19:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.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 19:10:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:59: 11000000 INFO @ Sun, 21 Jun 2020 19:11:01: 6000000 INFO @ Sun, 21 Jun 2020 19:11:03: 1000000 INFO @ Sun, 21 Jun 2020 19:11:05: 12000000 INFO @ Sun, 21 Jun 2020 19:11:07: 7000000 INFO @ Sun, 21 Jun 2020 19:11:09: 2000000 INFO @ Sun, 21 Jun 2020 19:11:11: 13000000 INFO @ Sun, 21 Jun 2020 19:11:13: 8000000 INFO @ Sun, 21 Jun 2020 19:11:16: 3000000 INFO @ Sun, 21 Jun 2020 19:11:18: 14000000 INFO @ Sun, 21 Jun 2020 19:11:19: 9000000 INFO @ Sun, 21 Jun 2020 19:11:22: 4000000 INFO @ Sun, 21 Jun 2020 19:11:24: 15000000 INFO @ Sun, 21 Jun 2020 19:11:25: 10000000 INFO @ Sun, 21 Jun 2020 19:11:29: 5000000 INFO @ Sun, 21 Jun 2020 19:11:30: 16000000 INFO @ Sun, 21 Jun 2020 19:11:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:11:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:11:31: #1 total tags in treatment: 16068918 INFO @ Sun, 21 Jun 2020 19:11:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:31: #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 19:11:31: 11000000 INFO @ Sun, 21 Jun 2020 19:11:31: #1 tags after filtering in treatment: 16068902 INFO @ Sun, 21 Jun 2020 19:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:32: #2 number of paired peaks: 182 WARNING @ Sun, 21 Jun 2020 19:11:32: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sun, 21 Jun 2020 19:11:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:32: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 19:11:32: #2 alternative fragment length(s) may be 4,51,80,108,573,583,598 bps INFO @ Sun, 21 Jun 2020 19:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.05_model.r WARNING @ Sun, 21 Jun 2020 19:11:32: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:32: #2 You may need to consider one of the other alternative d(s): 4,51,80,108,573,583,598 WARNING @ Sun, 21 Jun 2020 19:11:32: #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 19:11:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:35: 6000000 INFO @ Sun, 21 Jun 2020 19:11:37: 12000000 INFO @ Sun, 21 Jun 2020 19:11:41: 7000000 INFO @ Sun, 21 Jun 2020 19:11:42: 13000000 INFO @ Sun, 21 Jun 2020 19:11:48: 8000000 INFO @ Sun, 21 Jun 2020 19:11:49: 14000000 INFO @ Sun, 21 Jun 2020 19:11:54: 9000000 INFO @ Sun, 21 Jun 2020 19:11:55: 15000000 INFO @ Sun, 21 Jun 2020 19:12:01: 16000000 INFO @ Sun, 21 Jun 2020 19:12:01: 10000000 INFO @ Sun, 21 Jun 2020 19:12:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:01: #1 total tags in treatment: 16068918 INFO @ Sun, 21 Jun 2020 19:12:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:01: #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 19:12:02: #1 tags after filtering in treatment: 16068902 INFO @ Sun, 21 Jun 2020 19:12:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:03: #2 number of paired peaks: 182 WARNING @ Sun, 21 Jun 2020 19:12:03: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:03: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 19:12:03: #2 alternative fragment length(s) may be 4,51,80,108,573,583,598 bps INFO @ Sun, 21 Jun 2020 19:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.10_model.r WARNING @ Sun, 21 Jun 2020 19:12:03: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:03: #2 You may need to consider one of the other alternative d(s): 4,51,80,108,573,583,598 WARNING @ Sun, 21 Jun 2020 19:12:03: #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 19:12:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:07: 11000000 INFO @ Sun, 21 Jun 2020 19:12:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:13: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:12:19: 13000000 INFO @ Sun, 21 Jun 2020 19:12:25: 14000000 INFO @ Sun, 21 Jun 2020 19:12:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.05_summits.bed INFO @ Sun, 21 Jun 2020 19:12:26: Done! pass1 - making usageList (140 chroms): 1 millis pass2 - checking and writing primary data (1064 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:12:30: 15000000 INFO @ Sun, 21 Jun 2020 19:12:36: 16000000 INFO @ Sun, 21 Jun 2020 19:12:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:37: #1 total tags in treatment: 16068918 INFO @ Sun, 21 Jun 2020 19:12:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:37: #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 19:12:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:37: #1 tags after filtering in treatment: 16068902 INFO @ Sun, 21 Jun 2020 19:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:39: #2 number of paired peaks: 182 WARNING @ Sun, 21 Jun 2020 19:12:39: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:39: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 19:12:39: #2 alternative fragment length(s) may be 4,51,80,108,573,583,598 bps INFO @ Sun, 21 Jun 2020 19:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.20_model.r WARNING @ Sun, 21 Jun 2020 19:12:39: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:39: #2 You may need to consider one of the other alternative d(s): 4,51,80,108,573,583,598 WARNING @ Sun, 21 Jun 2020 19:12:39: #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 19:12:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.10_summits.bed INFO @ Sun, 21 Jun 2020 19:12:54: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287683/SRX287683.20_summits.bed INFO @ Sun, 21 Jun 2020 19:13:32: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 4 millis CompletedMACS2peakCalling