Job ID = 6455559 SRX = SRX287885 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:07:22 prefetch.2.10.7: 1) Downloading 'SRR870074'... 2020-06-21T10:07:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:12:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:12:42 prefetch.2.10.7: 1) 'SRR870074' was downloaded successfully Read 17355751 spots for SRR870074/SRR870074.sra Written 17355751 spots for SRR870074/SRR870074.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: 00:05:24 17355751 reads; of these: 17355751 (100.00%) were unpaired; of these: 1248895 (7.20%) aligned 0 times 10894778 (62.77%) aligned exactly 1 time 5212078 (30.03%) aligned >1 times 92.80% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 3083388 / 16106856 = 0.1914 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 19:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.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 19:23:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:25: 1000000 INFO @ Sun, 21 Jun 2020 19:23:31: 2000000 INFO @ Sun, 21 Jun 2020 19:23:36: 3000000 INFO @ Sun, 21 Jun 2020 19:23:42: 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 19:23:48: 5000000 INFO @ Sun, 21 Jun 2020 19:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.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 19:23:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:54: 6000000 INFO @ Sun, 21 Jun 2020 19:23:56: 1000000 INFO @ Sun, 21 Jun 2020 19:24:00: 7000000 INFO @ Sun, 21 Jun 2020 19:24:02: 2000000 INFO @ Sun, 21 Jun 2020 19:24:06: 8000000 INFO @ Sun, 21 Jun 2020 19:24:09: 3000000 INFO @ Sun, 21 Jun 2020 19:24:12: 9000000 INFO @ Sun, 21 Jun 2020 19:24:15: 4000000 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 19:24:18: 10000000 INFO @ Sun, 21 Jun 2020 19:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.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 19:24:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:22: 5000000 INFO @ Sun, 21 Jun 2020 19:24:24: 1000000 INFO @ Sun, 21 Jun 2020 19:24:25: 11000000 INFO @ Sun, 21 Jun 2020 19:24:28: 6000000 INFO @ Sun, 21 Jun 2020 19:24:30: 2000000 INFO @ Sun, 21 Jun 2020 19:24:31: 12000000 INFO @ Sun, 21 Jun 2020 19:24:35: 7000000 INFO @ Sun, 21 Jun 2020 19:24:36: 3000000 INFO @ Sun, 21 Jun 2020 19:24:37: 13000000 INFO @ Sun, 21 Jun 2020 19:24:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:38: #1 total tags in treatment: 13023468 INFO @ Sun, 21 Jun 2020 19:24:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:38: #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 19:24:38: #1 tags after filtering in treatment: 13023468 INFO @ Sun, 21 Jun 2020 19:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:39: #2 number of paired peaks: 847 WARNING @ Sun, 21 Jun 2020 19:24:39: Fewer paired peaks (847) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 847 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:39: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:24:39: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 19:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.05_model.r WARNING @ Sun, 21 Jun 2020 19:24:39: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:39: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 19:24:39: #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 19:24:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:41: 4000000 INFO @ Sun, 21 Jun 2020 19:24:41: 8000000 INFO @ Sun, 21 Jun 2020 19:24:46: 5000000 INFO @ Sun, 21 Jun 2020 19:24:48: 9000000 INFO @ Sun, 21 Jun 2020 19:24:52: 6000000 INFO @ Sun, 21 Jun 2020 19:24:55: 10000000 INFO @ Sun, 21 Jun 2020 19:24:57: 7000000 INFO @ Sun, 21 Jun 2020 19:25:02: 11000000 INFO @ Sun, 21 Jun 2020 19:25:02: 8000000 INFO @ Sun, 21 Jun 2020 19:25:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:08: 9000000 INFO @ Sun, 21 Jun 2020 19:25:08: 12000000 INFO @ Sun, 21 Jun 2020 19:25:13: 10000000 INFO @ Sun, 21 Jun 2020 19:25:15: 13000000 INFO @ Sun, 21 Jun 2020 19:25:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:16: #1 total tags in treatment: 13023468 INFO @ Sun, 21 Jun 2020 19:25:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:16: #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 19:25:16: #1 tags after filtering in treatment: 13023468 INFO @ Sun, 21 Jun 2020 19:25:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:17: #2 number of paired peaks: 847 WARNING @ Sun, 21 Jun 2020 19:25:17: Fewer paired peaks (847) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 847 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:17: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:25:17: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 19:25:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.10_model.r WARNING @ Sun, 21 Jun 2020 19:25:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:17: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 19:25:17: #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 19:25:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:19: 11000000 INFO @ Sun, 21 Jun 2020 19:25:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.05_summits.bed INFO @ Sun, 21 Jun 2020 19:25:19: Done! pass1 - making usageList (636 chroms): 1 millis pass2 - checking and writing primary data (2295 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:25:24: 12000000 INFO @ Sun, 21 Jun 2020 19:25:29: 13000000 INFO @ Sun, 21 Jun 2020 19:25:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:30: #1 total tags in treatment: 13023468 INFO @ Sun, 21 Jun 2020 19:25:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:30: #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 19:25:30: #1 tags after filtering in treatment: 13023468 INFO @ Sun, 21 Jun 2020 19:25:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:31: #2 number of paired peaks: 847 WARNING @ Sun, 21 Jun 2020 19:25:31: Fewer paired peaks (847) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 847 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:31: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:25:31: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 19:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.20_model.r WARNING @ Sun, 21 Jun 2020 19:25:31: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:31: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 19:25:31: #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 19:25:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:25:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.10_summits.bed INFO @ Sun, 21 Jun 2020 19:25:58: Done! INFO @ Sun, 21 Jun 2020 19:25:58: #3 Call peaks for each chromosome... pass1 - making usageList (522 chroms): 1 millis pass2 - checking and writing primary data (1968 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287885/SRX287885.20_summits.bed INFO @ Sun, 21 Jun 2020 19:26:10: Done! pass1 - making usageList (416 chroms): 1 millis pass2 - checking and writing primary data (1157 records, 4 fields): 13 millis CompletedMACS2peakCalling