Job ID = 6455328 SRX = SRX287697 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:04:25 prefetch.2.10.7: 1) Downloading 'SRR869885'... 2020-06-21T10:04:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:06:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:06:33 prefetch.2.10.7: 1) 'SRR869885' was downloaded successfully Read 19930693 spots for SRR869885/SRR869885.sra Written 19930693 spots for SRR869885/SRR869885.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: 00:05:52 19930693 reads; of these: 19930693 (100.00%) were unpaired; of these: 1532951 (7.69%) aligned 0 times 13015986 (65.31%) aligned exactly 1 time 5381756 (27.00%) aligned >1 times 92.31% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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] 2760340 / 18397742 = 0.1500 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 19:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.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 19:18:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:14: 1000000 INFO @ Sun, 21 Jun 2020 19:18:20: 2000000 INFO @ Sun, 21 Jun 2020 19:18:26: 3000000 INFO @ Sun, 21 Jun 2020 19:18:31: 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 19:18:37: 5000000 INFO @ Sun, 21 Jun 2020 19:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.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 19:18:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:43: 6000000 INFO @ Sun, 21 Jun 2020 19:18:45: 1000000 INFO @ Sun, 21 Jun 2020 19:18:49: 7000000 INFO @ Sun, 21 Jun 2020 19:18:51: 2000000 INFO @ Sun, 21 Jun 2020 19:18:55: 8000000 INFO @ Sun, 21 Jun 2020 19:18:57: 3000000 INFO @ Sun, 21 Jun 2020 19:19:01: 9000000 INFO @ Sun, 21 Jun 2020 19:19:03: 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 19:19:07: 10000000 INFO @ Sun, 21 Jun 2020 19:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.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 19:19:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:09: 5000000 INFO @ Sun, 21 Jun 2020 19:19:13: 11000000 INFO @ Sun, 21 Jun 2020 19:19:15: 1000000 INFO @ Sun, 21 Jun 2020 19:19:16: 6000000 INFO @ Sun, 21 Jun 2020 19:19:20: 12000000 INFO @ Sun, 21 Jun 2020 19:19:22: 2000000 INFO @ Sun, 21 Jun 2020 19:19:22: 7000000 INFO @ Sun, 21 Jun 2020 19:19:27: 13000000 INFO @ Sun, 21 Jun 2020 19:19:29: 3000000 INFO @ Sun, 21 Jun 2020 19:19:29: 8000000 INFO @ Sun, 21 Jun 2020 19:19:33: 14000000 INFO @ Sun, 21 Jun 2020 19:19:36: 9000000 INFO @ Sun, 21 Jun 2020 19:19:36: 4000000 INFO @ Sun, 21 Jun 2020 19:19:40: 15000000 INFO @ Sun, 21 Jun 2020 19:19:42: 10000000 INFO @ Sun, 21 Jun 2020 19:19:43: 5000000 INFO @ Sun, 21 Jun 2020 19:19:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:45: #1 total tags in treatment: 15637402 INFO @ Sun, 21 Jun 2020 19:19:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:45: #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 19:19:45: #1 tags after filtering in treatment: 15637402 INFO @ Sun, 21 Jun 2020 19:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:46: #2 number of paired peaks: 369 WARNING @ Sun, 21 Jun 2020 19:19:46: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:46: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:19:46: #2 alternative fragment length(s) may be 4,36 bps INFO @ Sun, 21 Jun 2020 19:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.05_model.r WARNING @ Sun, 21 Jun 2020 19:19:46: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:46: #2 You may need to consider one of the other alternative d(s): 4,36 WARNING @ Sun, 21 Jun 2020 19:19:46: #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 19:19:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:48: 11000000 INFO @ Sun, 21 Jun 2020 19:19:50: 6000000 INFO @ Sun, 21 Jun 2020 19:19:55: 12000000 INFO @ Sun, 21 Jun 2020 19:19:57: 7000000 INFO @ Sun, 21 Jun 2020 19:20:01: 13000000 INFO @ Sun, 21 Jun 2020 19:20:04: 8000000 INFO @ Sun, 21 Jun 2020 19:20:08: 14000000 INFO @ Sun, 21 Jun 2020 19:20:11: 9000000 INFO @ Sun, 21 Jun 2020 19:20:14: 15000000 INFO @ Sun, 21 Jun 2020 19:20:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:18: 10000000 INFO @ Sun, 21 Jun 2020 19:20:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:19: #1 total tags in treatment: 15637402 INFO @ Sun, 21 Jun 2020 19:20:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:19: #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 19:20:19: #1 tags after filtering in treatment: 15637402 INFO @ Sun, 21 Jun 2020 19:20:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:20: #2 number of paired peaks: 369 WARNING @ Sun, 21 Jun 2020 19:20:20: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sun, 21 Jun 2020 19:20:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:20: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:20:20: #2 alternative fragment length(s) may be 4,36 bps INFO @ Sun, 21 Jun 2020 19:20:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.10_model.r WARNING @ Sun, 21 Jun 2020 19:20:20: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:20:20: #2 You may need to consider one of the other alternative d(s): 4,36 WARNING @ Sun, 21 Jun 2020 19:20:20: #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 19:20:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:20:24: 11000000 INFO @ Sun, 21 Jun 2020 19:20:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.05_summits.bed INFO @ Sun, 21 Jun 2020 19:20:30: Done! pass1 - making usageList (586 chroms): 2 millis pass2 - checking and writing primary data (2449 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:20:31: 12000000 INFO @ Sun, 21 Jun 2020 19:20:37: 13000000 INFO @ Sun, 21 Jun 2020 19:20:44: 14000000 INFO @ Sun, 21 Jun 2020 19:20:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:50: 15000000 INFO @ Sun, 21 Jun 2020 19:20:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:55: #1 total tags in treatment: 15637402 INFO @ Sun, 21 Jun 2020 19:20:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:55: #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 19:20:55: #1 tags after filtering in treatment: 15637402 INFO @ Sun, 21 Jun 2020 19:20:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:56: #2 number of paired peaks: 369 WARNING @ Sun, 21 Jun 2020 19:20:56: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sun, 21 Jun 2020 19:20:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:56: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:20:56: #2 alternative fragment length(s) may be 4,36 bps INFO @ Sun, 21 Jun 2020 19:20:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.20_model.r WARNING @ Sun, 21 Jun 2020 19:20:56: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:20:56: #2 You may need to consider one of the other alternative d(s): 4,36 WARNING @ Sun, 21 Jun 2020 19:20:56: #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 19:20:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.10_summits.bed INFO @ Sun, 21 Jun 2020 19:21:03: Done! pass1 - making usageList (474 chroms): 1 millis pass2 - checking and writing primary data (1585 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:21:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:21:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287697/SRX287697.20_summits.bed INFO @ Sun, 21 Jun 2020 19:21:39: Done! pass1 - making usageList (219 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 6 millis CompletedMACS2peakCalling