Job ID = 6455247 SRX = SRX287589 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:57:55 prefetch.2.10.7: 1) Downloading 'SRR869732'... 2020-06-21T09:57:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:00:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:00:47 prefetch.2.10.7: 1) 'SRR869732' was downloaded successfully Read 21508050 spots for SRR869732/SRR869732.sra Written 21508050 spots for SRR869732/SRR869732.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: 00:05:48 21508050 reads; of these: 21508050 (100.00%) were unpaired; of these: 1497247 (6.96%) aligned 0 times 14283470 (66.41%) aligned exactly 1 time 5727333 (26.63%) aligned >1 times 93.04% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 4278338 / 20010803 = 0.2138 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 19:12:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.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 19:12:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:54: 1000000 INFO @ Sun, 21 Jun 2020 19:12:59: 2000000 INFO @ Sun, 21 Jun 2020 19:13:05: 3000000 INFO @ Sun, 21 Jun 2020 19:13:11: 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 19:13:17: 5000000 INFO @ Sun, 21 Jun 2020 19:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.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 19:13:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:23: 6000000 INFO @ Sun, 21 Jun 2020 19:13:24: 1000000 INFO @ Sun, 21 Jun 2020 19:13:30: 7000000 INFO @ Sun, 21 Jun 2020 19:13:31: 2000000 INFO @ Sun, 21 Jun 2020 19:13:36: 8000000 INFO @ Sun, 21 Jun 2020 19:13:37: 3000000 INFO @ Sun, 21 Jun 2020 19:13:43: 9000000 INFO @ Sun, 21 Jun 2020 19:13:44: 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 19:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.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 19:13:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:49: 10000000 INFO @ Sun, 21 Jun 2020 19:13:50: 5000000 INFO @ Sun, 21 Jun 2020 19:13:54: 1000000 INFO @ Sun, 21 Jun 2020 19:13:56: 11000000 INFO @ Sun, 21 Jun 2020 19:13:57: 6000000 INFO @ Sun, 21 Jun 2020 19:14:01: 2000000 INFO @ Sun, 21 Jun 2020 19:14:02: 12000000 INFO @ Sun, 21 Jun 2020 19:14:03: 7000000 INFO @ Sun, 21 Jun 2020 19:14:08: 3000000 INFO @ Sun, 21 Jun 2020 19:14:09: 13000000 INFO @ Sun, 21 Jun 2020 19:14:10: 8000000 INFO @ Sun, 21 Jun 2020 19:14:14: 4000000 INFO @ Sun, 21 Jun 2020 19:14:16: 14000000 INFO @ Sun, 21 Jun 2020 19:14:17: 9000000 INFO @ Sun, 21 Jun 2020 19:14:22: 5000000 INFO @ Sun, 21 Jun 2020 19:14:23: 15000000 INFO @ Sun, 21 Jun 2020 19:14:24: 10000000 INFO @ Sun, 21 Jun 2020 19:14:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:29: #1 total tags in treatment: 15732465 INFO @ Sun, 21 Jun 2020 19:14:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:29: #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 19:14:29: 6000000 INFO @ Sun, 21 Jun 2020 19:14:29: #1 tags after filtering in treatment: 15732465 INFO @ Sun, 21 Jun 2020 19:14:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:30: #2 number of paired peaks: 722 WARNING @ Sun, 21 Jun 2020 19:14:30: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:30: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:14:30: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 19:14:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.05_model.r WARNING @ Sun, 21 Jun 2020 19:14:30: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:30: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 19:14:30: #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 19:14:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:31: 11000000 INFO @ Sun, 21 Jun 2020 19:14:36: 7000000 INFO @ Sun, 21 Jun 2020 19:14:38: 12000000 INFO @ Sun, 21 Jun 2020 19:14:43: 8000000 INFO @ Sun, 21 Jun 2020 19:14:45: 13000000 INFO @ Sun, 21 Jun 2020 19:14:50: 9000000 INFO @ Sun, 21 Jun 2020 19:14:52: 14000000 INFO @ Sun, 21 Jun 2020 19:14:57: 10000000 INFO @ Sun, 21 Jun 2020 19:14:59: 15000000 INFO @ Sun, 21 Jun 2020 19:15:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:03: 11000000 INFO @ Sun, 21 Jun 2020 19:15:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:04: #1 total tags in treatment: 15732465 INFO @ Sun, 21 Jun 2020 19:15:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:04: #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 19:15:05: #1 tags after filtering in treatment: 15732465 INFO @ Sun, 21 Jun 2020 19:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:06: #2 number of paired peaks: 722 WARNING @ Sun, 21 Jun 2020 19:15:06: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:06: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:15:06: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 19:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.10_model.r WARNING @ Sun, 21 Jun 2020 19:15:06: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:06: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 19:15:06: #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 19:15:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:10: 12000000 INFO @ Sun, 21 Jun 2020 19:15:16: 13000000 INFO @ Sun, 21 Jun 2020 19:15:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.05_summits.bed INFO @ Sun, 21 Jun 2020 19:15:17: Done! pass1 - making usageList (673 chroms): 1 millis pass2 - checking and writing primary data (4889 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:22: 14000000 INFO @ Sun, 21 Jun 2020 19:15:28: 15000000 INFO @ Sun, 21 Jun 2020 19:15:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:33: #1 total tags in treatment: 15732465 INFO @ Sun, 21 Jun 2020 19:15:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:33: #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 19:15:34: #1 tags after filtering in treatment: 15732465 INFO @ Sun, 21 Jun 2020 19:15:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:35: #2 number of paired peaks: 722 WARNING @ Sun, 21 Jun 2020 19:15:35: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:35: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:15:35: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 19:15:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.20_model.r WARNING @ Sun, 21 Jun 2020 19:15:35: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:35: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 19:15:35: #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 19:15:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.10_summits.bed INFO @ Sun, 21 Jun 2020 19:15:50: Done! pass1 - making usageList (554 chroms): 2 millis pass2 - checking and writing primary data (3230 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287589/SRX287589.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:19: Done! pass1 - making usageList (443 chroms): 1 millis pass2 - checking and writing primary data (1825 records, 4 fields): 15 millis CompletedMACS2peakCalling