Job ID = 6455698 SRX = SRX287999 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:22:51 prefetch.2.10.7: 1) Downloading 'SRR870188'... 2020-06-21T10:22:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:53 prefetch.2.10.7: 1) 'SRR870188' was downloaded successfully Read 19240980 spots for SRR870188/SRR870188.sra Written 19240980 spots for SRR870188/SRR870188.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: 00:05:49 19240980 reads; of these: 19240980 (100.00%) were unpaired; of these: 1136389 (5.91%) aligned 0 times 12251572 (63.67%) aligned exactly 1 time 5853019 (30.42%) aligned >1 times 94.09% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 2703179 / 18104591 = 0.1493 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 19:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.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 19:38:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:22: 1000000 INFO @ Sun, 21 Jun 2020 19:38:28: 2000000 INFO @ Sun, 21 Jun 2020 19:38:34: 3000000 INFO @ Sun, 21 Jun 2020 19:38:40: 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 19:38:45: 5000000 INFO @ Sun, 21 Jun 2020 19:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.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 19:38:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:52: 6000000 INFO @ Sun, 21 Jun 2020 19:38:53: 1000000 INFO @ Sun, 21 Jun 2020 19:38:59: 7000000 INFO @ Sun, 21 Jun 2020 19:39:01: 2000000 INFO @ Sun, 21 Jun 2020 19:39:06: 8000000 INFO @ Sun, 21 Jun 2020 19:39:09: 3000000 INFO @ Sun, 21 Jun 2020 19:39:13: 9000000 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 19:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.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 19:39:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:17: 4000000 INFO @ Sun, 21 Jun 2020 19:39:20: 10000000 INFO @ Sun, 21 Jun 2020 19:39:23: 1000000 INFO @ Sun, 21 Jun 2020 19:39:25: 5000000 INFO @ Sun, 21 Jun 2020 19:39:27: 11000000 INFO @ Sun, 21 Jun 2020 19:39:31: 2000000 INFO @ Sun, 21 Jun 2020 19:39:33: 6000000 INFO @ Sun, 21 Jun 2020 19:39:34: 12000000 INFO @ Sun, 21 Jun 2020 19:39:38: 3000000 INFO @ Sun, 21 Jun 2020 19:39:41: 7000000 INFO @ Sun, 21 Jun 2020 19:39:42: 13000000 INFO @ Sun, 21 Jun 2020 19:39:46: 4000000 INFO @ Sun, 21 Jun 2020 19:39:49: 14000000 INFO @ Sun, 21 Jun 2020 19:39:49: 8000000 INFO @ Sun, 21 Jun 2020 19:39:54: 5000000 INFO @ Sun, 21 Jun 2020 19:39:56: 15000000 INFO @ Sun, 21 Jun 2020 19:39:57: 9000000 INFO @ Sun, 21 Jun 2020 19:39:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:39:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:39:59: #1 total tags in treatment: 15401412 INFO @ Sun, 21 Jun 2020 19:39:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:59: #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 19:40:00: #1 tags after filtering in treatment: 15401412 INFO @ Sun, 21 Jun 2020 19:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:01: #2 number of paired peaks: 711 WARNING @ Sun, 21 Jun 2020 19:40:01: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sun, 21 Jun 2020 19:40:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:01: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:40:01: #2 alternative fragment length(s) may be 3,37,541 bps INFO @ Sun, 21 Jun 2020 19:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.05_model.r WARNING @ Sun, 21 Jun 2020 19:40:01: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:40:01: #2 You may need to consider one of the other alternative d(s): 3,37,541 WARNING @ Sun, 21 Jun 2020 19:40:01: #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 19:40:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:01: 6000000 INFO @ Sun, 21 Jun 2020 19:40:05: 10000000 INFO @ Sun, 21 Jun 2020 19:40:08: 7000000 INFO @ Sun, 21 Jun 2020 19:40:13: 11000000 INFO @ Sun, 21 Jun 2020 19:40:16: 8000000 INFO @ Sun, 21 Jun 2020 19:40:21: 12000000 INFO @ Sun, 21 Jun 2020 19:40:23: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:40:29: 13000000 INFO @ Sun, 21 Jun 2020 19:40:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:30: 10000000 INFO @ Sun, 21 Jun 2020 19:40:37: 14000000 INFO @ Sun, 21 Jun 2020 19:40:38: 11000000 INFO @ Sun, 21 Jun 2020 19:40:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.05_summits.bed INFO @ Sun, 21 Jun 2020 19:40:43: Done! INFO @ Sun, 21 Jun 2020 19:40:45: 15000000 INFO @ Sun, 21 Jun 2020 19:40:45: 12000000 pass1 - making usageList (676 chroms): 1 millis pass2 - checking and writing primary data (2514 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:40:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:40:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:40:48: #1 total tags in treatment: 15401412 INFO @ Sun, 21 Jun 2020 19:40:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:48: #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 19:40:49: #1 tags after filtering in treatment: 15401412 INFO @ Sun, 21 Jun 2020 19:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:50: #2 number of paired peaks: 711 WARNING @ Sun, 21 Jun 2020 19:40:50: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sun, 21 Jun 2020 19:40:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:50: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:40:50: #2 alternative fragment length(s) may be 3,37,541 bps INFO @ Sun, 21 Jun 2020 19:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.10_model.r WARNING @ Sun, 21 Jun 2020 19:40:50: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:40:50: #2 You may need to consider one of the other alternative d(s): 3,37,541 WARNING @ Sun, 21 Jun 2020 19:40:50: #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 19:40:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:53: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:41:00: 14000000 INFO @ Sun, 21 Jun 2020 19:41:07: 15000000 INFO @ Sun, 21 Jun 2020 19:41:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:41:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:41:10: #1 total tags in treatment: 15401412 INFO @ Sun, 21 Jun 2020 19:41:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:10: #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 19:41:10: #1 tags after filtering in treatment: 15401412 INFO @ Sun, 21 Jun 2020 19:41:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:11: #2 number of paired peaks: 711 WARNING @ Sun, 21 Jun 2020 19:41:11: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sun, 21 Jun 2020 19:41:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:11: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:41:11: #2 alternative fragment length(s) may be 3,37,541 bps INFO @ Sun, 21 Jun 2020 19:41:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.20_model.r WARNING @ Sun, 21 Jun 2020 19:41:11: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:41:11: #2 You may need to consider one of the other alternative d(s): 3,37,541 WARNING @ Sun, 21 Jun 2020 19:41:11: #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 19:41:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:41:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.10_summits.bed INFO @ Sun, 21 Jun 2020 19:41:32: Done! pass1 - making usageList (528 chroms): 2 millis pass2 - checking and writing primary data (2067 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:41:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287999/SRX287999.20_summits.bed INFO @ Sun, 21 Jun 2020 19:41:54: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (1120 records, 4 fields): 12 millis CompletedMACS2peakCalling