Job ID = 6459478 SRX = SRX6827662 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:20:19 prefetch.2.10.7: 1) Downloading 'SRR10095442'... 2020-06-21T13:20:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:22:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:22:59 prefetch.2.10.7: 1) 'SRR10095442' was downloaded successfully Read 23060110 spots for SRR10095442/SRR10095442.sra Written 23060110 spots for SRR10095442/SRR10095442.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: 00:06:35 23060110 reads; of these: 23060110 (100.00%) were unpaired; of these: 818518 (3.55%) aligned 0 times 15725533 (68.19%) aligned exactly 1 time 6516059 (28.26%) aligned >1 times 96.45% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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] 3395781 / 22241592 = 0.1527 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 22:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.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 22:35:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:35:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:35:26: 1000000 INFO @ Sun, 21 Jun 2020 22:35:31: 2000000 INFO @ Sun, 21 Jun 2020 22:35:37: 3000000 INFO @ Sun, 21 Jun 2020 22:35:42: 4000000 INFO @ Sun, 21 Jun 2020 22:35:48: 5000000 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 22:35:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.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 22:35:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:35:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:35:53: 6000000 INFO @ Sun, 21 Jun 2020 22:35:57: 1000000 INFO @ Sun, 21 Jun 2020 22:35:59: 7000000 INFO @ Sun, 21 Jun 2020 22:36:04: 2000000 INFO @ Sun, 21 Jun 2020 22:36:05: 8000000 INFO @ Sun, 21 Jun 2020 22:36:10: 9000000 INFO @ Sun, 21 Jun 2020 22:36:11: 3000000 INFO @ Sun, 21 Jun 2020 22:36:16: 10000000 INFO @ Sun, 21 Jun 2020 22:36:17: 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 22:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.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 22:36:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:36:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:36:22: 11000000 INFO @ Sun, 21 Jun 2020 22:36:24: 5000000 INFO @ Sun, 21 Jun 2020 22:36:27: 1000000 INFO @ Sun, 21 Jun 2020 22:36:28: 12000000 INFO @ Sun, 21 Jun 2020 22:36:30: 6000000 INFO @ Sun, 21 Jun 2020 22:36:33: 2000000 INFO @ Sun, 21 Jun 2020 22:36:34: 13000000 INFO @ Sun, 21 Jun 2020 22:36:37: 7000000 INFO @ Sun, 21 Jun 2020 22:36:39: 3000000 INFO @ Sun, 21 Jun 2020 22:36:40: 14000000 INFO @ Sun, 21 Jun 2020 22:36:44: 8000000 INFO @ Sun, 21 Jun 2020 22:36:45: 4000000 INFO @ Sun, 21 Jun 2020 22:36:46: 15000000 INFO @ Sun, 21 Jun 2020 22:36:51: 9000000 INFO @ Sun, 21 Jun 2020 22:36:51: 5000000 INFO @ Sun, 21 Jun 2020 22:36:53: 16000000 INFO @ Sun, 21 Jun 2020 22:36:57: 6000000 INFO @ Sun, 21 Jun 2020 22:36:57: 10000000 INFO @ Sun, 21 Jun 2020 22:36:59: 17000000 INFO @ Sun, 21 Jun 2020 22:37:03: 7000000 INFO @ Sun, 21 Jun 2020 22:37:04: 11000000 INFO @ Sun, 21 Jun 2020 22:37:05: 18000000 INFO @ Sun, 21 Jun 2020 22:37:09: 8000000 INFO @ Sun, 21 Jun 2020 22:37:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:37:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:37:10: #1 total tags in treatment: 18845811 INFO @ Sun, 21 Jun 2020 22:37:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:37:10: #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 22:37:11: #1 tags after filtering in treatment: 18845757 INFO @ Sun, 21 Jun 2020 22:37:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:37:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:37:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:37:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:37:11: 12000000 INFO @ Sun, 21 Jun 2020 22:37:12: #2 number of paired peaks: 854 WARNING @ Sun, 21 Jun 2020 22:37:12: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Sun, 21 Jun 2020 22:37:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:37:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:37:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:37:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:37:12: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:37:12: #2 alternative fragment length(s) may be 2,48,588 bps INFO @ Sun, 21 Jun 2020 22:37:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.05_model.r WARNING @ Sun, 21 Jun 2020 22:37:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:37:12: #2 You may need to consider one of the other alternative d(s): 2,48,588 WARNING @ Sun, 21 Jun 2020 22:37:12: #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 22:37:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:37:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:37:15: 9000000 INFO @ Sun, 21 Jun 2020 22:37:17: 13000000 INFO @ Sun, 21 Jun 2020 22:37:21: 10000000 INFO @ Sun, 21 Jun 2020 22:37:24: 14000000 INFO @ Sun, 21 Jun 2020 22:37:27: 11000000 INFO @ Sun, 21 Jun 2020 22:37:30: 15000000 INFO @ Sun, 21 Jun 2020 22:37:32: 12000000 INFO @ Sun, 21 Jun 2020 22:37:37: 16000000 INFO @ Sun, 21 Jun 2020 22:37:38: 13000000 INFO @ Sun, 21 Jun 2020 22:37:44: 17000000 INFO @ Sun, 21 Jun 2020 22:37:44: 14000000 INFO @ Sun, 21 Jun 2020 22:37:50: 15000000 INFO @ Sun, 21 Jun 2020 22:37:51: 18000000 INFO @ Sun, 21 Jun 2020 22:37:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:37:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:37:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:37:56: #1 total tags in treatment: 18845811 INFO @ Sun, 21 Jun 2020 22:37:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:37:56: #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 22:37:57: 16000000 INFO @ Sun, 21 Jun 2020 22:37:57: #1 tags after filtering in treatment: 18845757 INFO @ Sun, 21 Jun 2020 22:37:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:37:57: #1 finished! INFO @ Sun, 21 Jun 2020 22:37:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:37:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:37:58: #2 number of paired peaks: 854 WARNING @ Sun, 21 Jun 2020 22:37:58: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Sun, 21 Jun 2020 22:37:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:37:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:37:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:37:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:37:59: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:37:59: #2 alternative fragment length(s) may be 2,48,588 bps INFO @ Sun, 21 Jun 2020 22:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.10_model.r WARNING @ Sun, 21 Jun 2020 22:37:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:37:59: #2 You may need to consider one of the other alternative d(s): 2,48,588 WARNING @ Sun, 21 Jun 2020 22:37:59: #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 22:37:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:38:02: 17000000 INFO @ Sun, 21 Jun 2020 22:38:07: 18000000 INFO @ Sun, 21 Jun 2020 22:38:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.05_summits.bed INFO @ Sun, 21 Jun 2020 22:38:10: Done! pass1 - making usageList (633 chroms): 1 millis pass2 - checking and writing primary data (3015 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:38:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:38:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:38:12: #1 total tags in treatment: 18845811 INFO @ Sun, 21 Jun 2020 22:38:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:12: #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 22:38:13: #1 tags after filtering in treatment: 18845757 INFO @ Sun, 21 Jun 2020 22:38:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:13: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:14: #2 number of paired peaks: 854 WARNING @ Sun, 21 Jun 2020 22:38:14: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Sun, 21 Jun 2020 22:38:14: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:15: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:38:15: #2 alternative fragment length(s) may be 2,48,588 bps INFO @ Sun, 21 Jun 2020 22:38:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.20_model.r WARNING @ Sun, 21 Jun 2020 22:38:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:15: #2 You may need to consider one of the other alternative d(s): 2,48,588 WARNING @ Sun, 21 Jun 2020 22:38:15: #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 22:38:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:38:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:38:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:38:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.10_summits.bed INFO @ Sun, 21 Jun 2020 22:38:57: Done! pass1 - making usageList (512 chroms): 1 millis pass2 - checking and writing primary data (2077 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827662/SRX6827662.20_summits.bed INFO @ Sun, 21 Jun 2020 22:39:11: Done! pass1 - making usageList (294 chroms): 1 millis pass2 - checking and writing primary data (678 records, 4 fields): 11 millis CompletedMACS2peakCalling