Job ID = 6458444 SRX = SRX5226998 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:51 prefetch.2.10.7: 1) Downloading 'SRR8417913'... 2020-06-21T12:31:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:37:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:37:52 prefetch.2.10.7: 1) 'SRR8417913' was downloaded successfully 2020-06-21T12:37:52 prefetch.2.10.7: 'SRR8417913' has 0 unresolved dependencies Read 24430431 spots for SRR8417913/SRR8417913.sra Written 24430431 spots for SRR8417913/SRR8417913.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: 00:08:53 24430431 reads; of these: 24430431 (100.00%) were unpaired; of these: 1015911 (4.16%) aligned 0 times 17538924 (71.79%) aligned exactly 1 time 5875596 (24.05%) aligned >1 times 95.84% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 3193242 / 23414520 = 0.1364 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 21:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.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 21:55:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:58: 1000000 INFO @ Sun, 21 Jun 2020 21:56:04: 2000000 INFO @ Sun, 21 Jun 2020 21:56:11: 3000000 INFO @ Sun, 21 Jun 2020 21:56:17: 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 21:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.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 21:56:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:23: 5000000 INFO @ Sun, 21 Jun 2020 21:56:28: 1000000 INFO @ Sun, 21 Jun 2020 21:56:30: 6000000 INFO @ Sun, 21 Jun 2020 21:56:35: 2000000 INFO @ Sun, 21 Jun 2020 21:56:36: 7000000 INFO @ Sun, 21 Jun 2020 21:56:41: 3000000 INFO @ Sun, 21 Jun 2020 21:56:43: 8000000 INFO @ Sun, 21 Jun 2020 21:56:48: 4000000 INFO @ Sun, 21 Jun 2020 21:56:49: 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 21:56:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.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 21:56:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:54: 5000000 INFO @ Sun, 21 Jun 2020 21:56:56: 10000000 INFO @ Sun, 21 Jun 2020 21:56:58: 1000000 INFO @ Sun, 21 Jun 2020 21:57:01: 6000000 INFO @ Sun, 21 Jun 2020 21:57:02: 11000000 INFO @ Sun, 21 Jun 2020 21:57:05: 2000000 INFO @ Sun, 21 Jun 2020 21:57:08: 7000000 INFO @ Sun, 21 Jun 2020 21:57:09: 12000000 INFO @ Sun, 21 Jun 2020 21:57:11: 3000000 INFO @ Sun, 21 Jun 2020 21:57:14: 8000000 INFO @ Sun, 21 Jun 2020 21:57:16: 13000000 INFO @ Sun, 21 Jun 2020 21:57:18: 4000000 INFO @ Sun, 21 Jun 2020 21:57:21: 9000000 INFO @ Sun, 21 Jun 2020 21:57:22: 14000000 INFO @ Sun, 21 Jun 2020 21:57:24: 5000000 INFO @ Sun, 21 Jun 2020 21:57:27: 10000000 INFO @ Sun, 21 Jun 2020 21:57:28: 15000000 INFO @ Sun, 21 Jun 2020 21:57:31: 6000000 INFO @ Sun, 21 Jun 2020 21:57:34: 11000000 INFO @ Sun, 21 Jun 2020 21:57:35: 16000000 INFO @ Sun, 21 Jun 2020 21:57:37: 7000000 INFO @ Sun, 21 Jun 2020 21:57:40: 12000000 INFO @ Sun, 21 Jun 2020 21:57:41: 17000000 INFO @ Sun, 21 Jun 2020 21:57:43: 8000000 INFO @ Sun, 21 Jun 2020 21:57:46: 13000000 INFO @ Sun, 21 Jun 2020 21:57:48: 18000000 INFO @ Sun, 21 Jun 2020 21:57:50: 9000000 INFO @ Sun, 21 Jun 2020 21:57:53: 14000000 INFO @ Sun, 21 Jun 2020 21:57:54: 19000000 INFO @ Sun, 21 Jun 2020 21:57:56: 10000000 INFO @ Sun, 21 Jun 2020 21:57:59: 15000000 INFO @ Sun, 21 Jun 2020 21:58:01: 20000000 INFO @ Sun, 21 Jun 2020 21:58:02: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:58:02: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:58:02: #1 total tags in treatment: 20221278 INFO @ Sun, 21 Jun 2020 21:58:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:02: #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 21:58:03: 11000000 INFO @ Sun, 21 Jun 2020 21:58:03: #1 tags after filtering in treatment: 20221176 INFO @ Sun, 21 Jun 2020 21:58:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:03: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:04: #2 number of paired peaks: 796 WARNING @ Sun, 21 Jun 2020 21:58:04: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:04: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:04: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:04: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:04: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:04: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 21:58:04: #2 alternative fragment length(s) may be 3,89 bps INFO @ Sun, 21 Jun 2020 21:58:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.05_model.r WARNING @ Sun, 21 Jun 2020 21:58:04: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:04: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Sun, 21 Jun 2020 21:58:04: #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 21:58:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:05: 16000000 INFO @ Sun, 21 Jun 2020 21:58:09: 12000000 INFO @ Sun, 21 Jun 2020 21:58:11: 17000000 INFO @ Sun, 21 Jun 2020 21:58:16: 13000000 INFO @ Sun, 21 Jun 2020 21:58:18: 18000000 INFO @ Sun, 21 Jun 2020 21:58:22: 14000000 INFO @ Sun, 21 Jun 2020 21:58:25: 19000000 INFO @ Sun, 21 Jun 2020 21:58:29: 15000000 INFO @ Sun, 21 Jun 2020 21:58:31: 20000000 INFO @ Sun, 21 Jun 2020 21:58:33: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:58:33: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:58:33: #1 total tags in treatment: 20221278 INFO @ Sun, 21 Jun 2020 21:58:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:33: #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 21:58:33: #1 tags after filtering in treatment: 20221176 INFO @ Sun, 21 Jun 2020 21:58:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:35: 16000000 INFO @ Sun, 21 Jun 2020 21:58:35: #2 number of paired peaks: 796 WARNING @ Sun, 21 Jun 2020 21:58:35: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:35: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 21:58:35: #2 alternative fragment length(s) may be 3,89 bps INFO @ Sun, 21 Jun 2020 21:58:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.10_model.r WARNING @ Sun, 21 Jun 2020 21:58:35: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:35: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Sun, 21 Jun 2020 21:58:35: #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 21:58:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:58:41: 17000000 INFO @ Sun, 21 Jun 2020 21:58:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:47: 18000000 INFO @ Sun, 21 Jun 2020 21:58:53: 19000000 INFO @ Sun, 21 Jun 2020 21:58:59: 20000000 INFO @ Sun, 21 Jun 2020 21:59:01: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:59:01: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:59:01: #1 total tags in treatment: 20221278 INFO @ Sun, 21 Jun 2020 21:59:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:01: #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 21:59:01: #1 tags after filtering in treatment: 20221176 INFO @ Sun, 21 Jun 2020 21:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:01: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:03: #2 number of paired peaks: 796 WARNING @ Sun, 21 Jun 2020 21:59:03: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:03: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 21:59:03: #2 alternative fragment length(s) may be 3,89 bps INFO @ Sun, 21 Jun 2020 21:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.20_model.r WARNING @ Sun, 21 Jun 2020 21:59:03: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:03: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Sun, 21 Jun 2020 21:59:03: #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 21:59:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.05_summits.bed INFO @ Sun, 21 Jun 2020 21:59:07: Done! pass1 - making usageList (474 chroms): 2 millis pass2 - checking and writing primary data (7202 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:59:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.10_summits.bed INFO @ Sun, 21 Jun 2020 21:59:37: Done! pass1 - making usageList (402 chroms): 2 millis pass2 - checking and writing primary data (3183 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226998/SRX5226998.20_summits.bed INFO @ Sun, 21 Jun 2020 22:00:06: Done! pass1 - making usageList (284 chroms): 1 millis pass2 - checking and writing primary data (1223 records, 4 fields): 10 millis CompletedMACS2peakCalling