Job ID = 6458340 SRX = SRX5011086 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:22:04 prefetch.2.10.7: 1) Downloading 'SRR8191535'... 2020-06-21T12:22:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:25:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:25:24 prefetch.2.10.7: 1) 'SRR8191535' was downloaded successfully Read 34576407 spots for SRR8191535/SRR8191535.sra Written 34576407 spots for SRR8191535/SRR8191535.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: 00:08:22 34576407 reads; of these: 34576407 (100.00%) were unpaired; of these: 4751046 (13.74%) aligned 0 times 22986597 (66.48%) aligned exactly 1 time 6838764 (19.78%) aligned >1 times 86.26% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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 16 files... [bam_rmdupse_core] 10429821 / 29825361 = 0.3497 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 21:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.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 21:41:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:36: 1000000 INFO @ Sun, 21 Jun 2020 21:41:42: 2000000 INFO @ Sun, 21 Jun 2020 21:41:47: 3000000 INFO @ Sun, 21 Jun 2020 21:41:53: 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 21:41:59: 5000000 INFO @ Sun, 21 Jun 2020 21:42:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.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 21:42:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:06: 6000000 INFO @ Sun, 21 Jun 2020 21:42:07: 1000000 INFO @ Sun, 21 Jun 2020 21:42:12: 7000000 INFO @ Sun, 21 Jun 2020 21:42:14: 2000000 INFO @ Sun, 21 Jun 2020 21:42:19: 8000000 INFO @ Sun, 21 Jun 2020 21:42:20: 3000000 INFO @ Sun, 21 Jun 2020 21:42:26: 9000000 INFO @ Sun, 21 Jun 2020 21:42:27: 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 21:42:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.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 21:42:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:33: 10000000 INFO @ Sun, 21 Jun 2020 21:42:34: 5000000 INFO @ Sun, 21 Jun 2020 21:42:39: 1000000 INFO @ Sun, 21 Jun 2020 21:42:41: 11000000 INFO @ Sun, 21 Jun 2020 21:42:42: 6000000 INFO @ Sun, 21 Jun 2020 21:42:47: 2000000 INFO @ Sun, 21 Jun 2020 21:42:48: 12000000 INFO @ Sun, 21 Jun 2020 21:42:49: 7000000 INFO @ Sun, 21 Jun 2020 21:42:55: 13000000 INFO @ Sun, 21 Jun 2020 21:42:56: 3000000 INFO @ Sun, 21 Jun 2020 21:42:57: 8000000 INFO @ Sun, 21 Jun 2020 21:43:03: 14000000 INFO @ Sun, 21 Jun 2020 21:43:04: 9000000 INFO @ Sun, 21 Jun 2020 21:43:04: 4000000 INFO @ Sun, 21 Jun 2020 21:43:10: 15000000 INFO @ Sun, 21 Jun 2020 21:43:12: 10000000 INFO @ Sun, 21 Jun 2020 21:43:13: 5000000 INFO @ Sun, 21 Jun 2020 21:43:18: 16000000 INFO @ Sun, 21 Jun 2020 21:43:19: 11000000 INFO @ Sun, 21 Jun 2020 21:43:21: 6000000 INFO @ Sun, 21 Jun 2020 21:43:26: 17000000 INFO @ Sun, 21 Jun 2020 21:43:26: 12000000 INFO @ Sun, 21 Jun 2020 21:43:30: 7000000 INFO @ Sun, 21 Jun 2020 21:43:33: 18000000 INFO @ Sun, 21 Jun 2020 21:43:34: 13000000 INFO @ Sun, 21 Jun 2020 21:43:38: 8000000 INFO @ Sun, 21 Jun 2020 21:43:41: 19000000 INFO @ Sun, 21 Jun 2020 21:43:41: 14000000 INFO @ Sun, 21 Jun 2020 21:43:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:43:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:43:44: #1 total tags in treatment: 19395540 INFO @ Sun, 21 Jun 2020 21:43:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:44: #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 21:43:44: #1 tags after filtering in treatment: 19395450 INFO @ Sun, 21 Jun 2020 21:43:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:44: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:46: #2 number of paired peaks: 800 WARNING @ Sun, 21 Jun 2020 21:43:46: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Sun, 21 Jun 2020 21:43:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:46: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:43:46: #2 alternative fragment length(s) may be 4,80 bps INFO @ Sun, 21 Jun 2020 21:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.05_model.r WARNING @ Sun, 21 Jun 2020 21:43:46: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:46: #2 You may need to consider one of the other alternative d(s): 4,80 WARNING @ Sun, 21 Jun 2020 21:43:46: #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 21:43:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:47: 9000000 INFO @ Sun, 21 Jun 2020 21:43:49: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:43:55: 10000000 INFO @ Sun, 21 Jun 2020 21:43:57: 16000000 INFO @ Sun, 21 Jun 2020 21:44:03: 11000000 INFO @ Sun, 21 Jun 2020 21:44:04: 17000000 INFO @ Sun, 21 Jun 2020 21:44:12: 18000000 INFO @ Sun, 21 Jun 2020 21:44:12: 12000000 INFO @ Sun, 21 Jun 2020 21:44:20: 19000000 INFO @ Sun, 21 Jun 2020 21:44:20: 13000000 INFO @ Sun, 21 Jun 2020 21:44:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:44:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:44:23: #1 total tags in treatment: 19395540 INFO @ Sun, 21 Jun 2020 21:44:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:23: #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 21:44:24: #1 tags after filtering in treatment: 19395450 INFO @ Sun, 21 Jun 2020 21:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:25: #2 number of paired peaks: 800 WARNING @ Sun, 21 Jun 2020 21:44:25: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Sun, 21 Jun 2020 21:44:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:25: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:44:25: #2 alternative fragment length(s) may be 4,80 bps INFO @ Sun, 21 Jun 2020 21:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.10_model.r WARNING @ Sun, 21 Jun 2020 21:44:25: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:44:25: #2 You may need to consider one of the other alternative d(s): 4,80 WARNING @ Sun, 21 Jun 2020 21:44:25: #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 21:44:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:44:28: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:44:36: 15000000 INFO @ Sun, 21 Jun 2020 21:44:44: 16000000 INFO @ Sun, 21 Jun 2020 21:44:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.05_summits.bed INFO @ Sun, 21 Jun 2020 21:44:46: Done! pass1 - making usageList (644 chroms): 2 millis pass2 - checking and writing primary data (4088 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:44:52: 17000000 INFO @ Sun, 21 Jun 2020 21:45:00: 18000000 INFO @ Sun, 21 Jun 2020 21:45:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:45:08: 19000000 INFO @ Sun, 21 Jun 2020 21:45:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:45:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:45:11: #1 total tags in treatment: 19395540 INFO @ Sun, 21 Jun 2020 21:45:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:11: #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 21:45:11: #1 tags after filtering in treatment: 19395450 INFO @ Sun, 21 Jun 2020 21:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:45:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:45:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:45:13: #2 number of paired peaks: 800 WARNING @ Sun, 21 Jun 2020 21:45:13: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Sun, 21 Jun 2020 21:45:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:45:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:45:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:45:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:45:13: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:45:13: #2 alternative fragment length(s) may be 4,80 bps INFO @ Sun, 21 Jun 2020 21:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.20_model.r WARNING @ Sun, 21 Jun 2020 21:45:13: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:45:13: #2 You may need to consider one of the other alternative d(s): 4,80 WARNING @ Sun, 21 Jun 2020 21:45:13: #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 21:45:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.10_summits.bed INFO @ Sun, 21 Jun 2020 21:45:23: Done! pass1 - making usageList (452 chroms): 2 millis pass2 - checking and writing primary data (2327 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:45:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011086/SRX5011086.20_summits.bed INFO @ Sun, 21 Jun 2020 21:46:15: Done! pass1 - making usageList (305 chroms): 1 millis pass2 - checking and writing primary data (1227 records, 4 fields): 10 millis CompletedMACS2peakCalling