Job ID = 6458436 SRX = SRX5226990 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:35:05 prefetch.2.10.7: 1) Downloading 'SRR8417905'... 2020-06-21T12:35:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:38:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:38:57 prefetch.2.10.7: 1) 'SRR8417905' was downloaded successfully 2020-06-21T12:38:57 prefetch.2.10.7: 'SRR8417905' has 0 unresolved dependencies Read 21789320 spots for SRR8417905/SRR8417905.sra Written 21789320 spots for SRR8417905/SRR8417905.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: 00:07:33 21789320 reads; of these: 21789320 (100.00%) were unpaired; of these: 994695 (4.57%) aligned 0 times 15544064 (71.34%) aligned exactly 1 time 5250561 (24.10%) aligned >1 times 95.43% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 2675302 / 20794625 = 0.1287 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 21:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.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 21:54:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:28: 1000000 INFO @ Sun, 21 Jun 2020 21:54:34: 2000000 INFO @ Sun, 21 Jun 2020 21:54:39: 3000000 INFO @ Sun, 21 Jun 2020 21:54:45: 4000000 INFO @ Sun, 21 Jun 2020 21:54:50: 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 21:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.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 21:54:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:56: 6000000 INFO @ Sun, 21 Jun 2020 21:54:59: 1000000 INFO @ Sun, 21 Jun 2020 21:55:02: 7000000 INFO @ Sun, 21 Jun 2020 21:55:06: 2000000 INFO @ Sun, 21 Jun 2020 21:55:08: 8000000 INFO @ Sun, 21 Jun 2020 21:55:14: 3000000 INFO @ Sun, 21 Jun 2020 21:55:14: 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 21:55:20: 10000000 INFO @ Sun, 21 Jun 2020 21:55:21: 4000000 INFO @ Sun, 21 Jun 2020 21:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.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 21:55:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:27: 11000000 INFO @ Sun, 21 Jun 2020 21:55:28: 5000000 INFO @ Sun, 21 Jun 2020 21:55:28: 1000000 INFO @ Sun, 21 Jun 2020 21:55:33: 12000000 INFO @ Sun, 21 Jun 2020 21:55:34: 2000000 INFO @ Sun, 21 Jun 2020 21:55:35: 6000000 INFO @ Sun, 21 Jun 2020 21:55:39: 13000000 INFO @ Sun, 21 Jun 2020 21:55:41: 3000000 INFO @ Sun, 21 Jun 2020 21:55:42: 7000000 INFO @ Sun, 21 Jun 2020 21:55:45: 14000000 INFO @ Sun, 21 Jun 2020 21:55:47: 4000000 INFO @ Sun, 21 Jun 2020 21:55:49: 8000000 INFO @ Sun, 21 Jun 2020 21:55:51: 15000000 INFO @ Sun, 21 Jun 2020 21:55:53: 5000000 INFO @ Sun, 21 Jun 2020 21:55:55: 9000000 INFO @ Sun, 21 Jun 2020 21:55:57: 16000000 INFO @ Sun, 21 Jun 2020 21:55:59: 6000000 INFO @ Sun, 21 Jun 2020 21:56:02: 10000000 INFO @ Sun, 21 Jun 2020 21:56:03: 17000000 INFO @ Sun, 21 Jun 2020 21:56:05: 7000000 INFO @ Sun, 21 Jun 2020 21:56:09: 11000000 INFO @ Sun, 21 Jun 2020 21:56:10: 18000000 INFO @ Sun, 21 Jun 2020 21:56:10: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:56:10: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:56:10: #1 total tags in treatment: 18119323 INFO @ Sun, 21 Jun 2020 21:56:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:10: #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 21:56:11: #1 tags after filtering in treatment: 18119195 INFO @ Sun, 21 Jun 2020 21:56:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:11: 8000000 INFO @ Sun, 21 Jun 2020 21:56:12: #2 number of paired peaks: 891 WARNING @ Sun, 21 Jun 2020 21:56:12: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:12: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 21:56:12: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 21:56:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.05_model.r WARNING @ Sun, 21 Jun 2020 21:56:12: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:12: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 21:56:12: #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 21:56:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:16: 12000000 INFO @ Sun, 21 Jun 2020 21:56:18: 9000000 INFO @ Sun, 21 Jun 2020 21:56:23: 13000000 INFO @ Sun, 21 Jun 2020 21:56:24: 10000000 INFO @ Sun, 21 Jun 2020 21:56:30: 11000000 INFO @ Sun, 21 Jun 2020 21:56:30: 14000000 INFO @ Sun, 21 Jun 2020 21:56:36: 12000000 INFO @ Sun, 21 Jun 2020 21:56:37: 15000000 INFO @ Sun, 21 Jun 2020 21:56:42: 13000000 INFO @ Sun, 21 Jun 2020 21:56:45: 16000000 INFO @ Sun, 21 Jun 2020 21:56:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:48: 14000000 INFO @ Sun, 21 Jun 2020 21:56:52: 17000000 INFO @ Sun, 21 Jun 2020 21:56:54: 15000000 INFO @ Sun, 21 Jun 2020 21:56:59: 18000000 INFO @ Sun, 21 Jun 2020 21:57:00: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:57:00: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:57:00: #1 total tags in treatment: 18119323 INFO @ Sun, 21 Jun 2020 21:57:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:57:00: #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 21:57:00: #1 tags after filtering in treatment: 18119195 INFO @ Sun, 21 Jun 2020 21:57:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:57:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:57:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:57:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:57:00: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:57:02: #2 number of paired peaks: 891 WARNING @ Sun, 21 Jun 2020 21:57:02: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Sun, 21 Jun 2020 21:57:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:57:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:57:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:57:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:57:02: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 21:57:02: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 21:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.10_model.r WARNING @ Sun, 21 Jun 2020 21:57:02: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:57:02: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 21:57:02: #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 21:57:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:57:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.05_summits.bed INFO @ Sun, 21 Jun 2020 21:57:05: Done! pass1 - making usageList (474 chroms): 2 millis pass2 - checking and writing primary data (6994 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:06: 17000000 INFO @ Sun, 21 Jun 2020 21:57:12: 18000000 INFO @ Sun, 21 Jun 2020 21:57:13: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:57:13: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:57:13: #1 total tags in treatment: 18119323 INFO @ Sun, 21 Jun 2020 21:57:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:57:13: #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 21:57:14: #1 tags after filtering in treatment: 18119195 INFO @ Sun, 21 Jun 2020 21:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:57:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:57:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:57:15: #2 number of paired peaks: 891 WARNING @ Sun, 21 Jun 2020 21:57:15: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Sun, 21 Jun 2020 21:57:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:57:15: start X-correlation... INFO @ Sun, 21 Jun 2020 21:57:15: end of X-cor INFO @ Sun, 21 Jun 2020 21:57:15: #2 finished! INFO @ Sun, 21 Jun 2020 21:57:15: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 21:57:15: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 21:57:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.20_model.r WARNING @ Sun, 21 Jun 2020 21:57:15: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:57:15: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 21:57:15: #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 21:57:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:57:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:57:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.10_summits.bed INFO @ Sun, 21 Jun 2020 21:57:55: Done! pass1 - making usageList (397 chroms): 1 millis pass2 - checking and writing primary data (3006 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:58:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226990/SRX5226990.20_summits.bed INFO @ Sun, 21 Jun 2020 21:58:08: Done! pass1 - making usageList (274 chroms): 1 millis pass2 - checking and writing primary data (1162 records, 4 fields): 10 millis CompletedMACS2peakCalling