Job ID = 6457881 SRX = SRX4828013 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:04:22 prefetch.2.10.7: 1) Downloading 'SRR7997149'... 2020-06-21T12:04:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:07:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:07:01 prefetch.2.10.7: 'SRR7997149' is valid 2020-06-21T12:07:01 prefetch.2.10.7: 1) 'SRR7997149' was downloaded successfully 2020-06-21T12:07:01 prefetch.2.10.7: 'SRR7997149' has 0 unresolved dependencies Read 25554421 spots for SRR7997149/SRR7997149.sra Written 25554421 spots for SRR7997149/SRR7997149.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: 00:06:31 25554421 reads; of these: 25554421 (100.00%) were unpaired; of these: 3645240 (14.26%) aligned 0 times 16671444 (65.24%) aligned exactly 1 time 5237737 (20.50%) aligned >1 times 85.74% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 5482271 / 21909181 = 0.2502 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 21:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.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 21:19:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:47: 1000000 INFO @ Sun, 21 Jun 2020 21:19:54: 2000000 INFO @ Sun, 21 Jun 2020 21:20:01: 3000000 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 21:20:08: 4000000 INFO @ Sun, 21 Jun 2020 21:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.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 21:20:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:16: 5000000 INFO @ Sun, 21 Jun 2020 21:20:18: 1000000 INFO @ Sun, 21 Jun 2020 21:20:23: 6000000 INFO @ Sun, 21 Jun 2020 21:20:27: 2000000 INFO @ Sun, 21 Jun 2020 21:20:31: 7000000 INFO @ Sun, 21 Jun 2020 21:20:35: 3000000 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 21:20:39: 8000000 INFO @ Sun, 21 Jun 2020 21:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.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 21:20:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:44: 4000000 INFO @ Sun, 21 Jun 2020 21:20:47: 9000000 INFO @ Sun, 21 Jun 2020 21:20:48: 1000000 INFO @ Sun, 21 Jun 2020 21:20:52: 5000000 INFO @ Sun, 21 Jun 2020 21:20:55: 10000000 INFO @ Sun, 21 Jun 2020 21:20:56: 2000000 INFO @ Sun, 21 Jun 2020 21:21:00: 6000000 INFO @ Sun, 21 Jun 2020 21:21:03: 11000000 INFO @ Sun, 21 Jun 2020 21:21:04: 3000000 INFO @ Sun, 21 Jun 2020 21:21:08: 7000000 INFO @ Sun, 21 Jun 2020 21:21:11: 12000000 INFO @ Sun, 21 Jun 2020 21:21:12: 4000000 INFO @ Sun, 21 Jun 2020 21:21:16: 8000000 INFO @ Sun, 21 Jun 2020 21:21:20: 13000000 INFO @ Sun, 21 Jun 2020 21:21:20: 5000000 INFO @ Sun, 21 Jun 2020 21:21:24: 9000000 INFO @ Sun, 21 Jun 2020 21:21:28: 6000000 INFO @ Sun, 21 Jun 2020 21:21:28: 14000000 INFO @ Sun, 21 Jun 2020 21:21:32: 10000000 INFO @ Sun, 21 Jun 2020 21:21:36: 7000000 INFO @ Sun, 21 Jun 2020 21:21:36: 15000000 INFO @ Sun, 21 Jun 2020 21:21:40: 11000000 INFO @ Sun, 21 Jun 2020 21:21:44: 8000000 INFO @ Sun, 21 Jun 2020 21:21:45: 16000000 INFO @ Sun, 21 Jun 2020 21:21:48: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:21:48: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:21:48: #1 total tags in treatment: 16426910 INFO @ Sun, 21 Jun 2020 21:21:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:48: #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 21:21:49: 12000000 INFO @ Sun, 21 Jun 2020 21:21:49: #1 tags after filtering in treatment: 16426833 INFO @ Sun, 21 Jun 2020 21:21:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:50: #2 number of paired peaks: 369 WARNING @ Sun, 21 Jun 2020 21:21:50: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sun, 21 Jun 2020 21:21:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:50: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 21:21:50: #2 alternative fragment length(s) may be 4,76,85 bps INFO @ Sun, 21 Jun 2020 21:21:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.05_model.r WARNING @ Sun, 21 Jun 2020 21:21:50: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:21:50: #2 You may need to consider one of the other alternative d(s): 4,76,85 WARNING @ Sun, 21 Jun 2020 21:21:50: #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 21:21:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:53: 9000000 INFO @ Sun, 21 Jun 2020 21:21:57: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:22:01: 10000000 INFO @ Sun, 21 Jun 2020 21:22:05: 14000000 INFO @ Sun, 21 Jun 2020 21:22:09: 11000000 INFO @ Sun, 21 Jun 2020 21:22:13: 15000000 INFO @ Sun, 21 Jun 2020 21:22:17: 12000000 INFO @ Sun, 21 Jun 2020 21:22:21: 16000000 INFO @ Sun, 21 Jun 2020 21:22:25: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:22:25: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:22:25: #1 total tags in treatment: 16426910 INFO @ Sun, 21 Jun 2020 21:22:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:25: #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 21:22:26: #1 tags after filtering in treatment: 16426833 INFO @ Sun, 21 Jun 2020 21:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:26: 13000000 INFO @ Sun, 21 Jun 2020 21:22:27: #2 number of paired peaks: 369 WARNING @ Sun, 21 Jun 2020 21:22:27: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sun, 21 Jun 2020 21:22:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:27: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 21:22:27: #2 alternative fragment length(s) may be 4,76,85 bps INFO @ Sun, 21 Jun 2020 21:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.10_model.r WARNING @ Sun, 21 Jun 2020 21:22:27: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:22:27: #2 You may need to consider one of the other alternative d(s): 4,76,85 WARNING @ Sun, 21 Jun 2020 21:22:27: #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 21:22:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:33: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:22:41: 15000000 INFO @ Sun, 21 Jun 2020 21:22:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.05_summits.bed INFO @ Sun, 21 Jun 2020 21:22:45: Done! pass1 - making usageList (561 chroms): 3 millis pass2 - checking and writing primary data (4119 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:22:48: 16000000 INFO @ Sun, 21 Jun 2020 21:22:52: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:22:52: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:22:52: #1 total tags in treatment: 16426910 INFO @ Sun, 21 Jun 2020 21:22:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:52: #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 21:22:52: #1 tags after filtering in treatment: 16426833 INFO @ Sun, 21 Jun 2020 21:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:54: #2 number of paired peaks: 369 WARNING @ Sun, 21 Jun 2020 21:22:54: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sun, 21 Jun 2020 21:22:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:54: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 21:22:54: #2 alternative fragment length(s) may be 4,76,85 bps INFO @ Sun, 21 Jun 2020 21:22:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.20_model.r WARNING @ Sun, 21 Jun 2020 21:22:54: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:22:54: #2 You may need to consider one of the other alternative d(s): 4,76,85 WARNING @ Sun, 21 Jun 2020 21:22:54: #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 21:22:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.10_summits.bed INFO @ Sun, 21 Jun 2020 21:23:21: Done! pass1 - making usageList (371 chroms): 1 millis pass2 - checking and writing primary data (1586 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:23:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828013/SRX4828013.20_summits.bed INFO @ Sun, 21 Jun 2020 21:23:46: Done! pass1 - making usageList (179 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 8 millis CompletedMACS2peakCalling