Job ID = 6458919 SRX = SRX5775924 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:44:52 prefetch.2.10.7: 1) Downloading 'SRR8997127'... 2020-06-21T12:44:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:47:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:47:58 prefetch.2.10.7: 1) 'SRR8997127' was downloaded successfully Read 19269924 spots for SRR8997127/SRR8997127.sra Written 19269924 spots for SRR8997127/SRR8997127.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: 00:06:54 19269924 reads; of these: 19269924 (100.00%) were unpaired; of these: 600909 (3.12%) aligned 0 times 13605708 (70.61%) aligned exactly 1 time 5063307 (26.28%) aligned >1 times 96.88% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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 8 files... [bam_rmdupse_core] 8895449 / 18669015 = 0.4765 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 22:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.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 22:00:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:39: 1000000 INFO @ Sun, 21 Jun 2020 22:00:45: 2000000 INFO @ Sun, 21 Jun 2020 22:00:52: 3000000 INFO @ Sun, 21 Jun 2020 22:00:58: 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 22:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.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 22:01:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:05: 5000000 INFO @ Sun, 21 Jun 2020 22:01:10: 1000000 INFO @ Sun, 21 Jun 2020 22:01:12: 6000000 INFO @ Sun, 21 Jun 2020 22:01:18: 2000000 INFO @ Sun, 21 Jun 2020 22:01:19: 7000000 INFO @ Sun, 21 Jun 2020 22:01:25: 3000000 INFO @ Sun, 21 Jun 2020 22:01:27: 8000000 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 22:01:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.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 22:01:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:33: 4000000 INFO @ Sun, 21 Jun 2020 22:01:34: 9000000 INFO @ Sun, 21 Jun 2020 22:01:40: 1000000 INFO @ Sun, 21 Jun 2020 22:01:40: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:01:40: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:01:40: #1 total tags in treatment: 9773566 INFO @ Sun, 21 Jun 2020 22:01:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:40: #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 22:01:41: 5000000 INFO @ Sun, 21 Jun 2020 22:01:41: #1 tags after filtering in treatment: 9773565 INFO @ Sun, 21 Jun 2020 22:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:42: #2 number of paired peaks: 1071 INFO @ Sun, 21 Jun 2020 22:01:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:42: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:01:42: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 22:01:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.05_model.r WARNING @ Sun, 21 Jun 2020 22:01:42: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:42: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 22:01:42: #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 22:01:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:48: 2000000 INFO @ Sun, 21 Jun 2020 22:01:48: 6000000 INFO @ Sun, 21 Jun 2020 22:01:55: 3000000 INFO @ Sun, 21 Jun 2020 22:01:56: 7000000 INFO @ Sun, 21 Jun 2020 22:02:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:03: 4000000 INFO @ Sun, 21 Jun 2020 22:02:04: 8000000 INFO @ Sun, 21 Jun 2020 22:02:10: 5000000 INFO @ Sun, 21 Jun 2020 22:02:12: 9000000 INFO @ Sun, 21 Jun 2020 22:02:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.05_summits.bed INFO @ Sun, 21 Jun 2020 22:02:12: Done! pass1 - making usageList (737 chroms): 1 millis pass2 - checking and writing primary data (2417 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:02:17: 6000000 INFO @ Sun, 21 Jun 2020 22:02:18: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:02:18: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:02:18: #1 total tags in treatment: 9773566 INFO @ Sun, 21 Jun 2020 22:02:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:18: #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 22:02:18: #1 tags after filtering in treatment: 9773565 INFO @ Sun, 21 Jun 2020 22:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:19: #2 number of paired peaks: 1071 INFO @ Sun, 21 Jun 2020 22:02:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:19: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:02:19: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 22:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.10_model.r WARNING @ Sun, 21 Jun 2020 22:02:19: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:19: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 22:02:19: #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 22:02:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:24: 7000000 INFO @ Sun, 21 Jun 2020 22:02:31: 8000000 INFO @ Sun, 21 Jun 2020 22:02:38: 9000000 INFO @ Sun, 21 Jun 2020 22:02:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:43: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:02:43: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:02:43: #1 total tags in treatment: 9773566 INFO @ Sun, 21 Jun 2020 22:02:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:02:44: #1 tags after filtering in treatment: 9773565 INFO @ Sun, 21 Jun 2020 22:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:45: #2 number of paired peaks: 1071 INFO @ Sun, 21 Jun 2020 22:02:45: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:45: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:45: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:45: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:45: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:02:45: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 22:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.20_model.r WARNING @ Sun, 21 Jun 2020 22:02:45: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:45: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 22:02:45: #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 22:02:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.10_summits.bed INFO @ Sun, 21 Jun 2020 22:02:51: Done! pass1 - making usageList (642 chroms): 1 millis pass2 - checking and writing primary data (1811 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:03:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775924/SRX5775924.20_summits.bed INFO @ Sun, 21 Jun 2020 22:03:16: Done! pass1 - making usageList (472 chroms): 1 millis pass2 - checking and writing primary data (1215 records, 4 fields): 15 millis CompletedMACS2peakCalling