Job ID = 6454636 SRX = SRX2422637 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:19:24 prefetch.2.10.7: 1) Downloading 'SRR5110251'... 2020-06-21T09:19:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:21:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:21:34 prefetch.2.10.7: 'SRR5110251' is valid 2020-06-21T09:21:34 prefetch.2.10.7: 1) 'SRR5110251' was downloaded successfully Read 12595880 spots for SRR5110251/SRR5110251.sra Written 12595880 spots for SRR5110251/SRR5110251.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: 00:04:47 12595880 reads; of these: 12595880 (100.00%) were unpaired; of these: 369763 (2.94%) aligned 0 times 7659186 (60.81%) aligned exactly 1 time 4566931 (36.26%) aligned >1 times 97.06% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 1739629 / 12226117 = 0.1423 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 18:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.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 18:30:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:51: 1000000 INFO @ Sun, 21 Jun 2020 18:30:56: 2000000 INFO @ Sun, 21 Jun 2020 18:31:02: 3000000 INFO @ Sun, 21 Jun 2020 18:31:07: 4000000 INFO @ Sun, 21 Jun 2020 18:31:13: 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 18:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.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 18:31:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:19: 6000000 INFO @ Sun, 21 Jun 2020 18:31:21: 1000000 INFO @ Sun, 21 Jun 2020 18:31:25: 7000000 INFO @ Sun, 21 Jun 2020 18:31:27: 2000000 INFO @ Sun, 21 Jun 2020 18:31:31: 8000000 INFO @ Sun, 21 Jun 2020 18:31:33: 3000000 INFO @ Sun, 21 Jun 2020 18:31:37: 9000000 INFO @ Sun, 21 Jun 2020 18:31:39: 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 18:31:43: 10000000 INFO @ Sun, 21 Jun 2020 18:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.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 18:31:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:45: 5000000 INFO @ Sun, 21 Jun 2020 18:31:47: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:31:47: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:31:47: #1 total tags in treatment: 10486488 INFO @ Sun, 21 Jun 2020 18:31:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:47: #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 18:31:47: #1 tags after filtering in treatment: 10486385 INFO @ Sun, 21 Jun 2020 18:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:48: #2 number of paired peaks: 2473 INFO @ Sun, 21 Jun 2020 18:31:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:48: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:31:48: #2 alternative fragment length(s) may be 3,71 bps INFO @ Sun, 21 Jun 2020 18:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.05_model.r WARNING @ Sun, 21 Jun 2020 18:31:48: #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 18:31:48: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Sun, 21 Jun 2020 18:31:48: #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 18:31:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:51: 1000000 INFO @ Sun, 21 Jun 2020 18:31:51: 6000000 INFO @ Sun, 21 Jun 2020 18:31:57: 2000000 INFO @ Sun, 21 Jun 2020 18:31:57: 7000000 INFO @ Sun, 21 Jun 2020 18:32:03: 3000000 INFO @ Sun, 21 Jun 2020 18:32:03: 8000000 INFO @ Sun, 21 Jun 2020 18:32:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:09: 4000000 INFO @ Sun, 21 Jun 2020 18:32:10: 9000000 INFO @ Sun, 21 Jun 2020 18:32:15: 5000000 INFO @ Sun, 21 Jun 2020 18:32:16: 10000000 INFO @ Sun, 21 Jun 2020 18:32:19: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:32:19: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:32:19: #1 total tags in treatment: 10486488 INFO @ Sun, 21 Jun 2020 18:32:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:19: #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 18:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.05_summits.bed INFO @ Sun, 21 Jun 2020 18:32:19: Done! INFO @ Sun, 21 Jun 2020 18:32:19: #1 tags after filtering in treatment: 10486385 INFO @ Sun, 21 Jun 2020 18:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:19: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (597 chroms): 1 millis pass2 - checking and writing primary data (2733 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:32:20: #2 number of paired peaks: 2473 INFO @ Sun, 21 Jun 2020 18:32:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:20: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:32:20: #2 alternative fragment length(s) may be 3,71 bps INFO @ Sun, 21 Jun 2020 18:32:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.10_model.r WARNING @ Sun, 21 Jun 2020 18:32:20: #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 18:32:20: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Sun, 21 Jun 2020 18:32:20: #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 18:32:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:21: 6000000 INFO @ Sun, 21 Jun 2020 18:32:27: 7000000 INFO @ Sun, 21 Jun 2020 18:32:33: 8000000 INFO @ Sun, 21 Jun 2020 18:32:39: 9000000 INFO @ Sun, 21 Jun 2020 18:32:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:32:44: 10000000 INFO @ Sun, 21 Jun 2020 18:32:47: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:32:47: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:32:47: #1 total tags in treatment: 10486488 INFO @ Sun, 21 Jun 2020 18:32:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:47: #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 18:32:48: #1 tags after filtering in treatment: 10486385 INFO @ Sun, 21 Jun 2020 18:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:49: #2 number of paired peaks: 2473 INFO @ Sun, 21 Jun 2020 18:32:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:49: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:32:49: #2 alternative fragment length(s) may be 3,71 bps INFO @ Sun, 21 Jun 2020 18:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.20_model.r WARNING @ Sun, 21 Jun 2020 18:32:49: #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 18:32:49: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Sun, 21 Jun 2020 18:32:49: #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 18:32:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.10_summits.bed INFO @ Sun, 21 Jun 2020 18:32:51: Done! pass1 - making usageList (524 chroms): 1 millis pass2 - checking and writing primary data (1917 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:33:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422637/SRX2422637.20_summits.bed INFO @ Sun, 21 Jun 2020 18:33:21: Done! pass1 - making usageList (459 chroms): 1 millis pass2 - checking and writing primary data (1344 records, 4 fields): 14 millis CompletedMACS2peakCalling