Job ID = 6457844 SRX = SRX4801808 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:11:22 prefetch.2.10.7: 1) Downloading 'SRR7968393'... 2020-06-21T12:11:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:24 prefetch.2.10.7: 'SRR7968393' is valid 2020-06-21T12:13:24 prefetch.2.10.7: 1) 'SRR7968393' was downloaded successfully Read 12595880 spots for SRR7968393/SRR7968393.sra Written 12595880 spots for SRR7968393/SRR7968393.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: 369836 (2.94%) aligned 0 times 7659070 (60.81%) aligned exactly 1 time 4566974 (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] 1740186 / 12226044 = 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 21:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.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 21:22:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:34: 1000000 INFO @ Sun, 21 Jun 2020 21:22:40: 2000000 INFO @ Sun, 21 Jun 2020 21:22:46: 3000000 INFO @ Sun, 21 Jun 2020 21:22:52: 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 21:22:58: 5000000 INFO @ Sun, 21 Jun 2020 21:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.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 21:22:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:04: 6000000 INFO @ Sun, 21 Jun 2020 21:23:05: 1000000 INFO @ Sun, 21 Jun 2020 21:23:10: 7000000 INFO @ Sun, 21 Jun 2020 21:23:11: 2000000 INFO @ Sun, 21 Jun 2020 21:23:17: 8000000 INFO @ Sun, 21 Jun 2020 21:23:17: 3000000 INFO @ Sun, 21 Jun 2020 21:23:24: 4000000 INFO @ Sun, 21 Jun 2020 21:23:24: 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 21:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.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 21:23:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:30: 5000000 INFO @ Sun, 21 Jun 2020 21:23:30: 10000000 INFO @ Sun, 21 Jun 2020 21:23:34: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:23:34: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:23:34: #1 total tags in treatment: 10485858 INFO @ Sun, 21 Jun 2020 21:23:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:34: #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 21:23:34: #1 tags after filtering in treatment: 10485749 INFO @ Sun, 21 Jun 2020 21:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:34: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:35: #2 number of paired peaks: 2466 INFO @ Sun, 21 Jun 2020 21:23:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:35: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:23:35: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 21:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.05_model.r WARNING @ Sun, 21 Jun 2020 21:23:35: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:23:35: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 21:23:35: #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 21:23:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:36: 1000000 INFO @ Sun, 21 Jun 2020 21:23:37: 6000000 INFO @ Sun, 21 Jun 2020 21:23:43: 2000000 INFO @ Sun, 21 Jun 2020 21:23:44: 7000000 INFO @ Sun, 21 Jun 2020 21:23:51: 3000000 INFO @ Sun, 21 Jun 2020 21:23:51: 8000000 INFO @ Sun, 21 Jun 2020 21:23:58: 9000000 INFO @ Sun, 21 Jun 2020 21:23:58: 4000000 INFO @ Sun, 21 Jun 2020 21:23:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:05: 10000000 INFO @ Sun, 21 Jun 2020 21:24:06: 5000000 INFO @ Sun, 21 Jun 2020 21:24:08: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:24:08: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:24:08: #1 total tags in treatment: 10485858 INFO @ Sun, 21 Jun 2020 21:24:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:24:08: #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 21:24:09: #1 tags after filtering in treatment: 10485749 INFO @ Sun, 21 Jun 2020 21:24:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:24:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:24:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:24:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:24:09: #2 number of paired peaks: 2466 INFO @ Sun, 21 Jun 2020 21:24:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:24:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:24:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:24:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:24:10: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:24:10: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 21:24:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.10_model.r WARNING @ Sun, 21 Jun 2020 21:24:10: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:24:10: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 21:24:10: #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 21:24:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.05_summits.bed INFO @ Sun, 21 Jun 2020 21:24:11: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (2697 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:24:13: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:24:20: 7000000 INFO @ Sun, 21 Jun 2020 21:24:27: 8000000 INFO @ Sun, 21 Jun 2020 21:24:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:34: 9000000 INFO @ Sun, 21 Jun 2020 21:24:41: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.10_summits.bed INFO @ Sun, 21 Jun 2020 21:24:43: Done! INFO @ Sun, 21 Jun 2020 21:24:44: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:24:44: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:24:44: #1 total tags in treatment: 10485858 INFO @ Sun, 21 Jun 2020 21:24:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:24:44: #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 21:24:45: #1 tags after filtering in treatment: 10485749 INFO @ Sun, 21 Jun 2020 21:24:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:24:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:24:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:24:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:24:46: #2 number of paired peaks: 2466 INFO @ Sun, 21 Jun 2020 21:24:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:24:46: start X-correlation... pass1 - making usageList (521 chroms): 1 millis INFO @ Sun, 21 Jun 2020 21:24:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:24:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:24:46: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:24:46: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 21:24:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.20_model.r WARNING @ Sun, 21 Jun 2020 21:24:46: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:24:46: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 21:24:46: #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 21:24:46: #3 Call peaks... pass2 - checking and writing primary data (1918 records, 4 fields): 18 millis INFO @ Sun, 21 Jun 2020 21:24:46: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801808/SRX4801808.20_summits.bed INFO @ Sun, 21 Jun 2020 21:25:19: Done! pass1 - making usageList (457 chroms): 1 millis pass2 - checking and writing primary data (1343 records, 4 fields): 14 millis CompletedMACS2peakCalling