Job ID = 6457851 SRX = SRX4801815 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:01:47 prefetch.2.10.7: 1) Downloading 'SRR7968400'... 2020-06-21T12:01:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:03:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:03:24 prefetch.2.10.7: 'SRR7968400' is valid 2020-06-21T12:03:24 prefetch.2.10.7: 1) 'SRR7968400' was downloaded successfully Read 10967021 spots for SRR7968400/SRR7968400.sra Written 10967021 spots for SRR7968400/SRR7968400.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: 00:03:55 10967021 reads; of these: 10967021 (100.00%) were unpaired; of these: 337392 (3.08%) aligned 0 times 6983321 (63.68%) aligned exactly 1 time 3646308 (33.25%) aligned >1 times 96.92% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 1370845 / 10629629 = 0.1290 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 21:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.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 21:11:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:29: 1000000 INFO @ Sun, 21 Jun 2020 21:11:34: 2000000 INFO @ Sun, 21 Jun 2020 21:11:39: 3000000 INFO @ Sun, 21 Jun 2020 21:11:45: 4000000 INFO @ Sun, 21 Jun 2020 21:11:50: 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 21:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.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 21:11:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:56: 6000000 INFO @ Sun, 21 Jun 2020 21:12:00: 1000000 INFO @ Sun, 21 Jun 2020 21:12:02: 7000000 INFO @ Sun, 21 Jun 2020 21:12:07: 2000000 INFO @ Sun, 21 Jun 2020 21:12:09: 8000000 INFO @ Sun, 21 Jun 2020 21:12:13: 3000000 INFO @ Sun, 21 Jun 2020 21:12:15: 9000000 INFO @ Sun, 21 Jun 2020 21:12:17: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:12:17: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:12:17: #1 total tags in treatment: 9258784 INFO @ Sun, 21 Jun 2020 21:12:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:12:17: #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 21:12:17: #1 tags after filtering in treatment: 9258653 INFO @ Sun, 21 Jun 2020 21:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:12:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:12:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:12:18: #2 number of paired peaks: 1971 INFO @ Sun, 21 Jun 2020 21:12:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:12:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:12:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:12:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:12:18: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:12:18: #2 alternative fragment length(s) may be 3,76 bps INFO @ Sun, 21 Jun 2020 21:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.05_model.r WARNING @ Sun, 21 Jun 2020 21:12:18: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:12:18: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Sun, 21 Jun 2020 21:12:18: #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 21:12:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:12:20: 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 21:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.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 21:12:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:26: 5000000 INFO @ Sun, 21 Jun 2020 21:12:31: 1000000 INFO @ Sun, 21 Jun 2020 21:12:33: 6000000 INFO @ Sun, 21 Jun 2020 21:12:38: 2000000 INFO @ Sun, 21 Jun 2020 21:12:39: 7000000 INFO @ Sun, 21 Jun 2020 21:12:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:12:45: 3000000 INFO @ Sun, 21 Jun 2020 21:12:46: 8000000 INFO @ Sun, 21 Jun 2020 21:12:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.05_summits.bed INFO @ Sun, 21 Jun 2020 21:12:51: Done! pass1 - making usageList (586 chroms): 2 millis pass2 - checking and writing primary data (2630 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:12:52: 4000000 INFO @ Sun, 21 Jun 2020 21:12:52: 9000000 INFO @ Sun, 21 Jun 2020 21:12:54: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:12:54: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:12:54: #1 total tags in treatment: 9258784 INFO @ Sun, 21 Jun 2020 21:12:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:12:54: #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 21:12:55: #1 tags after filtering in treatment: 9258653 INFO @ Sun, 21 Jun 2020 21:12:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:12:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:12:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:12:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:12:55: #2 number of paired peaks: 1971 INFO @ Sun, 21 Jun 2020 21:12:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:12:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:12:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:12:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:12:56: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:12:56: #2 alternative fragment length(s) may be 3,76 bps INFO @ Sun, 21 Jun 2020 21:12:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.10_model.r WARNING @ Sun, 21 Jun 2020 21:12:56: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:12:56: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Sun, 21 Jun 2020 21:12:56: #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 21:12:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:12:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:12:59: 5000000 INFO @ Sun, 21 Jun 2020 21:13:06: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:13:12: 7000000 INFO @ Sun, 21 Jun 2020 21:13:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:20: 8000000 INFO @ Sun, 21 Jun 2020 21:13:27: 9000000 INFO @ Sun, 21 Jun 2020 21:13:29: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:13:29: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:13:29: #1 total tags in treatment: 9258784 INFO @ Sun, 21 Jun 2020 21:13:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:29: #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 21:13:29: #1 tags after filtering in treatment: 9258653 INFO @ Sun, 21 Jun 2020 21:13:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:29: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.10_summits.bed INFO @ Sun, 21 Jun 2020 21:13:30: Done! INFO @ Sun, 21 Jun 2020 21:13:30: #2 number of paired peaks: 1971 INFO @ Sun, 21 Jun 2020 21:13:30: start model_add_line... pass1 - making usageList (485 chroms): 1 millis pass2 - checking and writing primary data (1577 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:13:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:30: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:13:30: #2 alternative fragment length(s) may be 3,76 bps INFO @ Sun, 21 Jun 2020 21:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.20_model.r WARNING @ Sun, 21 Jun 2020 21:13:30: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:13:30: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Sun, 21 Jun 2020 21:13:30: #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 21:13:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:13:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801815/SRX4801815.20_summits.bed INFO @ Sun, 21 Jun 2020 21:14:05: Done! pass1 - making usageList (310 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 10 millis CompletedMACS2peakCalling