Job ID = 6458895 SRX = SRX5736608 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:51:10 prefetch.2.10.7: 1) Downloading 'SRR8957018'... 2020-06-21T12:51:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:07 prefetch.2.10.7: 'SRR8957018' is valid 2020-06-21T12:53:07 prefetch.2.10.7: 1) 'SRR8957018' was downloaded successfully Read 13027879 spots for SRR8957018/SRR8957018.sra Written 13027879 spots for SRR8957018/SRR8957018.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: 00:03:36 13027879 reads; of these: 13027879 (100.00%) were unpaired; of these: 367163 (2.82%) aligned 0 times 9646197 (74.04%) aligned exactly 1 time 3014519 (23.14%) aligned >1 times 97.18% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 1418099 / 12660716 = 0.1120 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 22:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.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 22:00:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:28: 1000000 INFO @ Sun, 21 Jun 2020 22:00:33: 2000000 INFO @ Sun, 21 Jun 2020 22:00:38: 3000000 INFO @ Sun, 21 Jun 2020 22:00:43: 4000000 INFO @ Sun, 21 Jun 2020 22:00:48: 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 22:00:53: 6000000 INFO @ Sun, 21 Jun 2020 22:00:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.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 22:00:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:58: 7000000 INFO @ Sun, 21 Jun 2020 22:01:00: 1000000 INFO @ Sun, 21 Jun 2020 22:01:03: 8000000 INFO @ Sun, 21 Jun 2020 22:01:05: 2000000 INFO @ Sun, 21 Jun 2020 22:01:09: 9000000 INFO @ Sun, 21 Jun 2020 22:01:11: 3000000 INFO @ Sun, 21 Jun 2020 22:01:14: 10000000 INFO @ Sun, 21 Jun 2020 22:01:17: 4000000 INFO @ Sun, 21 Jun 2020 22:01:20: 11000000 INFO @ Sun, 21 Jun 2020 22:01:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:01:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:01:21: #1 total tags in treatment: 11242617 INFO @ Sun, 21 Jun 2020 22:01:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:21: #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 22:01:22: #1 tags after filtering in treatment: 11242500 INFO @ Sun, 21 Jun 2020 22:01:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:22: #2 looking for paired plus/minus strand peaks... 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 22:01:22: 5000000 INFO @ Sun, 21 Jun 2020 22:01:22: #2 number of paired peaks: 1346 INFO @ Sun, 21 Jun 2020 22:01:22: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:23: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 22:01:23: #2 alternative fragment length(s) may be 2,58 bps INFO @ Sun, 21 Jun 2020 22:01:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.05_model.r WARNING @ Sun, 21 Jun 2020 22:01:23: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:23: #2 You may need to consider one of the other alternative d(s): 2,58 WARNING @ Sun, 21 Jun 2020 22:01:23: #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 22:01:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.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 22:01:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:28: 6000000 INFO @ Sun, 21 Jun 2020 22:01:29: 1000000 INFO @ Sun, 21 Jun 2020 22:01:34: 2000000 INFO @ Sun, 21 Jun 2020 22:01:34: 7000000 INFO @ Sun, 21 Jun 2020 22:01:39: 3000000 INFO @ Sun, 21 Jun 2020 22:01:40: 8000000 INFO @ Sun, 21 Jun 2020 22:01:44: 4000000 INFO @ Sun, 21 Jun 2020 22:01:46: 9000000 INFO @ Sun, 21 Jun 2020 22:01:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:50: 5000000 INFO @ Sun, 21 Jun 2020 22:01:52: 10000000 INFO @ Sun, 21 Jun 2020 22:01:55: 6000000 INFO @ Sun, 21 Jun 2020 22:01:58: 11000000 INFO @ Sun, 21 Jun 2020 22:02:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:00: #1 total tags in treatment: 11242617 INFO @ Sun, 21 Jun 2020 22:02:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:00: #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 22:02:00: 7000000 INFO @ Sun, 21 Jun 2020 22:02:01: #1 tags after filtering in treatment: 11242500 INFO @ Sun, 21 Jun 2020 22:02:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.05_summits.bed INFO @ Sun, 21 Jun 2020 22:02:01: Done! INFO @ Sun, 21 Jun 2020 22:02:01: #2 number of paired peaks: 1346 INFO @ Sun, 21 Jun 2020 22:02:01: start model_add_line... pass1 - making usageList (479 chroms): 2 millis INFO @ Sun, 21 Jun 2020 22:02:01: start X-correlation... pass2 - checking and writing primary data (2529 records, 4 fields): 16 millis INFO @ Sun, 21 Jun 2020 22:02:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:01: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 22:02:01: #2 alternative fragment length(s) may be 2,58 bps INFO @ Sun, 21 Jun 2020 22:02:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.10_model.r WARNING @ Sun, 21 Jun 2020 22:02:01: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:01: #2 You may need to consider one of the other alternative d(s): 2,58 WARNING @ Sun, 21 Jun 2020 22:02:01: #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 22:02:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:01: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:02:05: 8000000 INFO @ Sun, 21 Jun 2020 22:02:10: 9000000 INFO @ Sun, 21 Jun 2020 22:02:16: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:21: 11000000 INFO @ Sun, 21 Jun 2020 22:02:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:22: #1 total tags in treatment: 11242617 INFO @ Sun, 21 Jun 2020 22:02:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:22: #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 22:02:23: #1 tags after filtering in treatment: 11242500 INFO @ Sun, 21 Jun 2020 22:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:24: #2 number of paired peaks: 1346 INFO @ Sun, 21 Jun 2020 22:02:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:24: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 22:02:24: #2 alternative fragment length(s) may be 2,58 bps INFO @ Sun, 21 Jun 2020 22:02:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.20_model.r WARNING @ Sun, 21 Jun 2020 22:02:24: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:24: #2 You may need to consider one of the other alternative d(s): 2,58 WARNING @ Sun, 21 Jun 2020 22:02:24: #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 22:02:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.10_summits.bed INFO @ Sun, 21 Jun 2020 22:02:39: Done! pass1 - making usageList (279 chroms): 1 millis pass2 - checking and writing primary data (919 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:02:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736608/SRX5736608.20_summits.bed INFO @ Sun, 21 Jun 2020 22:03:03: Done! pass1 - making usageList (107 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 5 millis CompletedMACS2peakCalling