Job ID = 6456602 SRX = SRX367040 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:06:24 prefetch.2.10.7: 1) Downloading 'SRR1015602'... 2020-06-21T11:06:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:13 prefetch.2.10.7: 1) 'SRR1015602' was downloaded successfully Read 32673564 spots for SRR1015602/SRR1015602.sra Written 32673564 spots for SRR1015602/SRR1015602.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: 00:06:18 32673564 reads; of these: 32673564 (100.00%) were unpaired; of these: 13162371 (40.28%) aligned 0 times 12561669 (38.45%) aligned exactly 1 time 6949524 (21.27%) aligned >1 times 59.72% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 10026533 / 19511193 = 0.5139 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 20:21:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.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 20:21:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:21:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:21:56: 1000000 INFO @ Sun, 21 Jun 2020 20:22:00: 2000000 INFO @ Sun, 21 Jun 2020 20:22:05: 3000000 INFO @ Sun, 21 Jun 2020 20:22:10: 4000000 INFO @ Sun, 21 Jun 2020 20:22:15: 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 20:22:20: 6000000 INFO @ Sun, 21 Jun 2020 20:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.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 20:22:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:25: 7000000 INFO @ Sun, 21 Jun 2020 20:22:26: 1000000 INFO @ Sun, 21 Jun 2020 20:22:30: 8000000 INFO @ Sun, 21 Jun 2020 20:22:31: 2000000 INFO @ Sun, 21 Jun 2020 20:22:35: 9000000 INFO @ Sun, 21 Jun 2020 20:22:36: 3000000 INFO @ Sun, 21 Jun 2020 20:22:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:22:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:22:38: #1 total tags in treatment: 9484660 INFO @ Sun, 21 Jun 2020 20:22:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:22:38: #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 20:22:39: #1 tags after filtering in treatment: 9484550 INFO @ Sun, 21 Jun 2020 20:22:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:22:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:22:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:22:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:22:40: #2 number of paired peaks: 1592 INFO @ Sun, 21 Jun 2020 20:22:40: start model_add_line... INFO @ Sun, 21 Jun 2020 20:22:40: start X-correlation... INFO @ Sun, 21 Jun 2020 20:22:40: end of X-cor INFO @ Sun, 21 Jun 2020 20:22:40: #2 finished! INFO @ Sun, 21 Jun 2020 20:22:40: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 20:22:40: #2 alternative fragment length(s) may be 2,42,579 bps INFO @ Sun, 21 Jun 2020 20:22:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.05_model.r WARNING @ Sun, 21 Jun 2020 20:22:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:22:40: #2 You may need to consider one of the other alternative d(s): 2,42,579 WARNING @ Sun, 21 Jun 2020 20:22:40: #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 20:22:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:22:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:22:41: 4000000 INFO @ Sun, 21 Jun 2020 20:22:46: 5000000 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 20:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.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 20:22:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:51: 6000000 INFO @ Sun, 21 Jun 2020 20:22:55: 1000000 INFO @ Sun, 21 Jun 2020 20:22:56: 7000000 INFO @ Sun, 21 Jun 2020 20:22:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:01: 2000000 INFO @ Sun, 21 Jun 2020 20:23:02: 8000000 INFO @ Sun, 21 Jun 2020 20:23:06: 3000000 INFO @ Sun, 21 Jun 2020 20:23:08: 9000000 INFO @ Sun, 21 Jun 2020 20:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.05_summits.bed INFO @ Sun, 21 Jun 2020 20:23:08: Done! pass1 - making usageList (706 chroms): 3 millis pass2 - checking and writing primary data (6635 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:23:11: 4000000 INFO @ Sun, 21 Jun 2020 20:23:11: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:23:11: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:23:11: #1 total tags in treatment: 9484660 INFO @ Sun, 21 Jun 2020 20:23:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:11: #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 20:23:11: #1 tags after filtering in treatment: 9484550 INFO @ Sun, 21 Jun 2020 20:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:12: #2 number of paired peaks: 1592 INFO @ Sun, 21 Jun 2020 20:23:12: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:12: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:12: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:12: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:12: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 20:23:12: #2 alternative fragment length(s) may be 2,42,579 bps INFO @ Sun, 21 Jun 2020 20:23:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.10_model.r WARNING @ Sun, 21 Jun 2020 20:23:12: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:23:12: #2 You may need to consider one of the other alternative d(s): 2,42,579 WARNING @ Sun, 21 Jun 2020 20:23:12: #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 20:23:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:16: 5000000 INFO @ Sun, 21 Jun 2020 20:23:21: 6000000 INFO @ Sun, 21 Jun 2020 20:23:26: 7000000 INFO @ Sun, 21 Jun 2020 20:23:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:31: 8000000 INFO @ Sun, 21 Jun 2020 20:23:36: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:23:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:23:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:23:39: #1 total tags in treatment: 9484660 INFO @ Sun, 21 Jun 2020 20:23:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:39: #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 20:23:40: #1 tags after filtering in treatment: 9484550 INFO @ Sun, 21 Jun 2020 20:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.10_summits.bed INFO @ Sun, 21 Jun 2020 20:23:40: Done! pass1 - making usageList (418 chroms): 2 millis pass2 - checking and writing primary data (2161 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:23:41: #2 number of paired peaks: 1592 INFO @ Sun, 21 Jun 2020 20:23:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:41: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 20:23:41: #2 alternative fragment length(s) may be 2,42,579 bps INFO @ Sun, 21 Jun 2020 20:23:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.20_model.r WARNING @ Sun, 21 Jun 2020 20:23:41: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:23:41: #2 You may need to consider one of the other alternative d(s): 2,42,579 WARNING @ Sun, 21 Jun 2020 20:23:41: #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 20:23:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX367040/SRX367040.20_summits.bed INFO @ Sun, 21 Jun 2020 20:24:09: Done! pass1 - making usageList (203 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 13 millis CompletedMACS2peakCalling