Job ID = 6454437 SRX = SRX2055965 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:13:09 prefetch.2.10.7: 1) Downloading 'SRR4069197'... 2020-06-21T09:13:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:19:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:19:55 prefetch.2.10.7: 1) 'SRR4069197' was downloaded successfully Read 19192206 spots for SRR4069197/SRR4069197.sra Written 19192206 spots for SRR4069197/SRR4069197.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: 00:05:42 19192206 reads; of these: 19192206 (100.00%) were unpaired; of these: 1979108 (10.31%) aligned 0 times 11781426 (61.39%) aligned exactly 1 time 5431672 (28.30%) aligned >1 times 89.69% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 1929424 / 17213098 = 0.1121 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 18:30:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.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 18:30:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:54: 1000000 INFO @ Sun, 21 Jun 2020 18:31:00: 2000000 INFO @ Sun, 21 Jun 2020 18:31:05: 3000000 INFO @ Sun, 21 Jun 2020 18:31:11: 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 18:31:16: 5000000 INFO @ Sun, 21 Jun 2020 18:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.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 18:31:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:23: 6000000 INFO @ Sun, 21 Jun 2020 18:31:26: 1000000 INFO @ Sun, 21 Jun 2020 18:31:29: 7000000 INFO @ Sun, 21 Jun 2020 18:31:33: 2000000 INFO @ Sun, 21 Jun 2020 18:31:36: 8000000 INFO @ Sun, 21 Jun 2020 18:31:40: 3000000 INFO @ Sun, 21 Jun 2020 18:31:42: 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 18:31:48: 4000000 INFO @ Sun, 21 Jun 2020 18:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.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 18:31:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:49: 10000000 INFO @ Sun, 21 Jun 2020 18:31:55: 1000000 INFO @ Sun, 21 Jun 2020 18:31:55: 5000000 INFO @ Sun, 21 Jun 2020 18:31:56: 11000000 INFO @ Sun, 21 Jun 2020 18:32:02: 2000000 INFO @ Sun, 21 Jun 2020 18:32:03: 12000000 INFO @ Sun, 21 Jun 2020 18:32:03: 6000000 INFO @ Sun, 21 Jun 2020 18:32:09: 3000000 INFO @ Sun, 21 Jun 2020 18:32:10: 13000000 INFO @ Sun, 21 Jun 2020 18:32:11: 7000000 INFO @ Sun, 21 Jun 2020 18:32:17: 4000000 INFO @ Sun, 21 Jun 2020 18:32:17: 14000000 INFO @ Sun, 21 Jun 2020 18:32:18: 8000000 INFO @ Sun, 21 Jun 2020 18:32:24: 5000000 INFO @ Sun, 21 Jun 2020 18:32:24: 15000000 INFO @ Sun, 21 Jun 2020 18:32:26: 9000000 INFO @ Sun, 21 Jun 2020 18:32:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:32:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:32:26: #1 total tags in treatment: 15283674 INFO @ Sun, 21 Jun 2020 18:32:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:26: #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 18:32:27: #1 tags after filtering in treatment: 15283603 INFO @ Sun, 21 Jun 2020 18:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:28: #2 number of paired peaks: 1695 INFO @ Sun, 21 Jun 2020 18:32:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:28: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:32:28: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.05_model.r WARNING @ Sun, 21 Jun 2020 18:32:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:28: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:32:28: #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 18:32:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:30: 6000000 INFO @ Sun, 21 Jun 2020 18:32:33: 10000000 INFO @ Sun, 21 Jun 2020 18:32:37: 7000000 INFO @ Sun, 21 Jun 2020 18:32:40: 11000000 INFO @ Sun, 21 Jun 2020 18:32:44: 8000000 INFO @ Sun, 21 Jun 2020 18:32:48: 12000000 INFO @ Sun, 21 Jun 2020 18:32:51: 9000000 INFO @ Sun, 21 Jun 2020 18:32:55: 13000000 INFO @ Sun, 21 Jun 2020 18:32:58: 10000000 INFO @ Sun, 21 Jun 2020 18:33:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:33:02: 14000000 INFO @ Sun, 21 Jun 2020 18:33:04: 11000000 INFO @ Sun, 21 Jun 2020 18:33:10: 15000000 INFO @ Sun, 21 Jun 2020 18:33:11: 12000000 INFO @ Sun, 21 Jun 2020 18:33:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:12: #1 total tags in treatment: 15283674 INFO @ Sun, 21 Jun 2020 18:33:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:12: #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 18:33:13: #1 tags after filtering in treatment: 15283603 INFO @ Sun, 21 Jun 2020 18:33:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:14: #2 number of paired peaks: 1695 INFO @ Sun, 21 Jun 2020 18:33:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:14: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:33:14: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:33:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.10_model.r WARNING @ Sun, 21 Jun 2020 18:33:14: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:14: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:33:14: #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 18:33:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.05_summits.bed INFO @ Sun, 21 Jun 2020 18:33:17: Done! pass1 - making usageList (646 chroms): 2 millis pass2 - checking and writing primary data (3175 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:17: 13000000 INFO @ Sun, 21 Jun 2020 18:33:23: 14000000 INFO @ Sun, 21 Jun 2020 18:33:29: 15000000 INFO @ Sun, 21 Jun 2020 18:33:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:31: #1 total tags in treatment: 15283674 INFO @ Sun, 21 Jun 2020 18:33:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:31: #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 18:33:31: #1 tags after filtering in treatment: 15283603 INFO @ Sun, 21 Jun 2020 18:33:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:33: #2 number of paired peaks: 1695 INFO @ Sun, 21 Jun 2020 18:33:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:33: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:33:33: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:33:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.20_model.r WARNING @ Sun, 21 Jun 2020 18:33:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:33: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:33:33: #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 18:33:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:33:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:00: Done! pass1 - making usageList (539 chroms): 3 millis pass2 - checking and writing primary data (2150 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055965/SRX2055965.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:22: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (969 records, 4 fields): 14 millis CompletedMACS2peakCalling