Job ID = 6458364 SRX = SRX507380 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:19:19 prefetch.2.10.7: 1) Downloading 'SRR1213167'... 2020-06-21T12:19:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:30 prefetch.2.10.7: 'SRR1213167' is valid 2020-06-21T12:20:30 prefetch.2.10.7: 1) 'SRR1213167' was downloaded successfully Read 5750891 spots for SRR1213167/SRR1213167.sra Written 5750891 spots for SRR1213167/SRR1213167.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: 00:01:30 5750891 reads; of these: 5750891 (100.00%) were unpaired; of these: 425453 (7.40%) aligned 0 times 3680427 (64.00%) aligned exactly 1 time 1645011 (28.60%) aligned >1 times 92.60% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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_rmdupse_core] 1466253 / 5325438 = 0.2753 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 21:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.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 21:24:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:30: 1000000 INFO @ Sun, 21 Jun 2020 21:24:37: 2000000 INFO @ Sun, 21 Jun 2020 21:24:44: 3000000 INFO @ Sun, 21 Jun 2020 21:24:49: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:24:49: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:24:49: #1 total tags in treatment: 3859185 INFO @ Sun, 21 Jun 2020 21:24:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:24:49: #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 21:24:50: #1 tags after filtering in treatment: 3859069 INFO @ Sun, 21 Jun 2020 21:24:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:24:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:24:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:24:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:24:50: #2 number of paired peaks: 1124 INFO @ Sun, 21 Jun 2020 21:24:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:24:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:24:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:24:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:24:50: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:24:50: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 21:24:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.05_model.r WARNING @ Sun, 21 Jun 2020 21:24:50: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:24:50: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 21:24:50: #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 21:24:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:24:50: #3 Pre-compute pvalue-qvalue table... 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 21:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.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 21:24:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:00: 1000000 INFO @ Sun, 21 Jun 2020 21:25:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.05_summits.bed INFO @ Sun, 21 Jun 2020 21:25:03: Done! pass1 - making usageList (492 chroms): 1 millis pass2 - checking and writing primary data (1892 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:06: 2000000 INFO @ Sun, 21 Jun 2020 21:25:13: 3000000 INFO @ Sun, 21 Jun 2020 21:25:19: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:25:19: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:25:19: #1 total tags in treatment: 3859185 INFO @ Sun, 21 Jun 2020 21:25:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:19: #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 21:25:20: #1 tags after filtering in treatment: 3859069 INFO @ Sun, 21 Jun 2020 21:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:20: #2 number of paired peaks: 1124 INFO @ Sun, 21 Jun 2020 21:25:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:20: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:25:20: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 21:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.10_model.r WARNING @ Sun, 21 Jun 2020 21:25:20: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:20: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 21:25:20: #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 21:25:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:20: #3 Pre-compute pvalue-qvalue table... 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 21:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.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 21:25:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:31: 1000000 INFO @ Sun, 21 Jun 2020 21:25:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.10_summits.bed INFO @ Sun, 21 Jun 2020 21:25:33: Done! pass1 - making usageList (309 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:39: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:25:47: 3000000 INFO @ Sun, 21 Jun 2020 21:25:53: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:25:53: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:25:53: #1 total tags in treatment: 3859185 INFO @ Sun, 21 Jun 2020 21:25:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:53: #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 21:25:54: #1 tags after filtering in treatment: 3859069 INFO @ Sun, 21 Jun 2020 21:25:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:54: #2 number of paired peaks: 1124 INFO @ Sun, 21 Jun 2020 21:25:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:54: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:25:54: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 21:25:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.20_model.r WARNING @ Sun, 21 Jun 2020 21:25:54: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:54: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 21:25:54: #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 21:25:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:26:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507380/SRX507380.20_summits.bed INFO @ Sun, 21 Jun 2020 21:26:07: Done! pass1 - making usageList (94 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 6 millis CompletedMACS2peakCalling