Job ID = 6509174 SRX = SRX706815 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:12:13 prefetch.2.10.7: 1) Downloading 'SRR1581496'... 2020-06-26T15:12:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:14:30 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:14:30 prefetch.2.10.7: 1) 'SRR1581496' was downloaded successfully Read 28322420 spots for SRR1581496/SRR1581496.sra Written 28322420 spots for SRR1581496/SRR1581496.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: 00:03:50 28322420 reads; of these: 28322420 (100.00%) were unpaired; of these: 14940559 (52.75%) aligned 0 times 11284207 (39.84%) aligned exactly 1 time 2097654 (7.41%) aligned >1 times 47.25% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 8809740 / 13381861 = 0.6583 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 @ Sat, 27 Jun 2020 00:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.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 @ Sat, 27 Jun 2020 00:22:18: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:22:18: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:22:23: 1000000 INFO @ Sat, 27 Jun 2020 00:22:28: 2000000 INFO @ Sat, 27 Jun 2020 00:22:33: 3000000 INFO @ Sat, 27 Jun 2020 00:22:38: 4000000 INFO @ Sat, 27 Jun 2020 00:22:41: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:22:41: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:22:41: #1 total tags in treatment: 4572121 INFO @ Sat, 27 Jun 2020 00:22:41: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:22:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:22:41: #1 tags after filtering in treatment: 4572068 INFO @ Sat, 27 Jun 2020 00:22:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:22:41: #1 finished! INFO @ Sat, 27 Jun 2020 00:22:41: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:22:42: #2 number of paired peaks: 1065 INFO @ Sat, 27 Jun 2020 00:22:42: start model_add_line... INFO @ Sat, 27 Jun 2020 00:22:42: start X-correlation... INFO @ Sat, 27 Jun 2020 00:22:42: end of X-cor INFO @ Sat, 27 Jun 2020 00:22:42: #2 finished! INFO @ Sat, 27 Jun 2020 00:22:42: #2 predicted fragment length is 50 bps INFO @ Sat, 27 Jun 2020 00:22:42: #2 alternative fragment length(s) may be 2,50,87,563 bps INFO @ Sat, 27 Jun 2020 00:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.05_model.r WARNING @ Sat, 27 Jun 2020 00:22:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:22:42: #2 You may need to consider one of the other alternative d(s): 2,50,87,563 WARNING @ Sat, 27 Jun 2020 00:22:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:22:42: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:22:42: #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 @ Sat, 27 Jun 2020 00:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.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 @ Sat, 27 Jun 2020 00:22:48: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:22:48: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:22:52: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:22:53: 1000000 INFO @ Sat, 27 Jun 2020 00:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.05_summits.bed INFO @ Sat, 27 Jun 2020 00:22:57: Done! pass1 - making usageList (346 chroms): 2 millis pass2 - checking and writing primary data (907 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:22:58: 2000000 INFO @ Sat, 27 Jun 2020 00:23:02: 3000000 INFO @ Sat, 27 Jun 2020 00:23:08: 4000000 INFO @ Sat, 27 Jun 2020 00:23:10: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:23:10: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:23:10: #1 total tags in treatment: 4572121 INFO @ Sat, 27 Jun 2020 00:23:10: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:23:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:23:11: #1 tags after filtering in treatment: 4572068 INFO @ Sat, 27 Jun 2020 00:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:23:11: #1 finished! INFO @ Sat, 27 Jun 2020 00:23:11: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:23:11: #2 number of paired peaks: 1065 INFO @ Sat, 27 Jun 2020 00:23:11: start model_add_line... INFO @ Sat, 27 Jun 2020 00:23:11: start X-correlation... INFO @ Sat, 27 Jun 2020 00:23:11: end of X-cor INFO @ Sat, 27 Jun 2020 00:23:11: #2 finished! INFO @ Sat, 27 Jun 2020 00:23:11: #2 predicted fragment length is 50 bps INFO @ Sat, 27 Jun 2020 00:23:11: #2 alternative fragment length(s) may be 2,50,87,563 bps INFO @ Sat, 27 Jun 2020 00:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.10_model.r WARNING @ Sat, 27 Jun 2020 00:23:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:23:11: #2 You may need to consider one of the other alternative d(s): 2,50,87,563 WARNING @ Sat, 27 Jun 2020 00:23:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:23:11: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:23:11: #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 @ Sat, 27 Jun 2020 00:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.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 @ Sat, 27 Jun 2020 00:23:18: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:23:18: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:23:22: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:23:23: 1000000 INFO @ Sat, 27 Jun 2020 00:23:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:23:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:23:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.10_summits.bed INFO @ Sat, 27 Jun 2020 00:23:27: Done! pass1 - making usageList (119 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:23:28: 2000000 INFO @ Sat, 27 Jun 2020 00:23:32: 3000000 INFO @ Sat, 27 Jun 2020 00:23:37: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:23:40: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:23:40: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:23:40: #1 total tags in treatment: 4572121 INFO @ Sat, 27 Jun 2020 00:23:40: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:23:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:23:40: #1 tags after filtering in treatment: 4572068 INFO @ Sat, 27 Jun 2020 00:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:23:40: #1 finished! INFO @ Sat, 27 Jun 2020 00:23:40: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:23:41: #2 number of paired peaks: 1065 INFO @ Sat, 27 Jun 2020 00:23:41: start model_add_line... INFO @ Sat, 27 Jun 2020 00:23:41: start X-correlation... INFO @ Sat, 27 Jun 2020 00:23:41: end of X-cor INFO @ Sat, 27 Jun 2020 00:23:41: #2 finished! INFO @ Sat, 27 Jun 2020 00:23:41: #2 predicted fragment length is 50 bps INFO @ Sat, 27 Jun 2020 00:23:41: #2 alternative fragment length(s) may be 2,50,87,563 bps INFO @ Sat, 27 Jun 2020 00:23:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.20_model.r WARNING @ Sat, 27 Jun 2020 00:23:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:23:41: #2 You may need to consider one of the other alternative d(s): 2,50,87,563 WARNING @ Sat, 27 Jun 2020 00:23:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:23:41: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:23:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:23:51: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706815/SRX706815.20_summits.bed INFO @ Sat, 27 Jun 2020 00:23:56: Done! pass1 - making usageList (86 chroms): 0 millis pass2 - checking and writing primary data (219 records, 4 fields): 5 millis CompletedMACS2peakCalling